Contacts of the helix formed by residues 313 - 344 (chain A) in PDB entry 3UMH
Residue contacts within the protein are
derived with the CSU software (Sobolev V., Sorokine A.,
Prilusky J., Abola E.E. and Edelman M. (1999) Automated
analysis of interatomic contacts in proteins.
Bioinformatics, 15, 327-332). A
short description of the analytical approach
is given at the end of the page.
Note:
Non-standard 3 letter residue
codes indicate a heterogroup. To identify
and analyse, use LPC software
Legend:
Dist - nearest distance (Å) between atoms of two residues
Surf - contact surface area (Å2) between two residues
HB - hydrophilic-hydrophilic contact (hydrogen bond)
Arom - aromatic-aromatic contact
Phob - hydrophobic-hydrophobic contact
DC - hydrophobic-hydrophilic contact (destabilizing contact)
+/- - indicates presence/absence of a specific contacts
* - indicates residues forming contacts by their side chain
(including CA atoms)
Residues in contact with HIS 313 (chain A).
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
1A CD 3.5 4.4 - - - -
314A ALA* 1.3 64.0 + - - +
315A HIS* 3.2 6.5 - - - +
316A PHE* 3.2 16.2 + - + +
317A GLN* 3.0 28.3 + - - +
382A HIS* 3.6 9.8 - + + -
386A VAL* 4.0 18.3 - - + +
428A LYS* 3.8 27.7 + - - -
432A HIS* 3.0 47.6 + + - -
----------------------------------------------------------
Back to top of page
Residues in contact with ALA 314 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
313A HIS* 1.3 77.0 - - - +
315A HIS* 1.3 68.6 + - + +
317A GLN* 4.1 8.6 - - - +
318A LYS* 2.9 28.4 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with HIS 315 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
313A HIS* 4.4 4.2 - - - +
314A ALA* 1.3 81.7 - - + +
316A PHE* 1.3 56.8 + - + +
318A LYS* 3.6 7.5 + - + +
319A ALA* 3.1 27.6 + - - +
385A ARG* 4.7 24.5 + - - -
----------------------------------------------------------
Back to top of page
Residues in contact with PHE 316 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
1A CD 4.6 2.0 - - - -
313A HIS* 3.2 12.7 + - + +
314A ALA 3.0 0.2 - - - -
315A HIS* 1.3 77.4 - - + +
317A GLN* 1.3 65.3 + - + +
318A LYS 3.1 1.8 - - - -
319A ALA* 3.2 4.7 + - - +
320A LYS* 2.8 42.8 + - + +
378A LEU* 3.8 29.6 - - + -
379A VAL* 3.9 24.7 - - + -
382A HIS* 3.5 61.5 - + + +
436A HIS* 4.4 11.2 - + - -
601A ACT 4.5 11.9 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with GLN 317 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
313A HIS 3.0 16.4 + - - +
314A ALA* 4.1 7.7 - - - +
316A PHE* 1.3 81.1 - - + +
318A LYS* 1.3 57.0 + - - +
320A LYS* 3.6 16.8 - - + +
321A GLU* 3.0 33.8 + - + +
----------------------------------------------------------
Back to top of page
Residues in contact with LYS 318 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
314A ALA 2.9 18.5 + - - +
315A HIS* 3.7 7.4 - - + +
317A GLN* 1.3 76.8 - - - +
319A ALA* 1.3 64.7 + - - +
321A GLU* 3.3 5.6 + - - +
322A ARG* 3.0 71.1 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with ALA 319 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
315A HIS 3.1 15.1 + - - +
316A PHE* 3.2 5.1 + - - +
318A LYS* 1.3 78.4 - - - +
320A LYS* 1.3 57.7 + - - +
322A ARG* 3.1 9.1 + - - +
323A LEU* 2.8 32.1 + - - +
378A LEU* 3.7 28.9 - - + +
----------------------------------------------------------
Back to top of page
Residues in contact with LYS 320 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
316A PHE* 2.8 30.0 + - + +
317A GLN* 3.6 18.4 - - + +
319A ALA* 1.3 76.8 - - - +
321A GLU* 1.3 74.7 + - - +
323A LEU* 3.2 5.7 + - - +
324A GLU* 3.1 27.9 + - + +
378A LEU* 3.7 16.5 - - + +
601A ACT 4.7 23.6 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with GLU 321 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
317A GLN* 3.0 23.5 + - + +
318A LYS* 3.7 5.8 - - - +
320A LYS* 1.3 91.8 - - - +
322A ARG* 1.3 63.5 + - + +
324A GLU* 3.3 27.8 + - - +
325A ALA* 3.1 21.2 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with ARG 322 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
318A LYS* 3.0 63.1 + - + +
319A ALA* 3.6 7.4 - - - +
321A GLU* 1.3 74.3 - - + +
323A LEU* 1.3 67.0 + - - +
325A ALA* 3.3 7.5 + - + +
326A LYS* 2.9 32.2 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with LEU 323 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
319A ALA 2.8 13.5 + - - +
320A LYS* 3.4 10.1 - - - +
322A ARG* 1.3 76.8 - - - +
324A GLU* 1.3 62.5 + - - +
326A LYS* 3.3 18.4 + - - +
327A HIS* 3.0 23.8 + - - +
371A ALA* 5.2 2.2 - - + +
374A GLU* 3.0 40.7 - - + +
375A ARG* 3.5 45.5 - - + +
378A LEU* 4.0 16.6 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with GLU 324 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
320A LYS* 3.1 15.9 + - + +
321A GLU* 3.4 31.1 - - - +
322A ARG 3.1 0.2 - - - -
323A LEU* 1.3 78.3 - - - +
325A ALA* 1.3 59.6 + - - +
327A HIS* 3.2 9.5 + - + +
328A ARG* 2.8 49.1 + - + +
375A ARG* 6.0 3.8 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with ALA 325 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
321A GLU 3.1 13.1 + - - +
322A ARG* 3.7 10.8 - - + +
324A GLU* 1.3 77.6 - - - +
326A LYS* 1.3 62.6 + - - +
328A ARG* 3.9 6.6 - - - +
329A GLU* 3.0 33.7 + - + +
----------------------------------------------------------
Back to top of page
Residues in contact with LYS 326 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
322A ARG* 2.9 18.5 + - - +
323A LEU* 3.4 22.0 - - - +
325A ALA* 1.3 77.8 - - - +
327A HIS* 1.3 64.0 + - - +
329A GLU* 3.1 7.9 + - - +
330A ARG* 2.9 32.0 + - - +
374A GLU* 4.6 17.4 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with HIS 327 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
5A CD 2.2 28.3 - - - -
323A LEU 3.0 13.2 + - - +
324A GLU* 3.7 8.3 - - + +
326A LYS* 1.3 79.5 - - - +
328A ARG* 1.3 61.8 + - + +
330A ARG* 3.2 6.8 + - - +
331A MET* 2.8 51.2 + - + +
367A LEU* 4.0 14.6 + - - +
368A GLU* 3.0 23.8 + - - -
371A ALA* 3.5 28.7 - - + +
374A GLU* 6.1 0.9 - - - +
375A ARG* 4.1 12.8 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with ARG 328 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
324A GLU* 2.8 39.4 + - + +
325A ALA* 3.9 6.7 - - - +
327A HIS* 1.3 78.8 - - + +
329A GLU* 1.3 61.2 + - + +
331A MET* 3.5 8.2 + - + +
332A SER* 2.8 28.5 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with GLU 329 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
325A ALA* 3.0 29.4 + - + +
326A LYS* 3.1 6.3 + - - +
328A ARG* 1.3 75.8 - - + +
330A ARG* 1.3 66.1 + - - +
332A SER* 3.2 11.1 + - - -
333A GLN* 3.1 33.8 + - - +
336A ARG* 4.6 5.9 + - - -
----------------------------------------------------------
Back to top of page
Residues in contact with ARG 330 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
326A LYS* 2.9 23.9 + - - +
327A HIS* 3.6 8.1 - - - +
329A GLU* 1.3 77.2 - - - +
331A MET* 1.3 62.1 + - - +
333A GLN* 3.4 20.4 + - - +
334A VAL* 3.2 26.7 + - - +
363A LYS* 4.4 10.5 - - - +
367A LEU* 3.1 26.7 - - + +
370A GLU* 2.4 47.9 + - - +
374A GLU* 4.9 3.0 + - - -
----------------------------------------------------------
Back to top of page
Residues in contact with MET 331 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
327A HIS* 2.8 46.2 + - + +
328A ARG* 3.7 10.3 - - + +
329A GLU 3.2 0.2 - - - -
330A ARG* 1.3 76.3 - - - +
332A SER* 1.3 59.9 + - - +
334A VAL* 3.5 3.8 + - - +
335A MET* 3.1 40.7 + - + +
364A VAL* 4.0 30.5 - - + -
367A LEU* 3.5 27.1 - - + -
368A GLU* 3.4 12.1 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with SER 332 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
328A ARG* 2.8 21.0 + - - +
329A GLU* 3.4 14.8 + - - -
330A ARG 3.1 0.6 - - - -
331A MET* 1.3 74.6 - - - +
333A GLN* 1.3 66.1 + - - +
335A MET* 3.2 8.6 + - - +
336A ARG* 3.1 40.0 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with GLN 333 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
329A GLU* 3.1 22.9 - - - +
330A ARG* 3.4 20.7 + - - +
332A SER* 1.3 75.8 - - - +
334A VAL* 1.3 59.3 + - + +
336A ARG* 3.3 35.9 + - - +
337A GLU* 2.9 32.0 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with VAL 334 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
330A ARG 3.2 5.7 + - - +
331A MET* 3.8 8.5 - - - +
332A SER 3.1 0.6 - - - -
333A GLN* 1.3 76.3 - - + +
335A MET* 1.3 63.6 + - - +
337A GLU* 3.4 10.1 + - - +
338A TRP* 2.9 28.0 + - + +
360A PHE* 3.8 18.4 - - + -
363A LYS* 3.2 45.3 - - + +
364A VAL* 4.0 26.7 - - + -
367A LEU* 3.4 17.5 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with MET 335 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
331A MET* 3.1 27.8 - - + +
332A SER* 3.2 7.9 + - - +
334A VAL* 1.3 78.9 - - - +
336A ARG* 1.3 61.8 + - + +
338A TRP* 3.5 37.8 - - + +
339A GLU* 3.2 19.2 + - - +
364A VAL* 4.7 13.2 - - - -
----------------------------------------------------------
Back to top of page
Residues in contact with ARG 336 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
329A GLU* 4.6 5.9 + - - -
332A SER* 3.1 22.7 + - - +
333A GLN* 3.4 48.5 + - - +
335A MET* 1.3 74.5 - - - +
337A GLU* 1.3 59.9 + - - +
338A TRP 2.9 1.1 - - - -
339A GLU* 2.6 35.1 + - - +
340A GLU* 3.0 20.8 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with GLU 337 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
333A GLN* 2.9 15.7 + - - +
334A VAL* 3.7 11.0 - - - +
336A ARG* 1.3 79.7 - - - +
338A TRP* 1.3 57.3 + - - +
340A GLU* 3.5 12.4 + - - +
341A ALA* 2.8 30.4 + - + +
359A HIS* 4.9 6.4 + - - -
360A PHE* 3.3 23.8 - - + -
363A LYS* 5.5 7.0 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with TRP 338 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
334A VAL* 2.9 19.7 + - + +
335A MET* 3.5 41.5 - - + +
337A GLU* 1.3 74.0 - - - +
339A GLU* 1.3 56.2 + - - +
341A ALA* 3.0 2.4 + - - +
342A GLU* 2.7 46.9 + - + +
356A VAL* 4.5 12.0 - - + +
357A ILE* 4.4 29.2 - - + +
360A PHE* 3.3 52.4 - + + +
361A GLN* 4.2 20.2 - - + -
364A VAL* 4.7 8.7 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with GLU 339 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
335A MET 3.2 9.5 + - - +
336A ARG* 2.6 22.2 + - - +
338A TRP* 1.3 74.7 - - - +
340A GLU* 1.3 67.7 + - + +
342A GLU* 3.0 13.5 + - - +
343A ARG* 2.9 58.5 + - + +
----------------------------------------------------------
Back to top of page
Residues in contact with GLU 340 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
336A ARG* 3.0 15.7 + - + +
337A GLU* 3.8 13.4 - - - +
339A GLU* 1.3 83.2 - - + +
341A ALA* 1.3 53.9 + - - +
343A ARG* 3.7 7.4 - - - +
344A GLN* 2.6 43.0 + - + +
----------------------------------------------------------
Back to top of page
Residues in contact with ALA 341 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
337A GLU* 2.8 18.8 + - + +
338A TRP 3.3 2.5 - - - +
340A GLU* 1.3 77.6 - - - +
342A GLU* 1.3 58.3 + - - +
344A GLN* 3.6 5.0 - - - +
345A ALA* 2.8 30.3 + - - +
356A VAL* 4.0 10.0 - - + +
360A PHE* 3.2 31.6 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with GLU 342 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
338A TRP* 2.7 24.4 + - + +
339A GLU* 3.1 13.4 - - - +
341A ALA* 1.3 77.4 - - - +
343A ARG* 1.3 77.5 + - - +
345A ALA* 3.1 6.5 + - - +
346A LYS* 3.1 31.9 + - + +
353A LYS* 5.4 1.7 - - - -
356A VAL* 4.5 10.1 - - + +
----------------------------------------------------------
Back to top of page
Residues in contact with ARG 343 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
339A GLU* 2.9 53.1 + - - +
340A GLU* 3.7 7.4 - - - +
342A GLU* 1.3 82.9 + - + +
344A GLN* 1.3 54.0 + - - +
345A ALA 2.5 18.0 + - - -
346A LYS* 2.9 52.6 + - + +
347A ASN 4.7 0.7 + - - -
----------------------------------------------------------
Back to top of page
Residues in contact with GLN 344 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
340A GLU* 2.6 25.0 + - + +
341A ALA* 3.6 5.2 - - - +
343A ARG* 1.3 70.2 - - - +
345A ALA* 1.3 58.9 + - - +
347A ASN* 6.5 0.2 - - - -
348A LEU* 4.3 4.9 - - - +
----------------------------------------------------------
Back to top of page
A short description of the
analytical approach
The contact analysis used in this page
is based upon the approach
developed in:
Sobolev V., Wade R.C., Vriend G.
and Edelman M. PROTEINS (1996)
25, 120-129.
Contact legitimacy depends on the hydrophobic-hydrophilic
properties of the contacting atoms. In order to
define it, for each inter-atomic contact,
eight atom classes have been introduced:
I Hydrophilic - N and O that can donate and accept hydrogen bonds
(e.g., oxygen of hydroxyl group of Ser. or Thr)
II Acceptor - N or O that can only accept a hydrogen bond
III Donor - N that can only donate a hydrogen bond
IV Hydrophobic - Cl, Br, I and all C atoms that are not in
aromatic rings and do not have a covalent bond to
a N or O atom
V Aromatic - C in aromatic rings irrespective of any other
bonds formed by the atom
VI Neutral - C atoms that have a covalent bond to at least one
atom of class I or two or more atoms from class II
or III; atoms; S, F, P, and metal atoms in all cases
VII Neutral-donor - C atoms that have a covalent bond with only one
atom of class III
VIII Neutral-acceptor - C atoms that have a covalent bond with only
one atom of class II
For each pair of contacts the state of legitimacy
is shown below:
Legend:
+, legitimate
-, illegitimate
------------------------------------------------------------
Atomic class I II III IV V VI VII VIII
------------------------------------------------------------
I (Hydrophilic) + + + - + + + +
II (Acceptor) + - + - + + + -
III (Donor) + + - - + + - +
IV (Hydrophobic) - - - + + + + +
V (Aromatic) + + + + + + + +
VI (Neutral) + + + + + + + +
VII (Neutral-donor) + + - + + + - +
VIII (Neutral-acceptor) + - + + + + + -
------------------------------------------------------------
Warning!
Atom classes for heterogroups are automatically
assigned based on the atomic coordinates. However, in
three cases (see below) the automatic assignment
is currently ambiguous. In these
cases, the user is advised to manually analyse
the full list of contacts using
LPC software.
1. Carbon atoms belonging to a 4-, 5- or 6-member ring are
considered "aromatic" (Class V) if the ring is approximately
planar, and "hydrophobic" (Class IV) or "neutral" (Classes
VI, VII, VIII) if the ring is non-planar.
2. The oxygen atom of a carbonyl or hydroxy group is considered
"hydroxy" (Class I) if the CO bond is longer than 1.29 Å, and
"carbonyl" (Class II) if shorter.
3. All nitrogen atoms are considered "hydrophilic" (Class I).
Please E-mail any
questions and/or suggestions concerning this page to
Vladimir.Sobolev@weizmann.ac.il