Contacts of the helix formed by residues 318 - 338 (chain A) in PDB entry 2ODP
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 ASN 318 (chain A).
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
278A PHE* 4.0 8.7 - - - +
279A ALA 2.8 11.8 + - - +
280A SER 3.2 29.0 + - - +
281A GLU* 5.8 0.6 - - - +
282A PRO* 5.8 0.3 - - - +
317A THR* 1.3 69.7 - - - +
319A THR* 1.3 62.2 + - - +
320A TYR* 3.5 4.7 + - - +
321A ALA* 3.0 37.5 + - + +
322A ALA 3.3 9.0 + - - -
361A MET* 3.4 32.9 - - + +
362A GLY* 3.4 19.1 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with THR 319 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
278A PHE* 3.7 20.2 - - + -
317A THR* 3.3 9.4 + - - +
318A ASN* 1.3 73.6 - - - +
320A TYR* 1.3 65.0 + - - +
322A ALA* 3.2 3.0 + - - +
323A LEU* 3.1 23.5 + - + +
353A LEU* 4.0 25.8 - - + -
355A THR* 5.0 2.9 + - + +
357A GLY* 5.9 1.2 - - - -
359A SER* 3.3 28.1 + - - -
361A MET 4.4 1.6 + - - -
365A PRO* 4.0 6.1 - - + -
402A GLU* 4.4 0.6 + - - +
406A LEU* 4.0 29.8 - - + +
----------------------------------------------------------
Back to top of page
Residues in contact with TYR 320 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
318A ASN* 3.2 5.1 + - - +
319A THR* 1.3 79.6 - - - +
321A ALA* 1.3 64.9 + - + +
323A LEU* 3.1 4.5 + - - +
324A ASN* 2.8 57.2 + - + -
361A MET 4.9 0.4 + - - -
362A GLY* 3.6 21.5 - - - +
363A GLY 3.5 22.3 + - - +
364A SER 3.5 18.6 - - - +
365A PRO* 4.0 12.2 - - + +
367A THR* 3.9 17.6 - - + +
368A ALA* 3.6 31.4 - - + -
371A HIS* 4.8 6.1 + - - -
----------------------------------------------------------
Back to top of page
Residues in contact with ALA 321 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
280A SER 4.7 0.9 - - - +
281A GLU* 5.1 0.9 - - + -
282A PRO* 3.5 29.1 - - + +
318A ASN* 3.0 37.3 + - + +
320A TYR* 1.3 88.7 - - + +
322A ALA* 1.3 57.4 + - - +
324A ASN* 3.4 4.8 + - - +
325A SER 3.0 22.2 + - - -
----------------------------------------------------------
Back to top of page
Residues in contact with ALA 322 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
238A LEU* 3.7 21.9 - - + +
276A ILE* 4.5 2.0 - - + +
278A PHE* 3.5 45.3 - - + +
282A PRO* 4.1 12.9 - - - +
318A ASN 3.3 5.1 + - - -
319A THR* 3.2 10.0 + - - +
321A ALA* 1.3 72.8 - - - +
323A LEU* 1.3 63.2 + - - +
325A SER* 3.2 17.8 - - - -
326A VAL* 3.4 5.7 + - - +
353A LEU* 5.1 1.3 - - + -
----------------------------------------------------------
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
----------------------------------------------------------
238A LEU* 4.1 7.2 - - + -
319A THR* 3.1 15.2 + - + +
320A TYR 3.7 2.5 - - - +
322A ALA* 1.3 74.4 - - - +
324A ASN* 1.3 66.4 + - - +
326A VAL* 3.2 7.1 + - + +
327A TYR* 3.0 17.0 + - - +
351A ILE* 4.0 38.8 - - + -
353A LEU* 4.2 15.0 - - + -
365A PRO* 3.9 27.4 - - + +
368A ALA* 3.7 18.2 - - + -
369A VAL* 4.1 14.6 - - + -
372A ILE* 3.7 11.9 - - + +
388A ILE* 5.0 7.6 - - + -
406A LEU* 4.1 15.5 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with ASN 324 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
320A TYR* 2.8 48.9 + - + +
321A ALA* 3.8 6.5 + - - +
322A ALA 3.3 0.2 - - - -
323A LEU* 1.3 78.6 - - - +
325A SER* 1.3 56.0 + - - +
327A TYR* 3.2 25.6 + - - +
328A LEU* 2.9 48.5 + - - +
368A ALA* 3.8 5.6 - - + +
371A HIS* 5.0 5.2 + - - -
----------------------------------------------------------
Back to top of page
Residues in contact with SER 325 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
276A ILE* 3.8 9.1 - - - +
282A PRO* 3.9 21.2 - - - +
284A VAL* 3.4 28.2 - - - +
321A ALA 3.0 13.8 + - - -
322A ALA 3.2 12.3 + - - -
324A ASN* 1.3 74.7 - - - +
326A VAL* 1.3 61.6 + - - +
328A LEU* 3.3 13.2 + - - +
329A MET* 3.0 24.6 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with VAL 326 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
236A TYR* 3.9 22.9 - - + -
238A LEU* 3.8 32.8 - - + -
276A ILE* 3.9 9.6 - - + -
322A ALA 3.4 9.4 + - - +
323A LEU* 3.2 9.7 + - - +
325A SER* 1.3 73.8 - - - +
327A TYR* 1.3 66.6 + - - +
329A MET* 3.1 8.4 + - - +
330A MET* 2.9 49.4 + - + +
351A ILE* 3.8 19.5 - - + -
372A ILE* 4.1 2.9 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with TYR 327 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
323A LEU 3.0 12.6 + - - +
324A ASN* 3.3 27.6 - - - +
326A VAL* 1.3 76.2 - - - +
328A LEU* 1.3 72.2 + - + +
330A MET* 3.2 7.0 + - - +
331A ASN* 2.9 43.5 + - + +
368A ALA* 5.0 1.6 - - + +
371A HIS* 3.5 50.6 - + + -
372A ILE* 3.9 16.5 - - + +
375A ILE* 3.9 29.5 - - + +
----------------------------------------------------------
Back to top of page
Residues in contact with LEU 328 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
324A ASN* 2.9 39.3 + - - +
325A SER* 3.6 13.2 - - - +
326A VAL 3.2 0.4 - - - -
327A TYR* 1.3 88.9 - - + +
329A MET* 1.3 56.8 + - - +
331A ASN* 3.4 9.2 + - + +
332A ASN* 2.8 38.7 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with MET 329 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
236A TYR* 3.8 12.6 - - + -
274A ALA* 3.8 16.8 - - + -
276A ILE* 4.4 11.0 - - + -
284A VAL* 3.8 28.0 - - + -
286A MET 4.0 3.8 - - - +
287A SER* 3.7 22.4 - - - +
288A VAL* 3.6 37.2 - - + -
289A LEU* 3.5 17.1 - - + +
325A SER 3.0 11.0 + - - +
326A VAL* 3.4 8.5 - - - +
328A LEU* 1.3 77.1 - - - +
330A MET* 1.3 54.9 + - - +
332A ASN* 3.3 6.0 + - - -
333A GLN* 2.9 26.0 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with MET 330 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
236A TYR* 3.7 20.4 - - + +
326A VAL* 2.9 39.8 + - + +
327A TYR* 3.5 6.3 - - - +
329A MET* 1.3 72.3 - - - +
331A ASN* 1.3 60.5 + - - +
333A GLN* 3.3 4.4 + - - +
334A MET* 2.9 32.2 + - - +
344A TRP* 3.5 16.0 - - + -
349A HIS* 3.6 30.3 - - + -
351A ILE* 4.4 4.5 - - + -
372A ILE* 3.8 31.0 - - + -
375A ILE* 4.1 14.4 - - + -
376A LEU* 3.8 24.5 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with ASN 331 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
327A TYR* 2.9 30.0 + - + +
328A LEU* 3.5 15.5 - - + +
330A MET* 1.3 73.8 - - - +
332A ASN* 1.3 74.5 + - - +
334A MET* 3.6 9.2 + - - +
335A ARG* 3.1 43.5 + - - +
375A ILE* 3.5 23.1 - - + +
----------------------------------------------------------
Back to top of page
Residues in contact with ASN 332 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
289A LEU* 3.8 18.7 - - + +
328A LEU* 2.8 27.9 + - - +
329A MET* 3.6 6.8 - - - +
331A ASN* 1.3 82.5 - - - +
333A GLN* 1.3 57.6 + - - +
335A ARG* 3.3 12.7 + - - +
336A LEU* 3.1 28.1 + - - +
----------------------------------------------------------
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
----------------------------------------------------------
234A ASN* 2.9 32.9 + - - +
236A TYR* 4.7 1.0 + - - -
272A SER* 5.8 0.2 + - - -
288A VAL* 3.7 26.6 - - - +
289A LEU* 3.6 20.5 - - + +
329A MET 2.9 16.6 + - - +
330A MET* 3.9 4.4 - - - +
331A ASN 3.2 0.2 - - - -
332A ASN* 1.3 74.8 - - - +
334A MET* 1.3 66.4 + - - +
336A LEU* 3.2 2.4 + - + -
337A LEU* 2.9 40.4 + - + +
344A TRP* 3.8 10.1 - - + -
347A ILE* 3.6 21.1 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with MET 334 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
330A MET 2.9 17.3 + - - +
331A ASN* 3.9 9.9 - - - +
333A GLN* 1.3 75.1 - - - +
335A ARG* 1.3 55.5 + - - +
338A GLY* 2.7 35.2 + - - -
339A MET* 3.6 43.4 + - + +
344A TRP* 3.4 49.8 - - + +
375A ILE* 3.7 38.1 - - + +
----------------------------------------------------------
Back to top of page
Residues in contact with ARG 335 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
331A ASN* 3.1 36.2 + - - +
332A ASN* 3.5 13.1 - - - +
334A MET* 1.3 79.2 - - - +
336A LEU* 1.3 63.1 + - - +
337A LEU 3.5 0.3 + - - -
338A GLY* 3.8 6.3 + - - -
339A MET* 6.5 0.7 - - - -
----------------------------------------------------------
Back to top of page
Residues in contact with LEU 336 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
289A LEU* 4.3 15.3 - - + -
332A ASN 3.1 17.3 + - - +
333A GLN* 3.2 4.5 + - + +
335A ARG* 1.3 79.7 - - - +
337A LEU* 1.3 63.6 + - + +
----------------------------------------------------------
Back to top of page
Residues in contact with LEU 337 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
333A GLN* 2.9 42.9 + - + +
335A ARG 4.4 0.2 - - - -
336A LEU* 1.3 83.1 - - + +
338A GLY* 1.3 59.8 + - - +
341A THR* 3.2 28.2 + - - +
343A ALA* 3.8 36.5 - - + +
344A TRP* 4.1 11.7 - - + +
347A ILE* 4.3 4.3 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with GLY 338 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
334A MET 2.7 16.4 + - - -
335A ARG* 3.8 5.4 + - - -
336A LEU 3.7 1.2 - - - -
337A LEU* 1.3 71.5 - - - +
339A MET* 1.3 67.3 + - - -
340A GLU* 2.9 15.8 + - - -
341A THR* 2.7 25.4 + - - -
344A TRP* 3.5 7.9 - - - +
----------------------------------------------------------
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