Contacts of the helix formed by residues 349 - 369 (chain A) in PDB entry 4RUH
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 THR 349 (chain A).
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
344A LEU* 3.8 4.9 - - - -
347A ASN 3.7 10.1 + - - +
348A MET* 1.3 77.9 - - - +
350A PRO* 1.3 71.2 - - + +
351A GLU* 3.7 6.0 + - - +
352A VAL* 3.2 33.7 + - + +
353A VAL* 2.9 30.7 + - - +
383A LYS* 4.9 14.8 - - + +
----------------------------------------------------------
Back to top of page
Residues in contact with PRO 350 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
214A CYS* 3.5 19.7 - - - -
344A LEU* 3.9 5.6 - - + -
349A THR* 1.3 87.9 - - - +
351A GLU* 1.3 60.1 + - - +
354A GLY* 3.1 16.8 + - - -
378A MET* 3.6 22.8 - - + +
381A GLY* 4.0 13.0 - - - +
382A GLY* 3.7 32.1 - - - +
383A LYS* 3.5 24.9 - - + +
----------------------------------------------------------
Back to top of page
Residues in contact with GLU 351 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
349A THR* 3.2 7.4 + - - +
350A PRO* 1.3 80.4 - - - +
352A VAL* 1.3 65.3 + - + +
354A GLY* 4.1 0.7 - - - -
355A GLU* 3.5 19.9 + - - +
378A MET* 5.4 2.5 - - - -
----------------------------------------------------------
Back to top of page
Residues in contact with VAL 352 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
348A MET* 6.3 0.7 - - - -
349A THR* 3.2 24.5 + - + +
351A GLU* 1.3 79.4 - - + +
353A VAL* 1.3 66.6 + - + +
355A GLU* 3.2 8.6 + - + +
356A GLN* 3.0 44.3 + - + +
----------------------------------------------------------
Back to top of page
Residues in contact with VAL 353 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
214A CYS* 3.9 21.5 - - + -
216A PHE* 4.1 12.6 - - + -
262A ILE* 4.0 22.4 - - + -
342A ILE* 4.4 6.1 - - + -
344A LEU* 4.2 11.0 - - + -
348A MET* 4.1 26.2 - - + -
349A THR 2.9 22.5 + - - +
352A VAL* 1.3 75.0 - - + +
354A GLY* 1.3 54.5 + - - +
356A GLN* 3.0 18.6 + - - +
357A VAL* 2.8 37.7 + - + +
----------------------------------------------------------
Back to top of page
Residues in contact with GLY 354 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
214A CYS* 4.8 0.2 - - - -
216A PHE* 4.2 17.6 - - - -
350A PRO 3.1 20.1 + - - -
351A GLU 4.1 1.3 - - - -
353A VAL* 1.3 77.9 - - - +
355A GLU* 1.3 53.7 + - - +
357A VAL* 4.1 1.0 - - - +
358A THR* 2.7 37.6 + - - -
378A MET* 4.5 10.1 - - - -
----------------------------------------------------------
Back to top of page
Residues in contact with GLU 355 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
351A GLU 3.5 12.1 + - - +
352A VAL* 3.2 11.2 + - - +
354A GLY* 1.3 73.7 - - - +
356A GLN* 1.3 63.2 + - + +
358A THR* 4.6 6.2 - - - +
359A SER* 2.8 48.9 + - - -
----------------------------------------------------------
Back to top of page
Residues in contact with GLN 356 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
259A ILE* 3.5 9.8 - - + +
260A PRO* 4.0 20.8 - - - +
261A GLY* 4.2 15.5 - - - -
262A ILE* 3.3 24.2 - - + +
352A VAL* 3.0 34.3 + - + +
353A VAL* 3.4 17.3 - - - +
355A GLU* 1.3 79.5 - - + +
357A VAL* 1.3 61.1 + - - +
359A SER* 4.2 3.0 - - - -
360A TYR* 3.2 23.4 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with VAL 357 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
216A PHE* 3.4 48.5 - - + -
259A ILE* 3.5 30.1 - - + -
262A ILE* 5.5 0.4 - - + -
340A PHE* 3.9 7.6 - - + -
342A ILE* 3.7 11.7 - - + -
353A VAL* 2.8 18.6 + - + +
354A GLY 4.1 0.2 - - - +
356A GLN* 1.3 71.1 - - + +
358A THR* 1.3 61.5 + - - +
360A TYR* 3.2 3.2 + - - +
361A LEU* 2.9 50.7 + - + +
376A VAL* 4.4 2.7 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with THR 358 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
216A PHE* 5.4 1.6 - - - -
354A GLY 2.7 23.2 + - - -
355A GLU* 4.1 7.4 - - - +
356A GLN 3.4 0.2 - - - -
357A VAL* 1.3 76.8 - - - +
359A SER* 1.3 63.7 + - - +
362A THR* 3.0 41.7 + - + +
376A VAL* 3.6 37.8 + - + +
377A TYR* 5.5 1.4 - - - -
----------------------------------------------------------
Back to top of page
Residues in contact with SER 359 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
355A GLU* 2.8 41.0 + - - -
356A GLN* 4.4 3.4 - - - -
358A THR* 1.3 77.1 - - - +
360A TYR* 1.3 62.6 + - - +
362A THR* 3.5 7.0 + - - -
363A LYS* 3.3 25.8 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with TYR 360 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
249A SER* 2.7 43.2 + - - -
250A LEU* 4.5 1.3 - - - -
258A LEU* 3.8 25.2 + - - +
259A ILE* 3.6 31.2 - - + -
260A PRO* 3.8 18.2 - - + -
356A GLN 3.2 19.8 + - - +
357A VAL 3.2 4.2 + - - +
358A THR 3.1 0.4 - - - -
359A SER* 1.3 78.1 - - - +
361A LEU* 1.3 70.5 + - + +
363A LYS* 3.1 17.5 + - + +
364A LYS* 3.0 57.3 + - + +
----------------------------------------------------------
Back to top of page
Residues in contact with LEU 361 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
218A ILE* 3.7 26.5 - - + -
246A LEU* 4.1 14.8 - - + +
249A SER* 4.0 15.3 - - - +
250A LEU* 4.2 11.4 - - + -
340A PHE* 4.3 4.9 - - + -
357A VAL* 2.9 33.5 + - + +
358A THR 4.2 1.3 - - - +
360A TYR* 1.3 87.5 - - + +
362A THR* 1.3 55.7 + - - +
364A LYS* 3.2 3.5 + - - +
365A PHE* 2.7 36.4 + - - +
374A PHE* 3.9 15.4 - - + -
376A VAL* 3.6 29.8 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with THR 362 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
358A THR* 3.0 41.3 + - + +
359A SER* 3.5 9.7 + - - -
361A LEU* 1.3 76.7 - - - +
363A LYS* 1.3 61.4 + - - +
365A PHE* 3.9 2.5 - - - +
366A ALA* 3.2 22.9 + - - +
374A PHE* 3.6 25.4 - - + -
376A VAL* 4.2 2.7 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with LYS 363 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
260A PRO* 6.0 4.0 - - - +
359A SER* 3.3 13.2 + - - +
360A TYR* 3.1 18.0 + - + +
361A LEU 3.1 0.6 - - - -
362A THR* 1.3 80.1 + - - +
364A LYS* 1.3 72.4 + - - +
366A ALA* 3.4 6.4 + - + +
367A GLU* 3.1 47.7 + - + +
----------------------------------------------------------
Back to top of page
Residues in contact with LYS 364 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
246A LEU* 3.5 20.9 - - + -
249A SER* 3.7 24.7 - - - +
360A TYR* 3.0 50.3 + - + +
361A LEU* 3.7 5.4 - - - +
363A LYS* 1.3 81.9 - - - +
365A PHE* 1.3 63.2 + - - +
367A GLU* 3.2 34.0 + - - +
368A LEU* 3.1 24.6 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with PHE 365 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
220A VAL* 4.9 2.0 - - + -
242A ASP* 3.9 13.2 - - + -
246A LEU* 3.9 13.9 - - + -
361A LEU 2.7 21.4 + - - +
362A THR* 3.9 4.3 - - - +
363A LYS 3.2 0.2 - - - -
364A LYS* 1.3 71.6 - - - +
366A ALA* 1.3 70.5 + - + +
368A LEU* 2.9 28.7 + - + +
369A ARG 3.5 2.6 + - - -
370A SER* 3.9 35.5 + - - -
372A ASN* 3.1 29.6 - - + -
374A PHE* 3.4 50.5 - + + -
----------------------------------------------------------
Back to top of page
Residues in contact with ALA 366 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
362A THR 3.2 19.8 + - - +
363A LYS* 3.6 6.5 - - - +
365A PHE* 1.3 79.7 - - + +
367A GLU* 1.3 59.2 + - + +
369A ARG* 2.9 30.5 + - - -
370A SER 5.9 0.2 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with GLU 367 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
363A LYS* 3.1 45.4 + - + +
364A LYS* 3.2 38.0 + - - +
365A PHE 3.2 0.4 - - - -
366A ALA* 1.3 77.5 - - + +
368A LEU* 1.3 62.6 + - + +
369A ARG* 3.2 8.1 + - - +
253B LYS* 4.4 13.6 - - + +
----------------------------------------------------------
Back to top of page
Residues in contact with LEU 368 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
237A HIS* 5.4 2.4 - - - -
242A ASP* 3.5 47.1 - - + +
245A LEU* 3.8 30.1 - - + -
246A LEU* 3.9 17.5 - - + -
364A LYS* 3.1 12.7 + - + +
365A PHE* 2.9 16.2 + - + +
367A GLU* 1.3 74.1 - - + +
369A ARG* 1.3 71.9 + - - +
370A SER* 4.2 11.7 - - - -
253B LYS* 3.4 31.0 - - + +
----------------------------------------------------------
Back to top of page
Residues in contact with ARG 369 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
237A HIS* 3.8 13.3 + - - -
365A PHE 3.5 1.0 + - - -
366A ALA 2.9 19.1 + - - -
367A GLU* 4.0 6.3 - - - +
368A LEU* 1.3 81.7 - - - +
370A SER* 1.3 59.6 + - - +
371A PRO* 4.3 0.7 - - - +
253B LYS 5.1 2.0 - - - +
----------------------------------------------------------
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