Contacts of the helix formed by residues 377 - 389 (chain H) in PDB entry 2VIG
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 PRO 377 (chain H).
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
289H CYS* 4.0 19.3 - - + -
375H GLU 4.8 0.2 - - - +
376H MET* 1.3 94.5 - - + +
378H ALA* 1.3 65.3 + - - +
379H GLU 3.4 2.5 - - - -
380H ARG* 3.2 34.0 + - + +
381H HIS* 3.1 40.3 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with ALA 378 (chain H).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
289H CYS* 4.6 5.1 - - - -
360H SER* 4.7 2.1 - - - +
363H ALA* 4.5 6.7 - - + -
364H ILE* 3.9 28.1 - - + +
367H LEU* 3.7 28.0 - - + -
371H GLY* 4.2 5.4 - - - +
376H MET* 3.4 1.8 - - + -
377H PRO* 1.3 79.9 - - - +
379H GLU* 1.3 57.3 + - - +
381H HIS* 3.2 14.0 + - - +
382H TYR* 2.9 28.2 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with GLU 379 (chain H).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
231G LEU* 3.3 35.9 - - + +
234G ARG* 5.4 1.2 + - - -
61H ASP* 4.8 0.2 - - - +
364H ILE* 4.1 8.3 - - - -
371H GLY 3.5 15.3 + - - +
372H TYR 4.5 2.0 - - - +
373H VAL 3.6 28.0 - - - +
374H THR* 3.3 27.2 - - - +
376H MET 4.3 4.1 + - - +
378H ALA* 1.3 78.4 - - - +
380H ARG* 1.3 68.3 + - - +
382H TYR* 3.3 3.2 + - - +
383H ARG* 2.9 64.7 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with ARG 380 (chain H).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
54H PHE* 6.2 2.2 - - - -
57H ALA* 3.6 36.9 + - - +
58H ALA* 4.4 10.2 - - - +
61H ASP* 3.6 35.0 - - - +
107H ARG 5.8 0.4 + - - -
108H GLY 4.5 5.9 + - - -
109H CYS* 5.2 4.8 - - - +
110H ALA* 5.3 2.2 - - - +
377H PRO* 3.2 34.6 + - + +
379H GLU* 1.3 84.6 - - - +
381H HIS* 1.3 78.0 + - - +
383H ARG* 3.2 20.0 + - - +
384H ASP* 2.9 54.6 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with HIS 381 (chain H).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
54H PHE* 6.4 0.2 - + - -
107H ARG 5.2 2.0 - - - -
282H ILE* 3.7 12.6 + - + +
285H THR* 3.3 38.9 + - + +
286H ALA* 3.9 26.9 - - + -
289H CYS* 4.9 3.0 - - + +
360H SER* 3.8 12.3 - - - -
363H ALA* 6.1 0.2 - - + -
377H PRO* 3.1 37.2 + - + +
378H ALA* 3.2 11.2 + - - +
380H ARG* 1.3 104.7 + - - +
382H TYR* 1.3 57.7 + - - +
384H ASP* 4.5 4.7 + - - -
385H ALA* 2.9 33.8 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with TYR 382 (chain H).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
231G LEU* 4.2 13.5 - - + -
357G THR* 3.8 7.8 + - - +
382G TYR* 3.2 55.3 + + - -
383G ARG* 5.8 0.9 - - + -
386G ARG* 3.6 28.7 - - + +
357H THR* 4.3 6.3 + - + -
360H SER* 3.4 22.0 - - - +
361H HIS* 3.4 45.1 - + + -
364H ILE* 3.7 19.7 - - + -
378H ALA 2.9 12.7 + - - +
379H GLU 3.5 8.7 - - - +
380H ARG 3.3 0.2 - - - -
381H HIS* 1.3 77.4 - - - +
383H ARG* 1.3 63.4 + - + +
385H ALA* 3.8 2.6 - - - +
386H ARG* 3.4 18.9 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with ARG 383 (chain H).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
231G LEU* 3.7 19.1 - - + -
234G ARG* 5.3 2.3 - - - +
372G TYR* 2.8 30.8 + - - -
382G TYR* 5.8 1.1 - - + -
383G ARG* 4.3 3.1 - - + +
61H ASP* 2.9 42.2 + - - -
231H LEU* 3.0 60.9 + - + +
232H GLY* 4.3 2.6 - - - -
234H ARG* 3.4 19.4 - - - +
374H THR* 5.3 1.4 - - - +
379H GLU* 2.9 51.9 + - - +
380H ARG* 3.2 14.6 + - - +
382H TYR* 1.3 78.4 - - + +
384H ASP* 1.3 57.5 + - - +
386H ARG* 3.5 8.0 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with ASP 384 (chain H).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
372G TYR* 3.8 4.5 - - - -
61H ASP* 4.6 4.2 - - - +
110H ALA* 3.5 33.4 + - + +
232H GLY* 3.5 5.0 - - - -
233H ILE* 3.0 25.3 + - + +
234H ARG 5.0 0.2 + - - -
282H ILE* 3.8 12.7 - - + +
380H ARG* 2.9 45.8 + - - +
381H HIS* 3.9 6.7 + - - +
383H ARG* 1.3 71.2 - - - +
385H ALA* 1.3 66.6 + - - +
386H ARG 3.1 2.0 - - - -
387H ILE* 3.1 24.4 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with ALA 385 (chain H).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
282H ILE* 3.8 14.1 - - + +
356H ALA* 3.6 38.8 - - + +
357H THR* 3.6 10.7 + - - +
360H SER* 3.7 5.8 - - - +
381H HIS 2.9 19.7 + - - +
382H TYR 3.8 2.7 - - - +
384H ASP* 1.3 76.8 - - - +
386H ARG* 1.3 61.6 + - - +
387H ILE 3.2 0.2 - - - -
388H THR* 2.7 25.0 + - - -
389H GLU 4.1 1.2 + - - -
----------------------------------------------------------
Back to top of page
Residues in contact with ARG 386 (chain H).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
361G HIS* 2.9 50.9 + - - -
364G ILE* 3.5 24.9 - - + +
365G GLN* 2.7 38.2 + - - +
372G TYR* 3.9 10.3 - - + -
382G TYR* 3.6 31.0 - - + +
231H LEU* 4.1 8.5 - - + -
357H THR* 4.0 5.1 + - - -
382H TYR 3.4 10.5 + - - +
383H ARG 3.6 13.2 - - - +
384H ASP 3.1 1.2 - - - -
385H ALA* 1.3 79.4 - - - +
387H ILE* 1.3 60.6 + - - +
388H THR 3.3 0.7 + - - -
389H GLU* 3.4 20.7 + - - +
390H ILE* 3.7 10.7 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with ILE 387 (chain H).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
372G TYR* 3.4 33.3 - - + +
233H ILE* 3.9 25.6 - - + -
278H GLN* 5.0 0.2 - - - +
384H ASP 3.1 19.9 + - - +
386H ARG* 1.3 77.3 - - - +
388H THR* 1.3 62.7 + - + +
390H ILE* 2.9 32.5 + - + -
391H TYR* 3.1 47.9 + - + +
501H FAD 3.7 39.0 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with THR 388 (chain H).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
275H ILE* 4.2 7.6 - - + -
278H GLN* 3.6 24.0 - - - +
279H ALA* 4.1 17.4 - - + +
282H ILE* 4.0 20.9 - - + -
349H LYS* 2.6 36.6 + - - -
353H SER* 3.3 31.0 + - - -
356H ALA* 4.3 1.9 - - - +
384H ASP 4.2 0.2 - - - +
385H ALA 2.7 20.4 + - - +
387H ILE* 1.3 81.6 - - + +
389H GLU* 1.3 49.7 + - - +
390H ILE 3.2 0.4 - - - -
391H TYR* 4.1 7.4 - - - -
----------------------------------------------------------
Back to top of page
Residues in contact with GLU 389 (chain H).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
361G HIS* 2.7 40.7 + - - -
365G GLN* 3.1 13.1 + - - +
349H LYS* 3.8 2.9 - - - +
353H SER* 3.7 30.1 - - - +
354H GLU* 3.5 21.9 - - + +
357H THR* 2.8 27.6 + - - +
386H ARG* 3.4 21.1 + - - +
387H ILE 3.1 1.0 + - - -
388H THR* 1.3 77.1 - - - +
390H ILE* 1.3 58.4 + - - +
394H THR* 3.3 0.5 - - - -
395H SER* 3.1 33.8 + - - +
----------------------------------------------------------
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