Contacts of the helix formed by residues 431 - 435 (chain M) in PDB entry 4G7H
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 431 (chain M).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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324M ASP* 2.8 32.7 + - - -
326M ASP* 3.3 34.1 - - + +
327M HIS* 3.6 10.6 + + - -
429M ASP* 3.6 7.0 + - + +
430M VAL* 1.3 78.9 - - - +
432M ARG* 1.3 92.1 + - + +
433M THR* 3.0 33.2 + - + +
434M HIS* 2.9 44.7 + - + +
1048N PRO* 5.0 4.3 - - + -
1071N PHE* 3.8 1.0 - - - -
1075N HIS* 4.2 0.7 - - - -
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Residues in contact with ARG 432 (chain M).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
324M ASP* 5.6 1.0 + - - -
327M HIS* 3.5 13.3 + - - -
430M VAL 3.9 1.4 + - - -
431M HIS* 1.3 88.1 + - + +
433M THR* 1.3 75.3 + - - +
434M HIS 3.2 1.0 + - - -
435M TYR* 3.3 21.1 + - - +
491M GLU* 5.4 3.5 + - - +
492M ASP* 2.7 43.4 + - - -
516M ARG* 5.0 2.9 + - - -
518M LYS* 3.2 42.0 + - - +
519M GLY* 3.8 15.0 - - - +
1048N PRO* 5.2 3.1 - - + +
1071N PHE* 3.6 16.1 - - + -
1075N HIS* 4.1 10.0 - - + +
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Residues in contact with THR 433 (chain M).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
327M HIS* 3.4 37.2 - - + +
328M LEU* 3.0 40.6 + - - +
431M HIS* 3.0 21.3 + - + +
432M ARG* 1.3 86.7 - - - +
434M HIS* 1.3 60.0 + - - +
435M TYR* 3.0 7.1 + - - -
437M ARG* 3.2 21.8 + - - +
488M ALA* 3.8 11.7 - - + -
491M GLU* 5.5 4.5 - - - +
492M ASP* 4.9 1.1 - - - +
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Residues in contact with HIS 434 (chain M).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
326M ASP 4.7 2.9 - - - -
328M LEU* 3.5 31.9 - - + +
331M ARG* 5.3 10.7 + - - -
427M VAL 5.6 1.4 + - - -
429M ASP 3.7 13.6 + - - -
430M VAL* 3.9 21.5 - - + -
431M HIS* 2.9 44.1 + - + +
433M THR* 1.3 75.6 - - - +
435M TYR* 1.3 63.9 + - - +
436M GLY 3.2 1.0 + - - -
437M ARG 2.9 2.1 + - - -
438M ILE* 2.9 66.2 + - + +
439M CYS 5.6 1.6 - - - -
440M PRO* 5.4 0.6 - - - +
453M THR* 5.8 3.2 - - + +
1071N PHE* 4.4 3.6 - - + -
1078N ARG* 5.5 2.5 - - - -
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Residues in contact with TYR 435 (chain M).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
432M ARG 3.3 16.8 + - - +
433M THR 3.0 1.1 - - - -
434M HIS* 1.3 75.8 - - - +
436M GLY* 1.3 63.9 + - - +
437M ARG* 2.9 33.1 + - - +
469M THR* 4.1 1.7 - - - +
471M TYR* 4.0 6.7 - + - -
491M GLU* 4.9 0.7 - - - +
498M GLN* 3.1 21.6 + - - -
516M ARG* 3.2 50.9 - - - +
533M ASP* 2.5 31.5 + - - -
538M GLN* 5.1 3.6 - - + -
539M VAL* 3.7 25.6 - - + +
1067N VAL* 4.1 5.3 - - + +
1068N LEU* 4.5 3.6 - - + -
1071N PHE* 3.7 46.0 - + + -
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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) + - + + + + + -
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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