Contacts of the helix formed by residues 316 - 322 (chain C) in PDB entry 2VGB
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 316 (chain C).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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287C PHE* 4.3 20.7 + - + +
288C VAL 4.9 1.8 - - - +
289C ARG* 3.5 39.4 + - - +
315C GLU* 1.3 81.5 - - - +
317C HIS* 1.3 64.6 + - - +
318C GLU* 3.4 6.5 + - - +
319C GLY* 2.9 22.9 + - - -
320C VAL* 3.0 24.6 + - - +
340C LEU* 3.5 12.1 - - - +
343C GLU* 3.8 26.4 + - + +
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Residues in contact with HIS 317 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
78A ILE* 3.5 23.5 - - + +
79A ASP* 3.2 34.9 + - - -
316C ASN* 1.3 72.9 - - - +
318C GLU* 1.3 63.8 + - - +
320C VAL* 2.9 6.9 + - - +
321C LYS* 2.8 45.0 + - + +
343C GLU* 4.6 6.0 - - + +
344C ILE* 4.0 21.9 - - + +
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Residues in contact with GLU 318 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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289C ARG* 3.7 43.6 + - + +
290C LYS* 5.9 1.3 - - - -
316C ASN* 3.4 8.2 + - - +
317C HIS* 1.3 80.8 + - - +
319C GLY* 1.3 56.9 + - - +
321C LYS* 3.1 6.8 + - + +
322C ARG* 2.9 60.2 + - - +
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Residues in contact with GLY 319 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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288C VAL 3.8 20.9 - - - -
289C ARG* 4.2 2.4 + - - +
314C ILE* 3.8 13.1 - - - +
316C ASN* 2.9 19.0 + - - -
318C GLU* 1.3 78.3 - - - +
320C VAL* 1.3 60.5 + - - +
322C ARG 3.5 0.2 + - - -
323C PHE* 3.1 23.9 + - - +
326C ILE* 3.6 11.6 - - - +
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Residues in contact with VAL 320 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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78A ILE* 3.9 31.4 - - + -
314C ILE* 3.8 13.7 - - + -
316C ASN 3.0 17.1 + - - +
317C HIS* 2.9 10.3 + - - +
319C GLY* 1.3 75.3 - - - +
321C LYS* 1.3 67.8 + - - +
323C PHE* 3.2 19.7 - - - +
340C LEU* 3.8 21.1 - - + -
344C ILE* 5.5 0.2 - - + -
352C ALA* 4.2 19.1 - - + -
355C MET* 4.0 24.2 - - + +
356C MET* 4.5 2.2 - - + -
359C ARG* 5.3 1.7 + - - -
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Residues in contact with LYS 321 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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77A ASP* 3.5 28.3 + - - -
78A ILE* 4.9 8.1 - - - -
79A ASP* 3.7 21.6 + - - +
317C HIS* 2.8 38.9 + - + +
318C GLU* 3.7 7.6 - - - +
320C VAL* 1.3 82.7 - - + +
322C ARG* 1.3 63.3 + - + +
323C PHE 3.3 1.8 + - - -
324C ASP 5.1 0.9 + - - -
359C ARG* 5.8 1.9 + - - -
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Residues in contact with ARG 322 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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289C ARG 3.6 15.9 - - - +
290C LYS* 3.4 28.8 - - - +
318C GLU* 2.9 46.6 + - + +
319C GLY 3.7 2.5 - - - -
321C LYS* 1.3 77.9 - - + +
323C PHE* 1.3 64.3 + - - +
324C ASP* 3.3 2.7 - - - -
325C GLU* 2.9 59.4 + - + +
326C ILE* 3.1 12.9 + - + +
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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
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Atomic class I II III IV V VI VII VIII
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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