Contacts of the strand formed by residues 69 - 74 (chain C) in PDB entry 2V1C
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 ALA 69 (chain C).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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34C LEU* 4.8 6.3 - - + -
35C LYS 3.9 15.8 + - - +
36C ALA* 3.4 3.3 - - - -
37C ILE* 3.2 24.2 + - - +
60C VAL* 3.7 31.9 - - + -
61C TYR 3.6 7.0 - - - +
62C GLN* 3.3 23.4 + - + +
67C ASP 4.3 0.2 - - - -
68C LEU* 1.3 78.6 - - - +
70C SER* 1.3 59.3 + - - +
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Residues in contact with SER 70 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
37C ILE* 3.3 13.9 - - - +
39C ARG* 3.9 23.9 + - - -
59C GLN 3.7 0.2 - - - +
60C VAL* 3.3 8.4 - - - -
61C TYR* 2.9 38.0 + - - -
68C LEU 5.0 1.8 - - - -
69C ALA* 1.3 76.5 - - - +
71C VAL* 1.3 63.7 + - - +
72C LYS* 2.9 28.4 + - - +
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Residues in contact with VAL 71 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
25C VAL* 5.0 4.5 - - + -
36C ALA* 4.2 19.5 - - + -
37C ILE 3.0 11.8 + - - +
38C ALA* 3.7 32.7 - - + +
39C ARG 5.5 0.7 + - - -
47C SER* 5.0 4.7 - - - +
50C LEU* 4.8 10.3 - - + -
58C VAL* 4.9 11.7 - - + -
59C GLN 3.6 3.8 - - - +
60C VAL* 4.6 5.4 - - + -
70C SER* 1.3 75.4 + - - +
72C LYS* 1.3 65.8 - - - +
73C GLN 3.6 25.8 - - - +
74C ALA* 4.3 10.8 - - + -
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Residues in contact with LYS 72 (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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5C THR* 5.3 6.3 - - + -
59C GLN* 2.7 36.0 + - - +
60C VAL 5.2 0.7 - - - -
61C TYR* 3.6 41.0 - - + +
70C SER* 2.9 27.4 + - - +
71C VAL* 1.3 77.4 - - - +
73C GLN* 1.3 76.2 + - - +
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Residues in contact with GLN 73 (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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7C ASN* 5.7 0.2 + - - -
47C SER* 4.9 4.8 + - - -
57C GLY 4.5 0.2 - - - -
58C VAL* 3.4 3.3 - - - -
59C GLN* 3.0 48.4 + - + +
71C VAL* 3.6 11.1 - - - +
72C LYS* 1.3 81.7 - - - +
74C ALA* 1.3 62.6 + - - +
75C VAL* 6.2 2.2 - - + -
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Residues in contact with ALA 74 (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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47C SER* 4.2 20.9 + - - +
49C SER* 6.3 1.6 - - - -
50C LEU* 4.1 30.1 - - + -
56C VAL* 4.5 0.4 - - + -
57C GLY 3.2 7.6 - - - +
58C VAL* 4.3 5.4 - - + -
71C VAL* 4.3 5.8 - - + -
73C GLN* 1.3 76.6 - - - +
75C VAL* 1.3 70.1 + - - +
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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