Contacts of the strand formed by residues 77 - 82 (chain C) in PDB entry 4CQM
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 VAL 77 (chain C).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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4C VAL* 4.2 13.2 - - + +
6C ALA* 4.5 13.7 - - + +
67C PHE* 5.1 7.6 - - + -
70C LEU* 4.2 35.4 - - + -
74C LEU* 6.0 0.4 - - + -
75C GLY 3.7 3.4 + - - +
76C ARG* 1.3 70.3 - - - +
78C ASN* 1.3 58.2 + - - +
79C PHE 3.5 20.9 - - - +
80C LEU* 4.9 2.9 - - + -
118C ALA* 5.0 8.7 - - + -
121C THR* 4.2 15.3 + - + +
122C MET* 3.7 22.9 - - + +
125C GLN* 2.6 28.5 + - - +
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Residues in contact with ASN 78 (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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3C LYS* 3.7 10.3 - - + +
4C VAL* 3.1 19.3 + - - +
76C ARG* 3.3 16.8 + - - +
77C VAL* 1.3 74.9 + - - +
79C PHE* 1.3 82.4 + - + +
122C MET* 3.4 5.4 - - - +
125C GLN* 2.6 40.4 + - - +
128C GLY* 3.4 8.2 - - - -
129C SER 3.1 23.4 + - - -
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Residues in contact with PHE 79 (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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3C LYS* 3.5 16.8 - - + -
4C VAL 3.1 9.2 + - - -
5C CYS* 3.3 22.7 - - + -
6C ALA 3.0 22.3 + - - -
22C MET* 4.8 0.9 - - + -
27C TYR* 3.5 40.6 - + - -
77C VAL* 3.5 9.2 - - - +
78C ASN* 1.3 92.2 - - + +
80C LEU* 1.3 61.1 + - - +
122C MET* 4.1 2.0 - - - -
129C SER* 3.5 23.1 - - - +
172C ARG* 5.0 0.4 - - - -
217C LEU* 3.2 45.3 - - + -
218C GLU* 5.1 1.3 - - + -
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Residues in contact with LEU 80 (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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6C ALA* 3.5 23.8 - - + +
8C PHE* 3.5 30.7 - - + -
67C PHE* 4.3 5.2 - - + -
77C VAL* 4.9 1.8 - - + -
79C PHE* 1.3 76.0 - - - +
81C VAL* 1.3 67.4 + - - +
82C ASN* 3.8 22.0 - - - +
114C THR* 3.8 16.4 - - - +
115C CYS* 4.0 5.6 - - - -
118C ALA* 3.7 24.0 - - + -
122C MET* 4.2 12.3 - - + -
129C SER 3.1 8.0 + - - +
130C ILE* 3.5 15.0 - - + +
131C VAL 3.0 26.2 + - - +
217C LEU* 4.2 1.6 - - - +
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Residues in contact with VAL 81 (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 CYS* 4.2 11.0 - - - -
6C ALA 2.8 13.2 + - - +
7C VAL* 4.2 18.6 - - + -
8C PHE* 2.8 30.3 + - - +
18C VAL* 4.2 20.4 - - + -
80C LEU* 1.3 79.6 - - - +
82C ASN* 1.3 63.7 + - - +
83C ALA* 3.5 7.6 + - + -
131C VAL 3.5 8.1 - - - +
133C VAL* 4.3 18.4 - - + -
213C VAL* 3.9 13.7 - - + -
217C LEU* 3.8 26.7 - - + -
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Residues in contact with ASN 82 (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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8C PHE* 4.1 11.4 - - + +
57C VAL* 5.8 0.3 - - - +
80C LEU* 3.8 14.4 - - - +
81C VAL* 1.3 70.9 - - - +
83C ALA* 1.3 59.5 + - - +
84C ALA* 3.5 2.9 - - + +
110C GLY 4.9 0.3 - - - -
111C SER* 3.6 23.5 + - - +
114C THR* 2.3 39.2 + - - +
115C CYS* 3.7 12.3 - - - -
130C ILE* 4.0 2.4 - - - +
131C VAL 3.1 8.3 + - - -
132C ASN* 2.7 29.9 + - - +
133C VAL* 2.9 29.5 + - - +
152C LYS* 5.3 0.9 + - - -
155C LEU* 5.9 0.3 - - - +
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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