Contacts of the helix formed by residues 80 - 87 (chain I) in PDB entry 4QOC
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 ASP 80 (chain I).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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60I TYR* 2.6 29.3 + - - -
64I LYS* 3.9 17.7 - - - +
66I LEU* 3.9 29.9 - - + +
77I CYS* 3.2 9.9 + - - +
78I SER 3.3 2.1 - - - +
79I ASN* 1.3 81.1 - - - +
81I LEU* 1.3 71.1 + - - +
82I LEU* 2.8 27.0 + - - +
83I GLY* 2.9 12.3 + - - -
84I ASP* 3.5 11.7 + - - +
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Residues in contact with LEU 81 (chain I).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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33I LEU* 4.0 16.5 - - + +
36I LYS* 4.5 19.3 - - - -
37I LEU* 3.8 30.3 - - + -
60I TYR* 4.5 5.4 - - - +
80I ASP* 1.3 80.2 + - - +
82I LEU* 1.3 58.2 + - - +
84I ASP* 2.9 21.7 + - - +
85I LEU* 2.9 26.7 + - - +
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Residues in contact with LEU 82 (chain I).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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37I LEU* 4.1 7.5 - - + +
57I LEU* 4.2 16.4 - - + -
60I TYR* 4.2 8.3 - - + -
61I ILE* 3.6 36.3 - - + -
66I LEU* 4.2 10.8 - - + -
75I VAL* 4.7 1.6 - - + -
77I CYS* 4.1 14.5 - - + -
80I ASP* 2.8 16.2 + - - +
81I LEU* 1.3 78.4 - - - +
83I GLY* 1.3 62.1 + - - +
85I LEU* 4.2 8.3 - - + -
86I PHE* 3.0 57.8 + - + +
91I PHE* 4.2 11.4 - - + -
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Residues in contact with GLY 83 (chain I).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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77I CYS* 3.1 27.1 + - - +
78I SER* 5.1 1.8 - - - -
80I ASP 2.9 7.7 + - - -
82I LEU* 1.3 79.1 - - - +
84I ASP* 1.3 56.6 + - - +
87I GLY* 2.7 33.1 + - - -
88I VAL 3.4 18.2 + - - +
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Residues in contact with ASP 84 (chain I).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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33I LEU* 4.3 11.2 - - + +
78I SER 5.7 1.2 - - - +
80I ASP 3.9 6.1 - - - +
81I LEU* 2.9 29.6 + - - +
83I GLY* 1.3 78.8 - - - +
85I LEU* 1.3 66.7 + - - +
87I GLY* 3.6 6.9 + - - -
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Residues in contact with LEU 85 (chain I).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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33I LEU* 3.6 34.5 - - + +
34I LEU* 3.6 37.0 - - + +
37I LEU* 3.9 17.0 - - + -
57I LEU* 5.1 0.2 - - + -
81I LEU 2.9 11.9 + - - +
82I LEU* 3.3 13.4 + - + +
84I ASP* 1.3 80.3 - - - +
86I PHE* 1.3 77.0 + - + +
105I ARG* 4.5 2.6 + - - -
106I ASN* 2.9 57.1 + - + +
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Residues in contact with PHE 86 (chain I).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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34I LEU* 5.8 0.2 - - + -
57I LEU* 4.2 11.2 - - + -
77I CYS* 5.6 0.2 - - - -
82I LEU* 3.0 28.7 + - + +
85I LEU* 1.3 102.1 - - + +
87I GLY* 1.3 61.7 + - - +
88I VAL* 3.6 15.7 + - + +
91I PHE* 3.8 35.4 - + - -
99I ILE* 4.7 2.0 - - + -
102I MET* 3.7 49.4 - - + -
103I ILE* 3.8 32.3 - - + -
105I ARG* 2.6 26.7 + - - +
201I 35T 4.2 7.9 - - + -
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Residues in contact with GLY 87 (chain I).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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83I GLY 2.7 21.1 + - - -
84I ASP 3.6 5.8 + - - -
85I LEU 3.4 2.6 - - - -
86I PHE* 1.3 74.7 - - - +
88I VAL* 1.3 61.8 + - - +
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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