Contacts of the helix formed by residues 81 - 90 (chain I) in PDB entry 3KOV
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 81 (chain I).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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80I THR* 1.3 76.2 + - - +
82I SER* 1.3 59.4 + - - +
84I ILE* 2.8 22.7 + - - +
85I VAL* 2.9 19.3 + - + +
33J TYR* 3.2 25.0 - - + -
36J SER* 3.2 22.8 + - - -
37J VAL* 4.1 10.1 - - - +
57J TYR* 2.7 25.9 + - - -
58J ALA 3.7 2.8 + - - -
59J SER* 3.5 21.1 + - - +
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Residues in contact with SER 82 (chain I).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
80I THR* 3.0 19.5 - - - +
81I ASN* 1.3 73.1 - - - +
83I ASP* 1.3 63.9 + - - -
84I ILE 2.7 1.9 + - - -
85I VAL* 3.1 8.7 + - - +
86I GLU* 2.9 36.4 + - - +
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Residues in contact with ASP 83 (chain I).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
78I SER 3.8 6.8 - - - +
79I ARG* 3.8 40.9 + - - +
80I THR* 2.9 39.5 + - - +
82I SER* 1.3 75.7 + - - +
84I ILE* 1.3 57.9 + - - +
86I GLU* 3.8 12.1 - - - +
87I ALA* 3.2 26.2 + - - +
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Residues in contact with ILE 84 (chain I).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
79I ARG* 4.4 20.9 - - + +
80I THR 3.1 18.4 - - - +
81I ASN* 2.8 12.1 + - - +
82I SER 2.7 1.0 + - - -
83I ASP* 1.3 78.0 - - - +
85I VAL* 1.3 67.5 + - - +
87I ALA* 3.1 5.8 + - - +
88I LEU* 2.8 34.7 + - + +
26J PHE* 4.3 18.4 - - + -
29J MET* 4.1 28.3 - - + +
30J LYS* 4.7 6.7 - - - -
33J TYR* 3.8 31.2 - - + -
57J TYR* 4.4 11.7 - - + -
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Residues in contact with VAL 85 (chain I).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
81I ASN* 2.9 18.3 + - + +
82I SER* 3.8 6.7 - - - +
84I ILE* 1.3 73.7 - - - +
86I GLU* 1.3 65.4 + - + +
88I LEU* 2.9 23.0 + - + +
89I ASN* 2.9 31.1 + - - +
33J TYR* 3.7 29.8 - - + +
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Residues in contact with GLU 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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82I SER* 2.9 28.7 + - - +
83I ASP* 3.8 10.2 - - - +
85I VAL* 1.3 78.9 - - + +
87I ALA* 1.3 63.6 + - - +
88I LEU 3.0 1.2 + - - -
89I ASN* 3.2 9.9 + - - +
90I LYS* 3.2 22.3 + - - +
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Residues in contact with ALA 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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79I ARG* 4.9 10.3 - - - +
83I ASP 3.2 16.4 + - - +
84I ILE* 3.1 8.3 + - - +
86I GLU* 1.3 80.2 - - - +
88I LEU* 1.3 63.1 + - - +
90I LYS* 3.4 21.8 - - - +
91I LYS* 3.8 14.2 - - - -
26J PHE* 4.6 17.7 - - + -
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Residues in contact with LEU 88 (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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84I ILE* 2.8 23.9 + - + +
85I VAL* 2.9 13.8 + - + +
87I ALA* 1.3 74.3 - - - +
89I ASN* 1.3 58.9 + - - +
90I LYS 3.0 1.8 - - - -
91I LYS* 2.6 41.8 + - - +
26J PHE* 4.0 25.1 - - + -
30J LYS* 4.4 27.6 - - + +
33J TYR* 4.0 28.3 - - + -
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Residues in contact with ASN 89 (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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85I VAL* 2.9 34.1 + - - +
86I GLU* 3.2 9.7 + - - +
88I LEU* 1.3 76.2 - - - +
90I LYS* 1.3 61.3 + - - +
91I LYS* 2.9 12.0 + - - +
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Residues in contact with LYS 90 (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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86I GLU 3.2 12.7 + - - +
87I ALA* 3.4 19.7 - - - +
88I LEU 2.9 0.8 + - - -
89I ASN* 1.3 75.2 - - - +
91I LYS* 1.3 62.9 + - + +
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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