Contacts of the strand formed by residues 73 - 79 (chain C) in PDB entry 5VOK
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 73 (chain C).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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66C CYS* 4.3 12.8 - - - -
67C LEU 3.2 9.9 - - - +
68C GLU* 3.0 25.8 + - - +
69C SER 2.9 22.5 + - - +
72C GLY* 1.3 89.0 - - - +
74C ILE* 1.3 64.2 + - - +
75C MET* 4.4 5.6 + - - -
86C VAL 3.9 0.2 - - - +
87C HIS* 3.4 2.4 - - - -
88C LYS* 2.6 43.5 + - + +
90C ALA* 4.2 16.1 - - + +
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Residues in contact with ILE 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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37C LEU* 5.1 8.7 - - + -
45C ILE* 5.9 0.7 - - + -
65C VAL 3.7 0.9 - - - +
66C CYS* 4.6 0.2 - - - -
67C LEU* 2.7 52.1 + - + +
72C GLY 5.4 0.9 - - - +
73C ASN* 1.3 78.5 - - - +
75C MET* 1.3 59.2 + - - +
76C ILE* 4.6 8.5 - - + +
85C ALA* 5.4 2.9 - - + -
86C VAL 3.1 22.0 - - - +
87C HIS* 3.4 24.7 - - + +
53D PHE* 3.1 44.2 - - + -
55D LEU* 4.6 10.5 - - + -
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Residues in contact with MET 75 (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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64C VAL* 4.0 23.1 - - + -
65C VAL 2.9 11.7 - - - +
66C CYS* 4.2 20.2 - - + -
73C ASN* 5.3 4.9 - - - +
74C ILE* 1.3 75.1 - - - +
76C ILE* 1.3 63.2 + - - +
77C GLN* 4.6 3.1 - - - +
85C ALA* 3.3 2.9 - - - -
86C VAL* 2.9 53.3 + - + +
88C LYS* 4.5 23.3 - - + +
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Residues in contact with ILE 76 (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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45C ILE* 4.0 22.0 - - + +
48C LEU* 4.4 22.9 - - + -
49C ALA* 4.1 11.7 - - + +
63C PRO 4.5 0.2 - - - -
64C VAL* 3.2 2.6 - - - +
65C VAL* 2.8 54.6 + - + +
67C LEU* 4.5 7.6 - - + -
74C ILE* 4.6 7.2 - - + +
75C MET* 1.3 83.9 - - - +
77C GLN* 1.3 73.3 + - - +
83C THR* 3.5 28.5 - - + -
84C VAL 3.4 8.5 - - - +
85C ALA* 3.6 15.9 - - + -
53D PHE* 5.9 1.1 - - + -
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Residues in contact with GLN 77 (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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49C ALA* 5.3 4.9 - - - +
62C ILE* 4.7 2.0 - - + -
63C PRO 2.9 28.9 - - - +
64C VAL* 3.8 17.1 - - + +
75C MET 4.6 1.7 - - - +
76C ILE* 1.3 87.7 + - - +
78C LYS* 1.3 60.6 + - - +
79C HIS* 2.8 38.2 + - + +
83C THR* 4.5 4.7 - - - -
84C VAL* 3.0 39.4 + - - +
86C VAL* 6.1 0.9 - - - +
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Residues in contact with LYS 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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49C ALA* 5.6 2.9 - - + +
62C ILE* 3.8 46.5 - - + +
77C GLN* 1.3 76.9 - - - +
79C HIS* 1.3 68.8 + - - +
80C ASP* 4.1 3.4 + - - +
81C GLY* 3.3 42.7 + - - +
82C ILE 3.6 4.7 - - - -
83C THR* 4.3 8.3 - - - +
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Residues in contact with HIS 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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5C LEU* 6.1 2.9 - - + -
8C HIS* 5.6 11.6 - + - -
77C GLN* 2.8 38.5 + - + -
78C LYS* 1.3 75.8 + - - +
80C ASP* 1.3 65.9 + - - +
82C ILE* 2.7 50.1 + - + +
84C VAL* 3.9 13.0 - - + +
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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