Contacts of the strand formed by residues 62 - 67 (chain B) in PDB entry 2OKD
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 CYS 62 (chain B).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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30A ALA* 5.9 0.2 - - - -
58B MET* 4.2 2.3 - - - +
59B PRO* 3.5 43.2 + - + +
60B LYS 3.2 6.0 - - - +
61B PHE* 1.3 79.0 - - - +
63B TYR* 1.3 85.6 + - - +
86B GLU* 3.7 17.0 + - - +
117B TYR* 3.8 25.1 - - - -
118B GLN 3.5 11.4 - - - +
120B ILE* 3.8 6.5 - - - +
122B TYR* 3.8 10.4 + - - -
121C TYR* 4.7 9.2 - - + -
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Residues in contact with TYR 63 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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30A ALA* 4.2 11.9 - - + -
65A ARG* 3.0 22.1 + - - -
116A ILE* 3.8 11.4 - - + -
118A GLN* 2.6 30.3 + - - -
58B MET* 4.4 2.0 - - - -
62B CYS* 1.3 82.6 - - - +
64B GLY* 1.3 83.4 + - - +
65B ARG* 3.4 12.8 + - + +
83B VAL* 3.7 26.2 - - + -
84B ILE 3.4 12.1 - - - +
85B ASP* 4.6 2.2 - - - -
116B ILE 3.3 1.2 - - - +
118B GLN* 2.8 55.6 + - + +
120B ILE* 3.5 38.1 - - + -
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Residues in contact with GLY 64 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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58B MET* 4.1 11.6 - - - -
63B TYR* 1.3 74.6 - - - +
65B ARG* 1.3 62.0 + - - -
66B ILE 3.9 0.2 - - - -
82B GLY 3.2 3.3 - - - +
84B ILE* 2.8 43.5 + - - +
115B LEU* 3.8 19.7 - - - -
116B ILE 3.3 8.3 - - - -
117B TYR* 4.7 2.2 - - - -
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Residues in contact with ARG 65 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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65A ARG* 3.7 19.3 - - - +
200A CL 3.6 7.9 - - - +
63B TYR* 3.4 26.0 + - + +
64B GLY* 1.3 71.0 - - - -
66B ILE* 1.3 73.8 + - - +
67B ALA* 3.2 15.5 + - + +
68B PRO* 3.9 23.2 - - - +
79B ILE* 6.1 0.2 - - - +
82B GLY 3.5 4.3 - - - +
115B LEU* 3.4 5.2 - - - -
116B ILE* 2.8 33.8 + - + +
118B GLN* 3.4 28.2 + - + +
63C TYR* 3.0 21.4 + - - -
65C ARG* 3.4 25.6 - - - +
81C GLY 5.3 4.9 + - - -
82C GLY 5.3 0.6 + - - -
83C VAL* 4.2 12.3 - - - +
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Residues in contact with ILE 66 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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34B LEU* 3.6 24.2 - - + -
65B ARG* 1.3 79.8 + - - +
67B ALA* 1.3 60.3 + - - +
79B ILE* 3.4 26.2 - - + +
80B GLY 5.7 0.2 - - - +
81B GLY 5.0 0.9 - - - +
82B GLY* 2.8 37.8 + - - +
84B ILE* 3.8 14.6 - - + -
92B ILE* 3.8 12.1 - - + -
93B GLY 4.0 5.6 - - - +
94B VAL* 3.9 31.2 - - + -
95B ILE 5.5 0.2 - - - +
113B ALA* 3.9 12.8 - - + -
114B GLN 3.7 2.9 - - - +
115B LEU* 3.7 14.4 - - + -
203B EDO 3.9 6.7 - - - +
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Residues in contact with ALA 67 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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65B ARG* 3.2 13.8 + - - +
66B ILE* 1.3 74.6 - - - +
68B PRO* 1.3 72.1 - - + +
79B ILE* 4.0 3.4 - - - -
113B ALA* 3.5 5.4 - - - +
114B GLN* 2.9 38.5 + - + +
116B ILE* 3.5 32.5 - - + -
83C VAL* 3.8 11.0 - - + -
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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