Contacts of the strand formed by residues 62 - 67 (chain C) 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 C).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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121A TYR* 4.3 24.7 - - - -
58C MET* 5.5 0.7 - - - -
59C PRO* 3.9 21.8 - - + +
60C LYS 3.1 12.9 - - - +
61C PHE* 1.3 81.4 - - - +
63C TYR* 1.3 66.4 + - - +
86C GLU* 3.7 15.4 - - - +
117C TYR* 4.4 5.2 - - + -
118C GLN 3.3 11.4 - - - +
119C ARG* 3.8 25.8 - - - -
120C ILE* 3.8 6.7 - - - -
122C TYR* 3.6 13.7 + - - -
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Residues in contact with TYR 63 (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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30B ALA* 3.7 19.3 - - + -
65B ARG* 3.0 18.7 + - - -
116B ILE* 3.8 19.1 - - + -
118B GLN* 2.7 29.0 + - - -
58C MET* 3.9 8.5 - - - -
62C CYS* 1.3 76.1 - - - +
64C GLY* 1.3 76.0 + - - +
65C ARG* 3.3 23.9 + - + +
83C VAL* 3.8 27.8 - - + -
84C ILE 3.5 11.0 - - - +
85C ASP* 4.8 0.7 - - - -
86C GLU 4.9 0.4 - - - +
116C ILE 3.3 0.7 - - - +
117C TYR* 3.5 3.0 - - - -
118C GLN* 2.9 51.9 + - + -
120C ILE* 3.6 19.5 - - + -
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Residues in contact with GLY 64 (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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58C MET* 3.3 18.3 - - - +
63C TYR* 1.3 73.9 - - - +
65C ARG* 1.3 61.6 + - - -
66C ILE 3.6 0.6 + - - -
82C GLY 3.1 4.2 - - - +
84C ILE* 2.8 43.9 + - - +
115C LEU* 3.7 15.5 - - - -
116C ILE 3.4 7.0 - - - -
117C TYR* 4.7 1.1 - - - -
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Residues in contact with ARG 65 (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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63A TYR* 3.0 27.7 + - - -
65A ARG* 3.6 23.4 - - - +
81A GLY 5.4 1.8 + - - -
82A GLY 5.5 0.8 + - - -
83A VAL* 4.0 11.5 - - - +
200A CL 3.8 6.8 - - - +
65B ARG* 3.4 19.3 - - - +
63C TYR* 3.3 27.8 + - + +
64C GLY* 1.3 71.0 - - - -
66C ILE* 1.3 72.2 + - - +
67C ALA* 3.1 17.7 + - - +
68C PRO* 3.7 20.0 - - - +
82C GLY 3.4 4.5 - - - +
114C GLN 3.3 0.9 - - - +
115C LEU* 3.3 2.5 - - - -
116C ILE* 2.8 39.3 + - + +
118C GLN* 3.2 31.0 + - + +
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Residues in contact with ILE 66 (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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34C LEU* 3.6 25.1 - - + -
64C GLY 3.6 0.2 + - - -
65C ARG* 1.3 74.9 + - - +
67C ALA* 1.3 58.1 + - - +
68C PRO* 4.5 0.7 - - - +
79C ILE* 3.4 24.4 - - + +
81C GLY 5.0 1.0 - - - +
82C GLY* 2.8 39.6 + - - +
84C ILE* 3.7 26.0 - - + -
92C ILE* 4.0 10.1 - - + -
93C GLY 4.6 6.1 - - - +
94C VAL* 3.8 24.5 - - + -
113C ALA* 3.7 25.8 - - + -
114C GLN 4.0 2.5 - - - -
115C LEU* 4.0 8.7 - - + +
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Residues in contact with ALA 67 (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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83A VAL* 3.8 7.4 - - + -
65C ARG* 3.1 17.1 + - - +
66C ILE* 1.3 75.6 - - - +
68C PRO* 1.3 71.2 - - + +
79C ILE* 4.1 2.0 - - - -
113C ALA* 3.5 6.2 - - - +
114C GLN* 2.7 45.3 + - + +
116C ILE* 3.6 28.5 - - + -
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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