Contacts of the strand formed by residues 32 - 35 (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 TYR 32 (chain C).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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121A TYR 4.6 2.0 - - - -
122A TYR* 3.1 12.6 - + - +
123A PRO* 2.3 47.8 + - + -
125A LEU* 3.5 28.3 - - + -
22C PRO* 3.9 17.9 - - + -
23C THR* 3.4 6.5 - - - +
24C ARG* 3.3 38.2 + - + -
30C ALA 5.1 0.7 - - - -
31C GLY* 1.3 77.9 - - - -
33C ASP* 1.3 63.8 + - - +
34C LEU* 3.5 1.6 + - - +
114C GLN* 4.2 0.4 - - - -
115C LEU* 2.8 49.1 + - + +
117C TYR* 3.4 31.9 - + + -
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Residues in contact with ASP 33 (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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22C PRO* 3.3 16.6 - - - +
23C THR* 2.7 22.2 + - - +
25C GLN* 3.6 12.1 + - - +
31C GLY 4.9 0.9 - - - -
32C TYR* 1.3 70.1 - - - +
34C LEU* 1.3 59.9 + - - +
35C TYR* 3.2 30.8 + - - +
69C ARG* 3.0 35.5 + - - -
111C ARG* 3.2 39.0 + - + -
113C ALA 3.5 7.4 - - - +
114C GLN* 3.7 3.8 - - - +
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Residues in contact with LEU 34 (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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20C LYS 6.1 0.2 - - - -
22C PRO* 4.1 24.7 - - + -
32C TYR 4.0 7.4 - - - +
33C ASP* 1.3 75.4 - - - +
35C TYR* 1.3 62.6 + - - +
52C THR* 4.2 16.6 - - + -
54C ILE* 5.5 4.7 - - + -
66C ILE* 3.6 33.4 - - + -
92C ILE* 4.2 16.4 - - + -
94C VAL* 4.0 14.1 - - + -
111C ARG* 3.5 4.3 - - - -
112C ILE* 2.9 34.6 + - + +
113C ALA* 3.0 13.6 + - + +
115C LEU* 4.0 26.5 - - + +
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Residues in contact with TYR 35 (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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20C LYS* 3.6 58.3 + - + +
21C SER 3.6 17.5 - - - -
23C THR* 2.9 20.6 + - - -
33C ASP* 3.2 31.9 + - + +
34C LEU* 1.3 75.0 - - - +
36C SER* 1.3 65.4 + - - +
37C ALA* 3.5 2.6 + - - -
52C THR* 3.6 23.9 - - - +
109C GLY 3.2 22.4 - - - +
110C ASP 3.2 5.8 - - - +
111C ARG* 3.8 25.6 - - + -
112C ILE* 4.1 4.7 - - - -
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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