Contacts of the strand formed by residues 137 - 141 (chain E) in PDB entry 2OCP
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 VAL 137 (chain E).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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39E ARG* 3.5 13.0 - - + +
41E LEU* 3.9 19.3 - - + -
65E TRP* 3.3 57.2 - - + +
66E HIS 2.9 25.8 + - - -
130E LEU* 3.1 11.5 - - - +
135E LYS* 3.7 8.0 + - + +
136E PRO* 1.3 79.7 - - - +
138E GLN* 1.3 62.7 + - - +
139E ILE* 3.9 7.9 - - + -
274E VAL* 3.6 19.1 - - + -
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Residues in contact with GLN 138 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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38E PRO* 4.7 1.1 - - + -
39E ARG 2.8 10.7 + - - +
40E ARG* 2.6 45.6 + - - +
41E LEU 2.9 26.7 + - - +
66E HIS* 3.2 37.1 + - - +
68E ALA* 5.3 1.1 - - + +
121E VAL 5.6 1.4 + - - -
124E GLU 5.4 3.3 + - - +
125E PRO 5.1 2.4 + - - -
126E PHE* 3.2 22.8 - - - +
127E PRO* 4.2 5.9 - - - +
130E LEU* 3.9 9.8 - - + +
137E VAL* 1.3 72.6 - - - +
139E ILE* 1.3 66.7 + - - +
140E PHE* 3.5 22.8 - - + -
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Residues in contact with ILE 139 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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41E LEU* 3.2 41.3 - - + +
43E ILE* 3.7 33.4 - - + -
58E LEU* 4.3 8.5 - - + -
65E TRP* 4.1 18.4 - - + -
66E HIS 2.7 10.4 + - - +
67E VAL* 3.3 25.6 - - + +
68E ALA* 2.8 30.0 + - - +
137E VAL* 3.9 13.9 - - + -
138E GLN* 1.3 74.5 - - - +
140E PHE* 1.3 67.8 + - - +
190E ILE* 4.6 13.5 - - + -
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Residues in contact with PHE 140 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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40E ARG* 3.5 36.3 - - + -
41E LEU 2.7 20.7 + - - +
42E SER* 3.1 8.0 - - - -
43E ILE* 2.8 30.1 + - - +
68E ALA* 3.7 23.8 - - + -
121E VAL* 3.6 34.1 - - + -
122E GLN* 3.8 19.3 - - + +
138E GLN* 3.5 31.2 - - + -
139E ILE* 1.3 77.0 - - - +
141E GLU* 1.3 61.7 + - - +
142E ARG 3.2 14.2 + - - +
186E LEU* 4.0 18.4 - - + -
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Residues in contact with GLU 141 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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43E ILE* 4.3 3.1 - - + -
51E LYS* 2.9 38.8 + - + +
52E SER* 4.3 7.7 + - - -
55E VAL* 4.1 29.1 - - + +
67E VAL* 4.3 12.2 - - + +
68E ALA 3.7 11.0 + - - +
69E THR* 3.8 8.7 + - - -
70E GLU* 2.7 63.5 + - + +
118E ARG* 5.3 0.3 - - - +
140E PHE* 1.3 69.8 - - - +
142E ARG* 1.3 64.9 + - - +
301E DTP 4.0 2.4 + - - -
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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