Contacts of the strand formed by residues 69 - 74 (chain B) in PDB entry 2OT3
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 69 (chain B).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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349A THR* 5.7 0.7 - - - +
17B ALA 5.6 3.5 + - - -
18B TYR 3.0 12.7 + - - +
19B SER* 3.5 22.5 + - - +
20B PHE* 2.9 30.1 + - - +
59B LYS 3.8 2.4 + - - -
60B LYS* 4.3 15.8 - - - +
67B ARG* 5.9 2.2 - - - +
68B VAL* 1.3 77.7 + - - +
70B LEU* 1.3 60.3 + - - +
71B ALA* 5.5 0.2 - - - +
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Residues in contact with LEU 70 (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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20B PHE* 3.9 4.9 - - + +
22B VAL* 3.5 31.6 - - + -
39B TYR* 3.8 26.7 - - + +
58B THR* 3.1 8.5 - - - +
59B LYS* 2.8 47.3 + - + +
61B LEU* 4.2 18.4 - - + -
68B VAL* 3.7 1.7 + - + -
69B ASN* 1.3 72.5 - - - +
71B ALA* 1.3 61.2 + - - +
72B ILE* 3.7 23.6 - - + -
173B PHE* 4.0 9.9 - - + -
176B LEU* 5.8 1.1 - - + -
177B CYS* 4.1 18.4 - - - -
180B MET* 4.1 4.5 - - + -
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Residues in contact with ALA 71 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
349A THR* 3.3 35.2 - - - +
20B PHE 3.1 14.7 + - - +
21B LYS* 4.9 0.7 - - - -
22B VAL* 3.0 29.3 + - - +
56B PHE* 4.0 11.0 - - + -
57B LEU 3.4 4.3 - - - -
58B THR* 4.1 3.6 - - + -
69B ASN 4.0 0.6 + - - +
70B LEU* 1.3 73.4 - - - +
72B ILE* 1.3 63.1 + - - +
73B TRP* 3.7 8.4 - - - +
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Residues in contact with ILE 72 (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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22B VAL* 3.5 17.7 - - + +
24B LEU* 4.1 23.6 - - + +
36B VAL* 4.1 28.7 - - + -
40B CYS* 4.4 7.9 - - - -
55B SER 3.6 2.1 - - - +
56B PHE* 3.4 8.1 - - - -
57B LEU* 2.5 48.2 + - + +
58B THR* 5.0 1.3 - - - +
70B LEU* 3.7 30.1 - - + -
71B ALA* 1.3 73.5 - - - +
73B TRP* 1.3 62.0 + - - +
74B ASP 4.8 0.9 - - - +
96B ILE* 5.7 0.9 - - + -
173B PHE* 3.7 23.8 - - + -
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Residues in contact with TRP 73 (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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347A LEU 3.9 9.4 - - - -
348A MET 3.8 15.3 - - - -
349A THR* 3.0 31.6 + - - -
353A GLY 3.5 20.0 - - - -
354A TYR* 3.5 38.4 - + + -
357A THR* 3.4 30.5 - - + -
21B LYS* 3.3 45.5 - - + +
22B VAL 2.8 12.6 + - - +
23B VAL* 3.4 10.7 - - + -
24B LEU* 3.0 24.3 + - - -
56B PHE* 3.5 9.9 - + - -
71B ALA* 3.7 13.4 - - - +
72B ILE* 1.3 75.5 - - - +
74B ASP* 1.3 64.4 + - - +
75B THR* 3.5 3.4 + - + +
88B TYR* 4.3 7.6 - + - -
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Residues in contact with ASP 74 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
311A SER* 3.6 7.8 - - - -
312A ALA* 2.8 26.9 + - + +
354A TYR* 2.6 28.4 + - - -
24B LEU* 3.4 24.1 - - + +
32B LYS* 2.8 41.5 + - - +
33B THR* 4.6 2.2 + - - -
54B ALA 4.1 5.7 - - - +
55B SER* 2.7 32.1 + - - +
72B ILE* 3.7 2.8 + - + +
73B TRP* 1.3 70.8 - - - +
75B THR* 1.3 63.8 + - - +
88B TYR* 3.7 4.5 - - - -
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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
------------------------------------------------------------
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