Contacts of the strand formed by residues 32 - 37 (chain B) in PDB entry 2OSL
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 ILE 32 (chain B).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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4B LEU* 4.0 11.7 - - + -
23B CYS* 4.5 0.4 - - - -
25B ALA* 6.2 0.2 - - + -
29B VAL* 4.1 2.9 - - + -
31B TYR* 1.3 73.6 - - - +
33B HIS* 1.3 71.7 + - - +
34B TRP* 3.6 27.4 - - + +
47B ILE 4.6 0.5 - - - +
48B TYR 4.4 0.2 - - - -
49B ALA 3.8 0.2 + - - -
50B THR* 2.7 41.0 + - - -
70B TYR* 3.4 49.8 - - + -
87B CYS* 3.7 26.2 - - - -
88B GLN 3.5 18.8 - - - +
89B GLN* 3.9 14.1 - - + -
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Residues in contact with HIS 33 (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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101A TYR* 5.9 0.4 - - - -
105A ASP* 2.9 34.3 + - + +
106A TRP 2.9 26.3 + - - -
107A TYR* 4.2 10.5 - + - +
31B TYR* 4.4 1.5 + - + -
32B ILE* 1.3 79.4 - - - +
34B TRP* 1.3 61.7 + - - +
35B PHE* 4.1 5.8 - + + -
47B ILE 3.4 6.3 - - - +
48B TYR* 3.4 27.9 - - + +
49B ALA* 3.4 18.9 + - - +
86B TYR 4.3 0.2 - - - -
87B CYS* 3.4 3.8 - - - -
88B GLN* 2.7 67.8 + - - +
90B TRP* 3.8 7.5 + + - -
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Residues in contact with TRP 34 (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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6B GLN* 3.5 25.6 - - + -
21B MET* 3.9 26.5 - - + -
22B THR 4.3 1.8 - - - -
23B CYS* 3.8 26.2 - - + -
32B ILE* 3.6 20.4 - - + +
33B HIS* 1.3 79.3 - - - +
35B PHE* 1.3 69.4 + - - +
46B TRP* 3.2 9.9 + - + -
47B ILE* 3.0 60.2 + - + +
50B THR* 4.7 5.7 + - - +
64B SER 5.6 0.2 + - - -
70B TYR* 4.5 1.4 - - - +
71B SER* 3.5 36.8 + - - +
72B LEU* 3.6 34.7 - - + +
85B TYR* 4.6 4.9 - - + -
86B TYR 3.1 15.0 - - - -
87B CYS* 4.3 2.5 - - + -
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Residues in contact with PHE 35 (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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107A TYR* 5.1 6.3 - + - -
108A PHE* 3.6 39.5 - + + -
111A TRP* 3.8 13.0 - + - -
33B HIS* 4.1 11.0 - - + -
34B TRP* 1.3 77.6 - - - +
36B GLN* 1.3 60.5 + - - +
37B GLN 4.0 0.2 + - - -
43B PRO* 4.1 16.2 - - + -
44B LYS 3.2 26.0 - - - +
45B PRO* 3.6 11.9 - - + -
46B TRP* 4.2 1.8 - - - -
47B ILE 5.8 0.4 - - - -
84B THR 3.7 0.3 - - - +
85B TYR* 3.2 5.6 - - - -
86B TYR* 2.6 53.6 + - + +
88B GLN* 3.2 37.5 - - + -
97B PHE* 3.7 21.3 - + + -
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Residues in contact with GLN 36 (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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35B PHE* 1.3 73.2 - - - +
37B GLN* 1.3 59.4 + - - +
38B LYS* 3.1 42.8 - - - +
44B LYS* 3.0 41.1 + - + +
46B TRP* 3.1 53.0 - - + +
61B PHE* 4.8 0.2 - - - -
80B GLU 4.6 5.8 + - - +
81B ASP* 5.0 0.2 - - - -
83B ALA* 4.0 5.4 - - + +
84B THR 3.5 4.3 - - - -
85B TYR* 3.2 38.2 + - + -
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Residues in contact with GLN 37 (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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39A GLN* 2.8 43.1 + - - -
95A TYR* 3.3 3.4 + - - -
36B GLN* 1.3 76.2 - - - +
38B LYS* 1.3 69.8 + - - +
39B PRO* 4.1 4.2 - - + +
40B GLY 5.8 0.6 - - - +
41B SER 2.7 27.7 + - - +
42B SER 4.8 1.6 - - - -
43B PRO* 3.2 29.7 - - + +
44B LYS* 5.9 0.4 - - - +
83B ALA* 3.8 1.7 - - - +
84B THR* 2.8 38.3 + - - +
86B TYR* 3.2 24.7 + - + -
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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