Contacts of the strand formed by residues 45 - 51 (chain B) in PDB entry 2O2V
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 45 (chain B).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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44B ASP* 1.3 69.5 - - - +
46B ARG* 1.3 69.4 + - - +
47B ILE* 3.7 17.0 + - + -
58B ILE 3.8 0.3 - - - +
59B ALA* 3.3 1.8 - - - -
60B PHE* 2.7 39.3 + - + +
62B ARG* 3.5 37.2 - - + +
64B VAL* 3.6 27.6 - - + -
104B ILE* 4.3 19.3 - - + -
107B LEU* 4.0 19.1 - - + -
116B LEU* 4.4 9.2 - - + -
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Residues in contact with ARG 46 (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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62A TYR* 5.2 1.0 + - - -
64A ASP* 4.6 1.2 - - - +
65A GLU* 2.9 40.8 + - - -
80A ALA* 5.1 5.1 + - + -
84A TYR* 3.9 31.0 - - - +
44B ASP* 3.5 10.0 + - + +
45B VAL* 1.3 75.8 - - - +
47B ILE* 1.3 63.1 + - - +
57B ILE* 3.9 35.7 - - + +
58B ILE 3.8 4.3 - - - -
59B ALA* 4.4 11.7 - - + +
107B LEU* 5.2 1.8 - - - +
114B LYS* 2.9 37.5 + - - +
115B SER* 3.2 11.7 - - - +
116B LEU* 2.9 25.3 + - - +
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Residues in contact with ILE 47 (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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45B VAL* 4.1 14.4 - - + -
46B ARG* 1.3 75.9 - - - +
48B LYS* 1.3 61.4 + - - +
49B PHE* 3.6 31.9 + - + -
56B ARG 3.5 2.3 - - - +
57B ILE* 3.2 5.0 - - - -
58B ILE 3.0 37.2 + - - +
60B PHE* 3.7 30.7 - - + -
64B VAL* 5.1 2.0 - - + -
69B VAL* 4.0 27.1 - - + -
100B LEU* 5.1 3.8 - - + -
115B SER* 5.0 0.2 - - - -
116B LEU* 3.5 20.0 - - + +
118B ILE* 3.6 24.5 - - + -
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Residues in contact with LYS 48 (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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64A ASP* 2.6 31.1 + - - +
66A ASP* 2.9 22.5 + - - -
68A ASP* 2.7 27.2 + - - +
70A ILE* 3.6 17.7 - - + -
46B ARG 4.1 0.8 + - - -
47B ILE* 1.3 69.6 - - - +
49B PHE* 1.3 66.9 + - - +
50B GLU* 4.0 6.4 - - - +
55B ARG* 4.3 9.4 - - + -
56B ARG 3.4 4.9 - - - +
57B ILE* 3.8 13.7 - - + -
115B SER* 3.9 19.5 - - - +
116B LEU 2.9 10.7 + - - +
117B ARG* 3.4 21.9 - - + +
118B ILE 2.9 26.1 + - - +
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Residues in contact with PHE 49 (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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47B ILE* 3.6 30.5 - - + -
48B LYS* 1.3 74.2 - - - +
50B GLU* 1.3 61.1 + - - +
54B GLU 3.9 0.3 - - - +
55B ARG* 3.1 5.5 - - - +
56B ARG* 2.7 41.3 + - + +
58B ILE* 4.3 22.2 - - + -
60B PHE* 4.1 22.0 - + - -
69B VAL* 4.1 19.5 - - + -
72B LYS* 4.9 2.9 - - + -
73B VAL* 3.4 27.6 - - + -
77B PHE* 3.9 26.9 - + + -
83B LEU* 4.6 0.4 - - + -
118B ILE* 3.3 10.8 - - + -
120B LEU* 3.8 26.9 - - + -
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Residues in contact with GLU 50 (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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48B LYS* 4.0 7.7 - - + +
49B PHE* 1.3 78.1 - - - +
51B HIS* 1.3 62.7 + - - +
54B GLU 3.4 7.2 - - - +
55B ARG* 3.8 23.8 + - + -
86B MET* 4.8 4.3 - - - +
117B ARG* 2.8 47.9 + - + +
118B ILE 2.8 17.0 + - - +
119B LEU* 3.7 25.0 - - + +
120B LEU* 2.8 28.2 + - - +
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Residues in contact with HIS 51 (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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49B PHE 4.3 0.2 - - - -
50B GLU* 1.3 76.1 - - - +
52B ASN* 1.3 100.7 + - + +
53B GLY 3.4 1.5 - - - +
54B GLU* 2.9 25.4 + - - +
77B PHE* 3.7 43.2 + + + +
79B GLN* 4.6 10.5 + - - -
81B LEU* 3.8 31.3 - - + +
119B LEU* 5.3 1.3 - - - -
120B LEU* 3.3 24.2 + - + -
121B LEU* 5.5 1.1 - - - -
122B SER* 5.5 2.2 - - - -
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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