Contacts of the strand formed by residues 74 - 83 (chain B) in PDB entry 2W99
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 LEU 74 (chain B).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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57B VAL* 4.0 9.0 - - + +
60B LEU* 3.3 52.4 + - + +
61B ARG* 3.0 33.0 + - - -
64B GLU* 3.8 8.4 - - - +
72B VAL 4.0 2.4 + - - -
73B ARG* 1.3 69.0 - - - +
75B MET* 1.3 58.3 + - - +
76B ASP 2.8 31.6 - - - +
77B VAL* 3.1 22.0 - - + -
91B LEU* 4.7 8.5 - - + -
92B VAL 3.2 11.9 - - - +
93B PHE* 4.1 21.0 - - + -
159B PHE* 4.8 2.9 - - + -
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Residues in contact with MET 75 (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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149A LYS* 5.4 2.9 + - - +
6B TYR* 5.5 2.7 - - - +
25B ASP* 5.0 9.9 - - - +
28B SER* 6.1 1.1 - - - +
30B HIS* 6.3 3.1 - - + -
32B VAL* 4.9 13.0 - - + -
61B ARG* 3.6 14.8 + - - -
64B GLU* 3.3 27.9 - - - +
73B ARG* 3.0 30.4 + - + +
74B LEU* 1.3 73.2 - - - +
76B ASP* 1.3 63.7 + - + +
92B VAL* 3.3 19.0 + - + +
93B PHE 4.1 2.0 - - - +
94B GLU* 3.9 19.1 - - - +
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Residues in contact with ASP 76 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
146A ASN 5.3 0.2 - - - +
149A LYS* 3.4 25.5 - - - +
5B ARG* 3.1 37.0 + - - -
6B TYR* 3.5 20.5 + - - +
61B ARG* 4.3 6.5 - - - +
74B LEU* 2.8 20.3 - - - +
75B MET* 1.3 79.3 - - - +
77B VAL* 1.3 96.3 + - - +
78B CYS* 5.7 1.8 - - - +
92B VAL* 3.0 29.3 + - + +
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Residues in contact with VAL 77 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
146A ASN* 4.3 4.0 - - - +
149A LYS* 4.3 5.6 + - - -
150A TRP* 3.6 38.6 - - + -
5B ARG* 5.7 0.3 + - - -
57B VAL* 3.7 20.0 - - + -
61B ARG* 3.9 6.5 - - - -
74B LEU* 3.1 24.5 - - + -
76B ASP* 1.3 105.0 + - - +
78B CYS* 1.3 67.8 + - - +
89B VAL* 3.4 26.7 - - + -
90B THR 3.5 5.4 - - - -
91B LEU* 3.8 12.3 - - + -
92B VAL* 4.6 1.3 - - - +
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Residues in contact with CYS 78 (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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146A ASN* 3.5 16.2 - - - -
150A TRP* 4.4 0.2 - - - -
3B THR 4.8 2.2 - - - -
4B SER* 4.5 8.3 - - - +
76B ASP* 5.3 2.2 - - - +
77B VAL* 1.3 79.3 - - - +
79B ALA* 1.3 67.0 + - - +
80B THR* 3.3 19.4 + - - -
89B VAL* 3.2 5.1 - - - -
90B THR* 2.9 53.0 + - + +
92B VAL* 5.9 2.5 - - + -
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Residues in contact with ALA 79 (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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142A LEU* 3.7 25.2 - - + +
146A ASN* 2.9 26.8 + - - +
150A TRP* 3.7 25.0 - - + +
78B CYS* 1.3 71.7 - - - +
80B THR* 1.3 63.9 + - - +
87B ILE* 3.1 22.6 - - + +
88B LYS 3.4 6.1 - - - -
89B VAL* 4.1 2.9 - - + -
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Residues in contact with THR 80 (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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142A LEU* 5.6 1.0 - - - +
2B ALA 3.8 19.8 + - - +
3B THR* 3.5 27.1 - - - +
4B SER* 4.3 0.2 - - - +
78B CYS* 3.9 11.2 - - - +
79B ALA* 1.3 74.9 - - - +
81B SER* 1.3 67.3 + - - -
82B ARG* 3.5 3.3 + - - +
88B LYS* 2.6 32.6 + - - +
90B THR* 3.7 27.3 - - + +
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Residues in contact with SER 81 (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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80B THR* 1.3 80.7 + - - +
82B ARG* 1.3 65.9 + - - +
83B THR* 4.6 6.4 + - - +
86B GLU 3.3 2.8 + - - +
87B ILE* 2.9 31.7 - - - -
88B LYS* 3.0 19.6 + - - -
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Residues in contact with ARG 82 (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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135A GLU* 3.7 18.2 + - - +
138A LEU* 4.1 28.2 - - - +
139A GLN* 2.9 44.0 + - - +
142A LEU* 4.1 25.3 - - + +
41B ASN* 3.8 24.6 + - - +
80B THR 3.5 5.4 + - - +
81B SER* 1.3 75.6 + - - +
83B THR* 1.3 71.5 + - - +
84B ASP* 5.4 5.1 + - - +
86B GLU 3.9 1.3 - - - -
87B ILE* 4.6 5.6 - - + +
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Residues in contact with THR 83 (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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41B ASN* 3.5 3.4 - - - +
81B SER* 4.7 7.0 - - - +
82B ARG* 1.3 81.2 + - - +
84B ASP* 1.3 66.7 + - + +
85B ARG 3.0 0.7 + - - -
86B GLU* 2.5 60.2 + - + +
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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