Contacts of the strand formed by residues 3 - 11 (chain B) in PDB entry 2W3B
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 SER 3 (chain B).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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1B VAL* 3.0 21.1 - - - +
2B GLY* 1.3 82.5 - - - +
4B LEU* 1.3 68.7 + - - +
5B ASN* 4.6 11.1 + - - -
112B VAL* 4.6 5.5 + - - +
130B HIS* 2.8 37.5 + - - -
132B LYS* 5.4 0.7 - - - -
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Residues in contact with LEU 4 (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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1B VAL* 3.8 16.6 - - + -
3B SER* 1.3 83.7 + - - +
5B ASN* 1.3 68.4 + - - +
93B LEU* 4.5 11.4 - - + -
97B LEU* 3.8 27.8 - - + -
112B VAL* 3.9 15.7 - - + -
114B ILE* 4.7 6.1 - - + -
124B ALA* 4.6 7.0 - - + +
127B HIS* 3.6 38.1 - - + -
130B HIS 3.2 5.5 + - - -
131B LEU* 3.3 27.9 - - + +
132B LYS 3.1 22.9 + - - -
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Residues in contact with ASN 5 (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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3B SER* 4.6 9.6 + - - -
4B LEU* 1.3 81.0 - - - +
6B CYS* 1.3 57.3 + - - +
111B MET* 3.5 33.6 - - - +
112B VAL 3.0 25.7 + - - +
113B TRP* 3.3 28.6 - - + -
114B ILE* 2.7 35.3 + - - +
132B LYS* 3.3 35.4 - - - +
134B PHE* 3.9 3.5 - - + -
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Residues in contact with CYS 6 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
5B ASN* 1.3 75.0 - - - +
7B ILE* 1.3 62.2 + - - +
8B VAL* 6.0 1.8 - - + -
113B TRP* 4.4 1.3 - - - -
114B ILE* 3.4 20.6 - - - +
121B TYR* 4.3 14.1 - - + -
124B ALA* 3.7 29.8 - - - -
125B MET* 4.3 9.0 - - + -
131B LEU* 4.1 6.7 - - - -
132B LYS 2.9 6.9 + - - +
133B LEU* 3.5 28.8 - - + -
134B PHE* 2.8 30.2 + - - +
148B PHE* 6.2 1.8 - - + -
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Residues in contact with ILE 7 (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 CYS* 1.3 76.4 - - - +
8B VAL* 1.3 58.9 + - - +
33B TYR* 4.1 16.8 - - + -
34B PHE* 3.8 42.6 - - + +
37B MET* 3.9 28.5 - - + -
38B THR* 3.8 13.2 - - + -
113B TRP* 3.9 11.4 - - + -
114B ILE 3.1 4.9 + - - +
115B VAL* 3.8 10.8 - - + -
121B TYR* 2.7 26.1 + - - -
134B PHE* 3.3 16.8 - - + +
301B VG9 3.0 24.8 + - - +
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Residues in contact with VAL 8 (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 CYS* 6.0 1.6 - - + -
7B ILE* 1.3 76.1 - - - +
9B ALA* 1.3 64.4 + - - +
10B VAL* 4.9 1.1 - - + -
16B ILE* 3.7 22.7 - - + -
121B TYR* 3.4 29.6 - - + +
134B PHE 3.0 13.6 + - - +
135B VAL* 4.0 23.1 - - + -
136B THR 2.9 23.4 + - - -
148B PHE* 3.9 25.4 - - + -
201B NDP 3.4 14.4 - - - +
301B VG9 3.5 11.3 + - - -
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Residues in contact with ALA 9 (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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8B VAL* 1.3 72.4 - - - +
10B VAL* 1.3 60.8 + - - +
16B ILE* 3.6 7.3 - - - +
24B TRP* 3.3 23.9 - - + +
30B GLU* 3.9 14.6 - - - +
136B THR* 3.5 13.9 - - - +
138B ILE* 4.2 5.6 - - + -
201B NDP 2.8 30.7 + - - +
301B VG9 3.6 18.1 + - + +
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Residues in contact with VAL 10 (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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8B VAL* 4.9 4.0 - - + -
9B ALA* 1.3 75.4 - - - +
11B SER* 1.3 73.4 + - - +
14B MET* 3.5 35.7 - - + +
15B GLY 3.4 4.9 - - - +
16B ILE* 4.4 4.0 - - + -
24B TRP* 3.9 1.9 - - - -
135B VAL* 3.5 24.9 - - + -
136B THR 2.9 19.0 + - - +
137B ARG* 3.7 17.4 - - - +
138B ILE* 2.9 27.1 + - - +
148B PHE* 4.0 17.7 - - + -
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Residues in contact with SER 11 (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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10B VAL* 1.3 80.9 - - - +
12B GLN* 1.3 60.7 + - - +
13B ASN* 2.7 23.9 + - - -
14B MET* 2.9 21.0 + - - +
15B GLY* 2.9 28.9 + - - -
24B TRP* 3.7 13.9 - - - -
137B ARG* 5.5 1.3 + - - -
138B ILE* 3.5 11.0 - - - -
140B GLN 3.4 9.0 - - - -
142B PHE* 4.0 16.2 + - - -
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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