Contacts of the strand formed by residues 6 - 13 (chain B) in PDB entry 1BWN
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 6 (chain B).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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88A GLU* 4.5 15.3 - - + -
4B VAL* 2.7 26.3 - - - +
5B ILE* 1.3 99.0 - - + +
7B GLU* 1.3 61.7 + - - +
31B LEU* 3.5 0.7 - - - -
32B LEU* 3.1 18.7 + - + +
123B ARG* 4.3 23.3 - - + +
124B TRP* 3.2 63.7 - - + +
127B GLN* 4.4 13.9 - - + -
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Residues in contact with GLU 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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88A GLU* 4.1 17.8 - - - +
89A MET* 4.9 10.2 + - + +
92A ILE* 3.9 23.3 - - + +
4B VAL* 4.1 10.8 - - + +
6B LEU* 1.3 81.4 - - - +
8B SER* 1.3 67.6 + - - +
29B LEU* 3.8 23.1 - - + +
30B PHE 3.2 6.1 - - - -
31B LEU* 2.7 31.0 - - + +
49B ARG* 6.3 0.2 - - - -
124B TRP* 3.8 0.2 - - - -
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Residues in contact with SER 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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88A GLU* 4.3 5.7 + - - +
91A GLN* 3.7 9.5 + - - -
92A ILE* 4.2 3.6 - - - -
7B GLU* 1.3 77.8 + - - +
9B ILE* 1.3 60.0 + - - +
10B PHE* 3.7 19.5 - - - -
29B LEU* 3.3 8.0 - - - +
30B PHE* 2.7 35.2 + - - +
120B LEU* 3.7 14.7 - - - +
124B TRP* 2.9 29.7 + - - -
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Residues in contact with ILE 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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44A PHE* 4.2 21.1 - - + -
91A GLN* 2.9 40.1 + - - +
92A ILE* 3.6 27.6 - - + -
95A ILE* 4.2 12.8 - - + -
8B SER* 1.3 72.2 - - - +
10B PHE* 1.3 71.6 + - - +
27B LYS* 4.5 3.4 - - + -
28B ARG 3.3 9.2 - - - +
29B LEU* 4.0 15.5 - - + +
42B TYR* 4.2 35.0 - - + -
95B ILE* 4.8 7.0 - - + -
98B PHE* 3.8 20.6 - - + -
116B PRO* 4.4 0.2 - - - +
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Residues in contact with PHE 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 SER* 3.7 8.7 - - - -
9B ILE* 1.3 78.9 - - - +
11B LEU* 1.3 58.9 + - - +
27B LYS* 3.2 3.7 - - - +
28B ARG* 2.6 40.5 + - - +
30B PHE* 3.6 25.8 - + + -
98B PHE* 4.1 7.4 - - - -
102B PHE* 4.2 12.1 - + - -
113B VAL* 3.5 26.2 - - + -
114B PHE 3.1 22.2 - - - +
115B SER* 3.5 29.2 - - - -
116B PRO* 4.0 1.3 - - + -
120B LEU* 4.0 12.8 - - + -
124B TRP* 3.3 57.2 - + + -
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Residues in contact with LEU 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 PHE* 1.3 75.0 - - - +
12B LYS* 1.3 64.0 + - - +
25B PHE* 3.6 24.0 - - + +
26B LYS 3.4 23.3 - - - +
27B LYS* 3.9 15.5 - - + +
76B GLU* 3.2 44.4 - - + +
77B ARG* 3.6 21.5 - - + +
98B PHE* 3.8 26.9 - - + -
113B VAL* 3.7 1.0 - - - -
114B PHE* 2.9 32.1 + - + -
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Residues in contact with LYS 12 (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 4IP 2.8 47.5 + - - +
11B LEU* 1.3 76.9 - - - +
13B ARG* 1.3 76.1 + - - +
14B SER* 4.1 1.6 - - - +
25B PHE* 3.1 6.6 - - - -
26B LYS* 2.9 37.9 + - - +
28B ARG* 3.9 8.7 - - + -
30B PHE* 3.9 21.5 - - + -
39B TYR* 3.4 46.9 - - + -
111B LEU* 4.2 10.3 - - + -
112B TYR 3.2 13.2 - - - +
113B VAL* 4.6 0.4 - - - -
114B PHE* 4.4 0.9 - - - -
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Residues in contact with ARG 13 (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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12B LYS* 1.3 86.9 + - - +
14B SER* 1.3 77.4 + - - +
15B GLN* 3.3 6.4 + - - +
16B GLN* 5.7 0.2 + - - -
23B LEU* 3.6 35.6 - - + +
24B ASN 3.1 8.3 - - - +
25B PHE* 3.8 32.3 - - + -
110B PRO* 5.5 0.8 + - - +
111B LEU* 4.6 2.4 - - - +
112B TYR* 3.0 61.9 + - + +
114B PHE* 4.4 2.4 - - + -
146B PHE* 4.0 14.5 - - - +
147B TRP* 3.0 36.3 + - - +
148B ILE* 4.3 9.2 - - - +
160B LYS* 6.2 0.8 - - - +
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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