Contacts of the strand formed by residues 109 - 115 (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 GLY 109 (chain B).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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15B GLN* 5.4 0.7 - - - -
105B VAL* 4.0 8.3 - - - -
106B TYR* 2.8 45.3 + - - -
107B ASP 3.3 0.2 - - - -
108B GLU* 1.3 81.4 - - - +
110B PRO* 1.3 70.2 - - - +
160B LYS 4.7 3.1 - - - -
161B ASN* 3.6 11.0 - - - -
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Residues in contact with PRO 110 (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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13B ARG* 5.7 0.4 - - - +
15B GLN* 4.5 9.7 - - - +
103B GLN* 4.4 2.9 - - + +
104B VAL 3.5 5.2 - - - +
105B VAL* 4.0 18.6 - - + -
106B TYR* 4.7 1.1 - - - -
109B GLY* 1.3 85.4 - - - +
111B LEU* 1.3 62.3 + - - +
112B TYR* 3.6 45.1 + - + +
147B TRP* 4.7 4.9 - - + -
152B TYR* 3.5 24.0 - - + +
160B LYS* 4.4 20.6 - - + -
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Residues in contact with LEU 111 (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* 4.2 28.0 - - + -
13B ARG 4.6 2.0 - - - +
15B GLN* 4.2 24.5 - - + +
30B PHE* 4.1 21.3 - - + -
37B LEU* 4.4 9.9 - - + -
39B TYR* 4.2 9.9 - - + -
56B ILE* 3.6 30.5 - - + -
103B GLN* 3.3 5.9 - - - +
104B VAL* 2.7 42.7 + - + +
106B TYR* 4.4 0.7 - - + -
109B GLY 3.8 0.8 + - - -
110B PRO* 1.3 72.0 - - - +
112B TYR* 1.3 74.0 + - - +
113B VAL* 3.8 13.7 + - + +
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Residues in contact with TYR 112 (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* 3.2 8.1 - - - +
13B ARG* 3.0 89.1 + - + -
15B GLN* 5.6 0.4 - - - +
67B VAL* 4.2 6.3 - - + -
102B PHE 3.9 0.9 - - - -
103B GLN* 3.9 27.3 + - + -
110B PRO* 3.6 42.4 + - + +
111B LEU* 1.3 74.9 - - - +
113B VAL* 1.3 60.7 + - - +
114B PHE* 3.7 10.7 - - + -
145B CYS 3.5 9.2 + - - -
146B PHE* 3.6 30.7 - + + -
147B TRP* 3.0 21.0 + - + -
152B TYR* 3.7 5.0 - - - -
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Residues in contact with VAL 113 (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* 3.5 30.5 - - + -
11B LEU 3.7 3.6 - - - +
12B LYS* 4.5 0.2 - - - +
30B PHE* 4.2 18.6 - - + -
37B LEU* 5.9 0.2 - - + -
101B PRO* 3.1 3.8 - - - +
102B PHE* 2.9 77.6 + - + +
104B VAL* 4.6 4.0 - - + -
111B LEU* 3.9 26.7 - - + +
112B TYR* 1.3 74.6 - - - +
114B PHE* 1.3 68.0 + - - +
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Residues in contact with PHE 114 (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* 3.1 25.2 - - - +
11B LEU* 2.9 30.1 + - + +
13B ARG* 4.4 2.9 - - + -
25B PHE* 4.1 25.8 - + - -
70B GLU* 4.2 8.3 - - + -
77B ARG* 3.5 26.0 - - + -
98B PHE* 3.6 27.1 - - + +
99B PRO 4.7 0.9 - - - -
100B TYR 3.5 2.2 - - - -
101B PRO* 3.6 36.8 - - + -
112B TYR* 3.7 23.8 - - + -
113B VAL* 1.3 76.8 - - - +
115B SER* 1.3 60.4 + - - +
146B PHE* 4.2 17.9 - + - -
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Residues in contact with SER 115 (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* 3.5 10.8 - - - -
98B PHE* 3.7 1.8 - - - -
99B PRO* 2.7 31.7 - - - +
100B TYR* 2.8 25.8 + - - -
102B PHE* 5.0 2.4 - - - -
113B VAL 4.1 0.2 + - - -
114B PHE* 1.3 72.9 - - - +
116B PRO* 1.3 58.7 - - - +
117B THR 2.7 28.5 + - - -
120B LEU* 3.1 21.7 - - - +
121B ARG* 3.2 11.7 + - - -
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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