Contacts of the strand formed by residues 85 - 91 (chain B) in PDB entry 2BME
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 85 (chain B).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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12B LYS 3.4 3.7 + - - +
13B PHE* 3.2 14.3 - - - -
14B LEU 3.0 20.3 + - - -
83B ALA* 3.4 6.6 - - - +
84B ALA* 1.3 82.5 - - - +
86B ALA* 1.3 60.3 + - - +
116B ILE* 3.9 4.5 - - - -
117B VAL 3.2 10.5 - - - -
167B CYS* 3.6 17.3 - - - -
171B ILE* 4.1 0.4 - - - -
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Residues in contact with ALA 86 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
13B PHE* 5.2 0.2 - - - -
14B LEU* 3.2 19.7 - - + +
16B ILE* 4.2 24.9 - - + -
85B GLY* 1.3 75.8 - - - +
87B LEU* 1.3 68.7 + - - +
88B LEU 3.9 0.2 - - - -
116B ILE* 4.1 13.9 - - + -
117B VAL 2.8 8.2 + - - +
118B ILE* 3.3 12.3 - - + -
119B ILE 3.0 24.1 + - - -
167B CYS* 3.9 2.4 - - - -
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Residues in contact with LEU 87 (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 PHE* 4.4 7.2 - - + -
14B LEU 2.9 11.6 + - - +
15B VAL* 3.5 15.3 - - + +
16B ILE* 3.0 28.4 + - - +
26B LEU* 5.6 6.5 - - + -
86B ALA* 1.3 77.6 - - - +
88B LEU* 1.3 59.4 + - - +
89B VAL* 4.0 1.8 - - + -
119B ILE* 3.5 6.7 - - + -
121B CYS* 4.0 18.8 - - - -
163B ALA* 3.9 30.3 - - + +
164B PHE* 3.5 53.8 - - + -
167B CYS* 4.2 12.8 - - + -
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Residues in contact with LEU 88 (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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16B ILE* 3.4 24.7 - - + +
17B GLY* 4.2 2.2 - - - -
86B ALA 3.9 1.2 + - - -
87B LEU* 1.3 71.7 - - - +
89B VAL* 1.3 62.4 + - - +
101B LEU* 3.6 26.0 - - + +
104B TRP* 3.6 33.9 - - + -
105B LEU* 3.8 37.5 - - + -
118B ILE* 3.8 18.6 - - + -
119B ILE 2.9 9.9 + - - +
120B LEU* 3.5 15.4 - - + +
121B CYS 2.8 25.8 + - - -
147B LEU* 4.9 2.0 - - + -
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Residues in contact with VAL 89 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
15B VAL* 3.9 19.7 - - + -
16B ILE 2.9 15.8 + - - +
17B GLY* 3.5 18.2 - - - -
18B ASN 4.0 0.9 + - - -
21B THR* 3.8 28.0 - - - +
23B LYS* 4.0 4.5 - - + -
26B LEU* 3.8 24.7 - - + -
87B LEU* 4.0 6.7 - - + +
88B LEU* 1.3 78.2 - - - +
90B TYR* 1.3 74.3 + - - +
97B THR 5.0 0.9 - - - +
101B LEU* 4.4 6.1 - - - +
104B TRP* 5.8 0.2 - - - -
121B CYS* 3.4 15.0 - - + +
123B ASN* 3.8 16.4 - - + -
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Residues in contact with TYR 90 (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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21B THR* 3.7 11.4 - - - -
89B VAL* 1.3 72.8 - - - +
91B ASP* 1.3 72.2 + - - +
92B ILE* 3.9 21.9 - - + +
97B THR* 3.6 25.4 - - - +
98B TYR* 3.8 23.1 - + + +
101B LEU* 3.8 19.1 - - + -
120B LEU* 4.0 17.0 - - + -
121B CYS 3.0 13.0 + - - +
122B GLY* 3.4 19.7 - - - -
123B ASN* 2.9 29.3 + - - +
133B VAL* 3.9 21.0 + - + +
138B ALA* 3.2 23.3 - - + +
149B PHE* 3.3 19.1 - + - -
151B GLU* 4.5 1.4 + - - -
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Residues in contact with ASP 91 (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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20B GLY 4.1 2.0 - - - +
21B THR* 3.7 18.7 - - + +
90B TYR* 1.3 79.2 - - - +
92B ILE* 1.3 64.7 + - - +
93B THR* 2.6 33.1 + - - +
94B SER* 3.0 32.4 + - - +
97B THR* 2.9 15.2 + - + +
123B ASN 3.7 4.9 - - - -
124B LYS* 2.9 38.9 + - - +
133B VAL* 4.6 0.5 - - - +
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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