Contacts of the strand formed by residues 87 - 93 (chain B) in PDB entry 1B8M
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 VAL 87 (chain B).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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86B TRP* 1.3 75.7 - - - +
88B SER* 1.3 56.6 + - - +
123B LEU* 3.6 2.6 - - - -
124B LEU* 2.6 55.4 + - + -
125B SER* 3.2 29.9 + - - +
126B ARG* 4.6 12.8 - - + -
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Residues in contact with SER 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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76B GLY 3.7 4.0 - - - +
77B GLY* 3.2 16.9 - - - -
78B CYS* 3.0 32.6 + - - -
81B VAL* 3.1 21.8 - - - +
83B ARG* 4.9 1.6 + - - +
86B TRP 3.9 2.5 + - - -
87B VAL* 1.3 77.9 - - - +
89B GLU* 1.3 66.0 + - - +
121B CYS* 4.1 2.7 - - - -
122B THR 3.1 12.3 - - - -
123B LEU* 4.1 8.1 - - - -
124B LEU* 4.4 4.4 - - - +
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Residues in contact with GLU 89 (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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76B GLY 4.2 9.6 - - - +
78B CYS* 3.8 4.2 - - - -
88B SER* 1.3 79.8 + - - +
90B CYS* 1.3 72.8 + - - +
91B LYS* 2.9 34.5 + - - +
122B THR* 2.7 41.8 + - - +
124B LEU* 3.9 22.8 - - + +
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Residues in contact with CYS 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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16B VAL 4.0 4.5 - - - -
17B CYS* 2.0 50.7 - - - -
18B ASP 5.0 0.9 - - - -
61B CYS* 4.1 8.4 - - + +
63B ALA* 5.5 10.0 - - + +
76B GLY 4.9 3.4 + - - -
77B GLY 4.7 4.3 - - - -
78B CYS* 4.1 11.7 - - - -
89B GLU* 1.3 79.9 - - - +
91B LYS* 1.3 59.8 + - - +
119B CYS* 3.9 13.9 - - - -
120B VAL 3.3 6.5 - - - -
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Residues in contact with LYS 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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9A GLU* 3.1 31.3 + - - +
61B CYS* 3.6 5.6 - - - -
89B GLU* 2.9 30.4 + - - +
90B CYS* 1.3 73.5 - - - +
92B ALA* 1.3 68.2 + - - +
119B CYS* 3.4 1.9 - - - -
120B VAL* 2.8 36.3 + - + +
122B THR* 3.8 23.2 - - - +
124B LEU* 4.4 15.0 - - - +
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Residues in contact with ALA 92 (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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9A GLU* 5.4 3.3 - - - +
60B ARG* 4.9 7.4 - - + -
61B CYS* 3.9 11.0 - - - +
91B LYS* 1.3 85.2 - - - +
93B LYS* 1.3 64.0 + - - +
94B GLN* 3.6 8.6 - - - +
116B ASP* 4.0 27.8 - - + +
118B ALA 3.1 11.7 - - - +
120B VAL* 5.1 0.9 - - - +
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Residues in contact with LYS 93 (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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9A GLU* 5.3 9.0 - - - +
11A SER* 4.0 21.7 + - - -
15A SER* 3.6 21.8 + - - -
56A THR* 5.0 10.2 - - + +
107A THR 5.5 5.4 - - - +
108A SER* 5.4 3.6 - - - -
92B ALA* 1.3 74.8 - - - +
94B GLN* 1.3 71.4 + - - +
116B ASP* 3.4 5.4 - - - -
117B THR* 2.9 26.2 + - - +
118B ALA* 2.8 19.7 + - + +
120B VAL* 4.1 33.2 - - + -
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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