Contacts of the strand formed by residues 155 - 162 (chain B) in PDB entry 6ISB
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 ILE 155 (chain B).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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5B TRP* 3.5 27.2 - - + -
7B THR* 3.2 4.9 - - - +
8B SER* 2.8 42.0 + - - +
112B PHE* 3.8 30.1 - - + -
113B GLU* 5.3 2.5 - - - +
148B GLU* 4.0 21.3 - - + +
149B LYS 3.3 9.4 - - - +
150B ILE* 4.1 32.8 - - + -
154B GLN* 1.3 77.0 - - - +
156B ASP* 1.3 62.7 + - - +
203B ARG* 6.0 3.1 - - - +
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Residues in contact with ASP 156 (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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5B TRP* 4.8 0.7 - - - -
6B HIS 3.3 2.9 - - - +
7B THR* 2.6 35.7 + - - +
102B LYS* 5.1 0.9 + - - -
148B GLU* 3.2 7.9 - - - +
149B LYS* 2.9 35.6 + - + +
151B GLN* 2.9 18.6 + - - +
154B GLN* 2.8 28.3 + - - +
155B ILE* 1.3 75.2 - - - +
157B LEU* 1.3 61.5 + - - +
158B LEU* 3.6 0.7 + - - +
173B PHE* 3.2 36.5 - - + -
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Residues in contact with LEU 157 (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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5B TRP* 3.8 10.9 - - - +
6B HIS* 2.7 28.3 + - + +
146B ARG* 3.8 30.7 - - + +
147B TRP 3.4 13.5 - - - +
148B GLU* 4.4 2.7 - - + -
156B ASP* 1.3 71.3 - - - +
158B LEU* 1.3 54.6 + - - +
159B THR* 3.2 28.7 - - - +
160B TYR* 3.9 12.3 - - + -
169B PHE* 3.4 40.6 - - + +
171B SER* 2.8 30.0 + - - -
172B LYS 4.5 0.9 + - - -
173B PHE* 3.5 10.0 + - - +
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Residues in contact with LEU 158 (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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147B TRP* 2.7 22.1 + - + +
148B GLU 3.9 12.6 - - - +
149B LYS* 4.0 17.3 - - + +
156B ASP 4.6 0.7 - - - +
157B LEU* 1.3 74.8 - - - +
159B THR* 1.3 64.8 + - - +
171B SER* 3.0 21.2 + - - -
173B PHE* 3.4 38.6 - - + -
175B ARG* 5.7 0.2 - - + -
177B ILE* 4.1 30.1 - - + +
189B ILE* 4.0 16.6 - - + -
202B TYR* 3.6 33.9 - - + -
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Residues in contact with THR 159 (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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145B VAL* 4.5 1.1 - - + +
146B ARG* 3.5 0.9 - - - -
147B TRP* 2.9 50.2 + - + -
157B LEU* 3.2 10.4 - - - +
158B LEU* 1.3 84.5 + - - +
160B TYR* 1.3 64.9 + - - +
161B CYS* 3.8 22.4 - - - -
171B SER* 4.8 2.7 - - - +
177B ILE* 3.8 11.4 + - - +
179B SER* 3.0 37.4 + - - +
181B CYS* 4.3 2.9 - - - -
189B ILE* 3.9 1.0 - - + +
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Residues in contact with TYR 160 (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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4B LEU* 4.6 15.5 - - + +
144B ALA* 3.6 21.5 - - + +
145B VAL 3.3 12.6 - - - -
146B ARG* 3.6 23.3 - - + -
157B LEU* 3.9 14.8 - - + +
159B THR* 1.3 76.6 - - - +
161B CYS* 1.3 70.3 + - - +
162B ASN* 3.0 46.6 + - + -
168B ASN* 4.4 7.6 - - - -
169B PHE* 3.3 53.9 + + + +
171B SER 5.7 1.0 - - - +
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Residues in contact with CYS 161 (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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144B ALA* 3.3 2.4 - - - -
145B VAL* 2.8 42.8 + - + +
159B THR* 3.8 11.2 - - - -
160B TYR* 1.3 89.8 - - - +
162B ASN* 1.3 62.1 + - - +
163B LEU* 3.8 7.4 + - + +
180B ASN 4.7 1.6 - - - -
181B CYS* 2.0 55.0 - - + -
186B TRP* 4.3 8.7 - - + -
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Residues in contact with ASN 162 (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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143B GLN* 4.0 12.1 + - - +
144B ALA* 4.2 7.2 - - - +
160B TYR* 3.0 35.0 + - + +
161B CYS* 1.3 72.5 - - - +
163B LEU* 1.3 64.0 + - - +
164B VAL* 2.9 46.9 + - + +
168B ASN* 4.7 18.1 + - - +
93C TYR* 4.3 13.6 + - - -
99C THR* 6.0 1.8 - - - +
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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