Contacts of the strand formed by residues 170 - 176 (chain B) in PDB entry 4WB7
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 ASN 170 (chain B).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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128B ILE* 4.0 14.4 - - + +
129B LEU 3.2 7.6 - - - +
130B ASP* 3.4 21.7 + - - +
131B LYS* 3.8 1.7 - - - +
166B LYS* 3.3 6.4 - - - +
167B ASP* 2.8 36.1 + - - +
169B SER* 1.3 85.7 - - - +
171B LEU* 1.3 65.4 + - - +
172B TYR* 3.0 33.7 + - + +
390B ILE* 3.8 19.4 - - - +
391B ARG 3.8 14.8 + - - +
392B VAL* 4.5 0.8 - - - +
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Residues in contact with LEU 171 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
127B LYS 3.7 0.5 - - - +
128B ILE* 3.5 4.5 - - - -
129B LEU* 2.8 48.5 + - + +
131B LYS* 3.7 24.7 - - + -
134B VAL* 4.7 4.0 - - + -
143B THR* 3.7 28.3 - - + -
165B PHE 3.9 2.7 - - - -
166B LYS* 3.8 21.1 - - + -
170B ASN* 1.3 74.0 - - - +
172B TYR* 1.3 64.1 - - - +
173B MET* 5.8 0.4 - - - -
402B PHE* 3.7 34.5 - - + -
405B PHE* 3.9 29.8 - - + -
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Residues in contact with TYR 172 (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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95B LEU* 3.5 28.8 - - + +
126B MET* 3.9 21.1 - - + -
127B LYS 3.3 4.0 - - - +
128B ILE* 3.9 28.5 - - + -
164B SER* 3.3 8.8 - - - -
165B PHE* 2.9 75.8 + + + +
166B LYS* 4.1 0.7 - - - -
167B ASP* 2.5 39.5 + - - -
170B ASN* 3.0 32.9 + - + -
171B LEU* 1.3 77.7 - - - +
173B MET* 1.3 65.8 + - - +
174B VAL* 4.1 0.9 - - - -
390B ILE* 4.1 2.9 - - + +
392B VAL* 4.0 1.7 - - - +
405B PHE* 3.8 2.2 - - - -
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Residues in contact with MET 173 (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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125B ALA 3.6 2.4 - - - +
127B LYS* 2.8 51.0 + - + +
129B LEU* 3.6 27.8 - - + -
143B THR* 4.7 6.7 - - + -
146B GLU* 3.5 36.1 - - + +
147B LYS* 4.0 28.5 - - + -
150B LEU* 5.6 4.9 - - + -
161B LEU* 3.7 20.0 - - + -
163B PHE 3.8 3.8 - - - -
164B SER* 4.7 0.4 - - - -
171B LEU* 5.9 0.4 - - + -
172B TYR* 1.3 78.0 - - - +
174B VAL* 1.3 64.3 + - - +
175B MET* 3.6 6.1 + - + +
405B PHE* 3.9 13.7 - - + -
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Residues in contact with VAL 174 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
98B PHE* 4.2 15.0 - - + -
115B VAL* 4.8 0.7 - - + -
124B TYR* 3.5 31.9 - - + -
125B ALA 3.7 4.0 - - - +
126B MET* 3.9 22.7 - - + +
161B LEU* 3.5 2.7 - - - +
162B GLU* 2.8 25.1 + - - +
163B PHE* 2.8 41.4 + - + +
165B PHE* 3.8 29.6 - - + -
173B MET* 1.3 75.0 - - - +
175B MET* 1.3 57.3 + - - +
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Residues in contact with MET 175 (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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112B VAL* 4.4 4.0 - - + -
124B TYR* 3.3 9.5 - - - +
125B ALA 2.8 38.8 + - - +
127B LYS* 3.9 32.1 - - + +
150B LEU* 4.5 10.3 - - + -
159B VAL* 4.1 13.2 - - + -
160B LYS 3.3 14.1 - - - +
161B LEU* 4.2 14.6 - - + -
162B GLU* 4.1 3.6 - - - -
173B MET* 4.1 4.9 - - + +
174B VAL* 1.3 77.4 - - - +
176B GLU* 1.3 73.6 + - - +
238B THR* 3.5 22.4 - - - +
239B ASP 5.2 1.6 - - - -
501B ATP 3.6 27.8 - - + +
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Residues in contact with GLU 176 (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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124B TYR* 4.5 4.7 - - - -
159B VAL* 3.7 9.9 - - + +
160B LYS* 3.0 47.2 + - + +
162B GLU* 3.7 17.5 - - - +
175B MET* 1.3 70.1 - - - +
177B TYR* 1.3 71.0 + - - +
178B VAL* 3.5 4.3 + - + +
236B GLN* 3.6 19.8 - - - +
501B ATP 2.9 25.1 + - - -
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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