Contacts of the strand formed by residues 167 - 175 (chain B) in PDB entry 4GWF
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 167 (chain B).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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123B GLU* 3.8 42.6 - - + +
126B LEU* 3.7 41.3 - - + -
127B THR* 4.9 5.4 - - - +
150B SER* 5.6 0.2 - - - -
151B VAL 3.4 4.5 - - - +
152B ARG* 4.0 15.5 - - + -
166B LYS* 1.3 76.5 - - - +
168B THR* 1.3 60.2 + - - +
169B HIS* 3.5 19.2 + - + +
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Residues in contact with THR 168 (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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149B LEU 3.4 3.8 - - - +
150B SER* 3.5 1.4 - - - -
151B VAL* 2.9 36.5 + - - +
153B THR* 4.0 11.6 - - - +
166B LYS* 4.7 5.4 - - - +
167B VAL* 1.3 71.9 - - - +
169B HIS* 1.3 66.6 + - - +
170B VAL* 4.0 3.8 + - + -
204B GLU* 3.5 39.4 + - - +
210B LEU* 3.7 30.8 - - + +
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Residues in contact with HIS 169 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
119B GLY 4.6 1.2 + - - -
122B ALA* 5.4 0.2 - - - +
123B GLU* 3.3 45.1 + - + +
138B ARG* 3.3 21.1 + - - +
148B VAL* 4.0 9.9 - - + -
149B LEU 3.5 4.3 - - - -
150B SER* 3.2 30.9 + - - -
167B VAL* 3.5 22.1 + - + +
168B THR* 1.3 74.7 - - - +
170B VAL* 1.3 62.9 + - - +
171B MET* 4.1 9.2 + - + +
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Residues in contact with VAL 170 (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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148B VAL* 3.5 1.4 - - - -
149B LEU* 2.7 62.2 + - + +
151B VAL* 5.2 1.3 - - + -
168B THR* 4.6 7.0 - - + +
169B HIS* 1.3 75.9 - - - +
171B MET* 1.3 68.8 + - - +
172B ILE* 3.7 0.5 + - - +
181B VAL* 3.8 34.5 - - + +
202B MET* 3.9 13.5 - - + -
210B LEU* 3.8 28.9 - - + -
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Residues in contact with MET 171 (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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138B ARG* 5.7 1.3 - - - +
140B SER* 4.7 10.3 - - - +
142B SER* 4.9 8.7 - - - +
146B ASP* 6.0 4.0 - - + +
147B PHE 3.9 5.6 - - - +
148B VAL* 3.9 30.7 - - + -
169B HIS* 4.1 10.2 + - + +
170B VAL* 1.3 77.0 - - - +
172B ILE* 1.3 60.9 + - - +
173B ARG* 4.0 8.7 + - + +
180B ASP 4.0 0.2 - - - +
181B VAL* 3.6 24.8 - - - +
182B GLY 4.6 0.2 + - - -
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Residues in contact with ILE 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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137B VAL* 4.4 13.7 - - + -
146B ASP* 3.4 5.2 - - - +
147B PHE* 2.8 45.4 + - + +
148B VAL 4.5 0.4 - - - -
149B LEU* 3.7 30.7 - - + +
170B VAL 4.1 4.9 - - - +
171B MET* 1.3 75.4 - - - +
173B ARG* 1.3 68.9 + - - +
179B TYR* 4.1 7.6 - - + -
180B ASP 3.4 4.9 - - - +
181B VAL* 4.0 15.7 - - + -
190B LEU* 3.8 31.4 - - + -
193B LEU* 3.9 33.9 - - + -
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Residues in contact with ARG 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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26A ASP* 5.8 1.6 + - - +
99A LYS* 6.3 1.4 - - - +
100A TYR* 4.9 4.0 + - - -
143B HIS* 4.5 17.2 - - - -
146B ASP* 3.4 21.0 + - - +
171B MET* 4.0 8.2 + - + +
172B ILE* 1.3 75.4 - - - +
174B CYS* 1.3 60.2 + - - +
175B GLN* 3.4 42.9 + - + +
178B LYS 3.7 0.7 - - - +
179B TYR* 3.4 6.6 - - - +
180B ASP* 2.9 45.2 + - - +
182B GLY* 5.6 6.5 - - - +
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Residues in contact with CYS 174 (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 GLY* 3.6 26.2 - - - +
146B ASP* 3.4 14.8 + - - +
147B PHE* 4.8 0.2 - - + -
172B ILE 3.9 0.6 + - - -
173B ARG* 1.3 72.5 - - - +
175B GLN* 1.3 62.6 + - - +
176B GLU 4.3 0.7 + - - -
177B LEU* 4.7 17.7 - - - -
178B LYS 3.4 7.0 - - - -
179B TYR* 3.7 35.2 - - + -
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Residues in contact with GLN 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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25A VAL* 3.7 30.8 - - + +
26A ASP* 4.6 8.3 + - - +
100A TYR* 3.3 24.5 + - - -
173B ARG* 3.4 46.6 + - + +
174B CYS* 1.3 75.7 - - - +
176B GLU* 1.3 63.3 + - + +
177B LEU 3.4 1.3 - - - -
178B LYS* 2.9 15.3 + - - +
180B ASP* 3.1 26.8 + - - +
186B ARG* 2.8 24.6 + - - +
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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