Contacts of the helix formed by residues 171 - 183 (chain B) in PDB entry 2WP9
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 171 (chain B).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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156B SER* 4.0 2.0 - - - -
162B PHE* 3.8 9.4 - - - -
169B PHE* 3.2 30.0 - - - -
170B ILE* 1.3 78.6 - - - +
172B PRO* 1.3 78.0 - - - +
173B ALA 3.4 2.0 - - - -
174B GLY 3.3 0.7 + - - -
175B LEU* 3.1 22.8 + - - +
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Residues in contact with PRO 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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155B CYS* 3.6 10.1 - - + +
156B SER* 3.2 39.5 - - - +
159B CYS* 4.1 17.3 - - + -
162B PHE* 4.9 0.2 - - + -
169B PHE* 4.3 5.1 - - + -
171B GLY* 1.3 84.1 - - - +
173B ALA* 1.3 61.9 + - - +
175B LEU* 3.7 1.0 - - - +
176B LEU* 2.8 23.7 + - - +
212B CYS* 3.8 16.2 - - + -
222B PRO* 3.5 31.4 - - + +
226B ILE* 4.2 12.5 - - + +
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Residues in contact with ALA 173 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
110B PHE* 3.5 33.9 - - + -
114B TYR* 5.7 1.6 - - - -
149B CYS* 4.7 16.7 - - - -
151B LEU* 5.6 3.0 - - + +
155B CYS* 3.5 22.7 - - - -
156B SER* 3.3 3.6 + - - -
172B PRO* 1.3 77.9 - - - +
174B GLY* 1.3 64.9 + - - +
176B LEU* 3.1 11.7 + - - +
177B ALA* 3.0 20.1 + - - +
222B PRO* 5.5 0.4 - - - -
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Residues in contact with GLY 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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110B PHE* 5.3 1.2 - - - -
113B GLN* 5.6 0.2 - - - -
114B TYR* 4.7 19.1 - - - -
117B ILE* 3.8 4.6 - - - +
156B SER* 4.7 0.4 + - - -
170B ILE* 3.5 23.8 + - - -
171B GLY 3.3 4.6 + - - -
172B PRO 3.3 0.4 - - - -
173B ALA* 1.3 78.0 - - - +
175B LEU* 1.4 56.8 + - - +
177B ALA* 3.0 11.2 + - - +
178B ALA* 2.8 26.5 + - - +
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Residues in contact with LEU 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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169B PHE* 3.7 30.7 - - + -
170B ILE* 3.7 23.8 - - + -
171B GLY 3.1 15.3 + - - +
172B PRO 3.8 1.1 - - - +
174B GLY* 1.4 71.1 - - - +
176B LEU* 1.3 66.8 + - - +
178B ALA* 3.5 9.4 - - + +
179B TYR* 2.9 21.3 + - - +
197B LEU* 4.8 4.0 - - + -
202B SER 3.8 8.3 - - - +
203B VAL* 3.9 29.4 - - + +
225B ALA* 5.1 2.5 - - - -
226B ILE* 3.7 32.8 - - + -
229B ILE* 3.6 18.5 - - + +
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Residues in contact with LEU 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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145B GLY 3.8 8.5 - - - +
146B LEU* 3.6 48.2 - - + +
149B CYS* 3.7 27.4 - - + -
172B PRO 2.8 14.0 + - - +
173B ALA* 3.2 11.0 - - - +
175B LEU* 1.3 78.4 - - - +
177B ALA* 1.3 56.8 + - - +
179B TYR* 3.2 3.5 + - - +
180B ARG* 3.1 24.3 + - - +
220B LEU* 4.1 16.2 - - + -
221B ASN 4.4 5.4 - - - +
222B PRO* 4.3 20.2 - - + -
225B ALA* 3.9 18.5 - - + +
226B ILE* 5.2 0.6 - - - +
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Residues in contact with ALA 177 (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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114B TYR* 3.6 33.9 - - + -
117B ILE* 4.1 7.9 - - + -
119B PRO* 4.9 2.0 - - + -
146B LEU 5.7 1.1 - - - -
149B CYS* 6.5 1.6 - - + -
151B LEU* 6.1 0.2 - - + -
173B ALA 3.0 10.1 + - - +
174B GLY 3.0 10.2 + - - +
176B LEU* 1.3 74.0 - - - +
178B ALA* 1.3 66.6 + - - +
179B TYR 3.1 1.3 - - - -
180B ARG* 3.0 26.3 + - - +
181B PHE* 3.3 11.9 + - + -
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Residues in contact with ALA 178 (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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117B ILE* 3.7 33.5 - - + +
174B GLY 2.8 15.4 + - - +
175B LEU* 3.2 13.9 + - + +
177B ALA* 1.3 72.2 - - - +
179B TYR* 1.3 58.4 + - - +
181B PHE* 3.1 5.7 + - - +
182B LEU* 2.8 33.1 + - + +
193B ARG* 5.3 2.2 - - - +
197B LEU* 4.4 13.2 - - + -
229B ILE* 4.4 9.0 - - + -
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Residues in contact with TYR 179 (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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142B LYS* 5.3 1.8 - - - +
146B LEU* 3.6 30.3 - - + -
175B LEU 2.9 17.2 + - - +
176B LEU 3.7 4.0 - - - +
177B ALA 3.1 0.2 - - - -
178B ALA* 1.3 78.0 - - - +
180B ARG* 1.3 63.1 + - - +
182B LEU* 4.0 11.7 - - + -
183B ILE* 2.9 69.2 + - + +
225B ALA* 4.0 17.9 - - + -
228B HIS* 3.4 45.0 + + + +
229B ILE* 4.0 22.4 - - + -
232B MET* 4.1 13.7 - - + -
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Residues in contact with ARG 180 (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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103A GLY* 3.1 28.5 + - - -
105A PRO* 4.4 10.4 - - - +
148A THR* 5.5 1.0 + - - -
151A GLN* 4.7 9.4 + - - +
143B LEU* 3.5 21.2 - - - +
146B LEU* 3.8 27.5 - - + +
147B TYR* 4.3 24.9 - - - +
176B LEU 3.1 11.6 + - - +
177B ALA* 3.0 16.5 + - + +
179B TYR* 1.3 78.1 - - - +
181B PHE* 1.3 99.7 + - + +
184B ASP* 2.9 37.6 + - - +
186B ARG* 4.1 0.6 - - - +
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Residues in contact with PHE 181 (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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102A MET 5.7 0.4 - - - -
151A GLN* 3.5 26.0 - - - -
118B LYS 4.3 1.6 - - - -
119B PRO* 3.1 39.0 - - + -
120B TYR* 3.3 32.5 - - - -
121B LEU* 3.5 15.3 - - + -
177B ALA* 3.3 20.2 + - + -
178B ALA* 3.1 5.5 + - - +
179B TYR 3.1 0.4 - - - -
180B ARG* 1.3 111.6 - - + +
182B LEU* 1.3 68.6 + - - +
183B ILE 3.2 2.6 + - - -
184B ASP* 3.3 9.6 + - + +
187B ASP* 3.5 22.5 - - - +
190B THR* 5.2 0.3 + - - -
193B ARG* 3.5 27.8 - - - +
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Residues in contact with LEU 182 (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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178B ALA* 2.8 24.7 + - + +
179B TYR* 3.7 12.3 - - + +
181B PHE* 1.3 77.6 - - - +
183B ILE* 1.3 60.7 + - - +
184B ASP 3.9 1.6 + - - +
190B THR* 3.6 36.2 + - + +
193B ARG* 3.8 28.9 - - + +
194B LEU* 3.5 39.5 - - + -
197B LEU* 4.4 8.5 - - + -
229B ILE* 3.9 32.1 - - + -
232B MET* 4.2 11.9 - - - +
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Residues in contact with ILE 183 (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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139B GLN 5.0 1.9 - - - +
142B LYS* 3.4 42.8 - - + +
143B LEU* 3.4 21.7 - - + +
146B LEU* 3.4 21.5 - - + -
179B TYR* 2.9 60.2 + - + +
180B ARG 3.7 1.1 - - - +
182B LEU* 1.3 77.8 - - - +
184B ASP* 1.3 63.4 + - - +
185B SER* 3.2 4.6 + - - -
232B MET* 4.9 8.3 - - + -
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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