Contacts of the helix formed by residues 172 - 184 (chain B) in PDB entry 3P3W
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 GLN 172 (chain B).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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170B ASP* 3.3 17.8 + - - +
171B VAL* 1.3 81.6 - - + +
173B GLU* 1.3 64.0 + - - +
174B PHE 3.2 0.4 - - - -
175B ARG* 3.1 55.8 + - - +
176B ARG* 3.4 46.3 + - - +
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Residues in contact with GLU 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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168B ILE* 3.9 20.9 - - + -
170B ASP* 3.5 25.3 + - + +
171B VAL 3.2 0.4 - - - -
172B GLN* 1.3 79.2 - - - +
174B PHE* 1.3 61.4 + - - +
176B ARG* 3.4 20.3 + - - +
177B ILE* 3.5 21.6 + - + +
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Residues in contact with PHE 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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165B VAL* 3.8 38.1 - - + -
168B ILE* 3.7 35.9 - - + -
169B LYS 5.3 2.0 - - - -
170B ASP 3.6 16.8 - - - -
171B VAL* 3.3 22.5 + - + +
172B GLN 3.2 1.2 - - - -
173B GLU* 1.3 78.9 - - - +
175B ARG* 1.3 58.1 + - - +
177B ILE* 4.2 13.6 - - + +
178B ILE* 3.3 28.1 - - - +
197B ARG* 4.7 10.5 - - + -
200B THR* 5.1 12.1 - - - -
201B ILE* 4.3 27.6 - - + -
204B GLN* 4.1 17.0 - - + +
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Residues in contact with ARG 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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171B VAL* 3.6 6.3 + - - +
172B GLN* 3.1 48.3 + - - +
174B PHE* 1.3 81.1 - - - +
176B ARG* 1.3 60.8 + - + +
177B ILE 3.6 0.2 - - - -
178B ILE* 4.1 8.0 + - - +
179B GLU* 3.9 15.4 + - - +
204B GLN* 3.7 33.6 + - + +
207B ILE* 3.2 37.2 - - - +
208B LEU* 4.5 17.0 - - + +
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Residues in contact with ARG 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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170B ASP* 4.9 3.8 + - - -
172B GLN* 3.4 52.2 + - - +
173B GLU* 3.4 11.1 + - - +
174B PHE 3.4 0.2 - - - -
175B ARG* 1.3 78.1 - - - +
177B ILE* 1.3 63.7 + - + +
178B ILE 3.3 0.9 - - - -
179B GLU* 3.4 19.2 - - + +
180B GLU* 3.4 15.2 + - - +
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Residues in contact with ILE 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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136B LEU* 4.1 31.9 - - + -
163B ARG* 4.0 23.9 + - + +
165B VAL* 5.3 9.9 - - + -
173B GLU* 3.5 16.8 + - + +
174B PHE* 4.2 15.7 - - + +
176B ARG* 1.3 76.9 - - + +
178B ILE* 1.3 76.1 + - + +
180B GLU* 3.3 38.8 - - - +
181B MET* 3.5 14.5 + - + +
189B TYR* 6.3 0.9 - - + -
151D GLU* 5.9 2.7 - - - +
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Residues in contact with ILE 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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136B LEU* 5.9 3.6 - - + -
174B PHE 3.3 22.9 - - - +
175B ARG* 4.3 7.6 - - - +
176B ARG 3.3 0.4 - - - -
177B ILE* 1.3 83.9 - - + +
179B GLU* 1.3 64.9 + - - +
180B GLU 3.1 0.4 - - - -
181B MET* 3.2 13.9 + - - +
182B ASP* 3.3 15.2 + - - +
189B TYR* 3.6 26.7 - - + +
201B ILE* 5.1 9.4 - - + +
204B GLN* 4.7 18.4 - - + +
205B VAL* 5.0 14.4 - - + -
208B LEU* 6.2 2.7 - - + -
211B HIS* 3.7 31.2 - - + +
217B TYR* 5.5 2.9 - - - +
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Residues in contact with GLU 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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175B ARG 3.9 8.1 + - - +
176B ARG* 3.4 16.9 + - + +
177B ILE 3.3 0.2 - - - -
178B ILE* 1.3 79.3 - - - +
180B GLU* 1.3 61.5 + - - +
182B ASP* 3.4 18.6 + - - +
183B ARG* 3.3 25.5 + - - +
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Residues in contact with GLU 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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163B ARG* 2.2 47.0 + - - +
176B ARG* 3.5 12.1 - - - +
177B ILE* 3.3 24.3 + - - +
178B ILE 3.1 0.6 - - - -
179B GLU* 1.3 78.0 - - - +
181B MET* 1.3 63.3 + - + +
183B ARG* 3.4 50.5 + - - +
184B ARG* 3.5 12.1 + - - +
154D VAL* 4.2 7.4 - - + +
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Residues in contact with MET 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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134B VAL* 3.7 39.0 - - + -
136B LEU* 5.9 1.3 - - + -
161B THR* 4.1 20.6 - - + -
163B ARG* 3.6 33.9 - - + +
177B ILE* 3.8 11.7 - - + +
178B ILE 3.2 4.0 + - - +
180B GLU* 1.3 81.0 - - + +
182B ASP* 1.3 61.1 + - - +
183B ARG 3.2 1.3 - - - -
184B ARG* 3.1 14.0 + - - +
185B GLN 2.9 8.8 + - - -
186B GLU* 2.9 37.8 + - + +
189B TYR* 3.3 25.6 - - + +
154D VAL* 4.2 7.2 - - + -
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Residues in contact with ASP 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 ILE* 3.3 17.9 + - - +
179B GLU* 3.7 14.0 - - - +
180B GLU 3.4 0.2 - - - -
181B MET* 1.3 76.7 - - - +
183B ARG* 1.3 61.5 + - - +
185B GLN* 3.2 24.3 + - - +
186B GLU 4.1 6.1 - - - +
189B TYR* 3.7 10.4 + - - -
211B HIS* 3.5 20.2 + - - -
215B TYR* 3.4 23.2 + - - -
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Residues in contact with ARG 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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176B ARG 5.3 0.2 + - - -
179B GLU* 3.3 19.4 + - - +
180B GLU* 3.5 50.3 + - - +
181B MET 3.2 0.2 - - - -
182B ASP* 1.3 75.5 - - - +
184B ARG* 1.3 60.9 + - + +
185B GLN* 3.2 6.0 + - - +
154D VAL* 3.9 19.6 + - - +
155D GLN* 5.5 1.6 - - - +
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Residues in contact with ARG 184 (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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132B LYS* 3.5 21.3 + - - -
161B THR* 4.0 20.2 + - - +
180B GLU 3.5 10.7 + - - +
181B MET* 3.1 23.8 + - - +
183B ARG* 1.3 78.4 - - + +
185B GLN* 1.3 68.4 + - - +
186B GLU* 3.4 14.4 + - + +
153D ALA* 3.0 28.7 + - - +
154D VAL* 3.5 24.7 + - - +
157D ASN* 3.1 27.5 + - - +
158D TRP 4.2 6.1 + - - -
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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