Contacts of the helix formed by residues 172 - 186 (chain B) in PDB entry 2GH0
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 172 (chain B).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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168B LEU 3.4 4.6 + - - +
169B CYS 3.0 9.4 + - - +
171B LEU* 1.3 76.2 - - - +
173B ASP* 1.3 69.2 + - - +
174B LYS* 3.4 12.6 + - - +
175B CYS* 3.0 25.8 + - + +
176B ASP* 2.8 23.4 + - - +
211B HIS* 3.7 34.1 + - + -
146D ARG* 3.4 0.9 - - - -
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Residues in contact with ASP 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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171B LEU 3.6 1.2 + - - -
172B ASN* 1.3 72.1 - - - +
174B LYS* 1.3 63.9 + - - +
176B ASP* 3.8 1.0 - - - +
177B ARG* 2.8 71.3 + - - +
146D ARG* 3.2 32.3 + - - +
148D ARG* 3.8 2.8 + - - -
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Residues in contact with LYS 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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172B ASN* 3.3 10.5 + - - +
173B ASP* 1.3 84.3 + - - +
175B CYS* 1.3 62.5 + - - +
177B ARG* 3.5 5.2 + - - +
178B LEU* 3.3 29.0 + - + +
206B LYS* 3.0 33.1 + - - -
207B ALA* 4.1 7.2 - - - +
208B ALA* 3.8 20.2 - - - +
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Residues in contact with CYS 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 CYS* 2.1 61.7 - - - +
172B ASN* 3.0 20.0 + - + +
174B LYS* 1.3 75.1 - - - +
176B ASP* 1.3 60.3 + - - +
178B LEU* 3.3 8.9 + - - +
179B ARG 2.9 26.0 + - - -
203B PHE* 4.0 15.7 - - - -
207B ALA* 4.6 6.1 - - + +
208B ALA 5.9 0.7 - - - +
211B HIS* 3.7 26.5 - - + +
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Residues in contact with ASP 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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169B CYS* 3.1 9.4 + - - +
170B THR* 3.3 36.7 + - - +
172B ASN 2.8 22.2 + - - +
173B ASP 3.8 3.5 - - - +
175B CYS* 1.3 71.5 - - - +
177B ARG* 1.3 58.2 + - - +
179B ARG* 3.8 6.6 + - - +
180B LYS* 2.7 64.3 + - - +
146D ARG* 3.2 26.2 + - - +
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Residues in contact with ARG 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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173B ASP* 2.8 50.4 + - - +
174B LYS* 3.9 5.8 - - - +
175B CYS 3.2 0.2 - - - -
176B ASP* 1.3 81.0 - - - +
178B LEU* 1.3 61.3 + - + +
180B LYS* 3.9 17.3 - - - +
181B ALA* 3.2 23.6 + - - +
148D ARG* 3.8 19.0 - - - +
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Residues in contact with LEU 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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174B LYS* 3.3 27.3 + - + +
175B CYS* 3.3 5.2 + - - +
177B ARG* 1.3 77.2 - - + +
179B ARG* 1.3 63.0 + - - +
181B ALA* 3.5 7.2 + - + +
182B TYR* 3.4 18.9 + - - +
199B GLN 5.0 0.9 - - - +
202B THR* 4.2 21.3 - - + +
203B PHE* 3.6 23.4 - - + +
206B LYS* 3.7 27.1 - - + +
207B ALA* 3.5 37.7 - - + +
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Residues in contact with ARG 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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166B ALA* 4.1 8.7 - - - +
167B MET* 4.3 0.6 - - - +
169B CYS* 3.8 24.7 - - - -
170B THR* 3.7 19.2 + - - +
175B CYS 2.9 20.6 + - - +
176B ASP* 3.9 7.5 + - - +
178B LEU* 1.3 67.6 - - - +
180B LYS* 1.3 62.7 + - - +
181B ALA 3.1 2.0 + - - -
182B TYR* 3.4 16.1 + - + -
183B GLY* 2.9 27.2 + - - -
203B PHE* 3.7 11.6 - - + -
215B LEU* 4.0 22.7 - - - +
230B ARG* 3.3 11.7 - - - +
234B THR* 6.0 0.2 - - - +
143D GLU* 3.0 40.0 + - - -
144D LEU 5.7 0.6 + - - -
145D VAL* 6.2 1.4 - - - +
197D SER 5.0 5.1 + - - -
199D MET* 4.2 3.0 - - - +
205D TRP* 3.5 35.4 - - + -
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Residues in contact with LYS 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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176B ASP* 2.7 55.0 + - - +
177B ARG* 3.9 15.2 - - - +
179B ARG* 1.3 78.4 - - - +
181B ALA* 1.3 58.8 + - - +
183B GLY* 3.7 0.6 - - - +
184B GLU* 2.9 33.5 + - - +
145D VAL* 6.6 0.2 - - + -
146D ARG* 4.0 14.6 + - - +
148D ARG* 4.0 23.0 - - - +
194D GLU* 5.3 10.4 + - - +
195D ALA 4.7 14.4 - - - +
196D VAL* 5.5 1.3 - - - -
197D SER* 3.8 27.2 + - - +
205D TRP* 5.3 2.5 - - - -
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Residues in contact with ALA 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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177B ARG 3.2 15.0 + - - +
178B LEU* 3.7 8.5 - - + +
179B ARG 3.1 1.0 - - - -
180B LYS* 1.3 81.9 - - - +
182B TYR* 1.3 61.7 + - - +
184B GLU* 3.5 8.2 + - - +
185B ALA* 3.1 21.7 + - - +
199B GLN* 3.7 21.4 - - - +
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Residues in contact with TYR 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 LEU 3.4 11.8 + - - -
179B ARG* 3.4 27.3 + - + +
181B ALA* 1.3 75.2 - - - +
183B GLY* 1.3 58.5 + - - +
185B ALA 3.0 0.7 + - - -
186B CYS* 2.7 48.5 + - + -
199B GLN* 3.6 35.8 - - + +
200B LEU* 3.6 24.0 - - + +
203B PHE* 3.9 30.5 - + + -
204B PHE* 5.8 1.7 - + - -
215B LEU* 3.7 8.3 - - + +
234B THR* 2.6 47.0 + - - +
235B ILE* 4.4 3.1 - - + +
205D TRP* 3.6 24.5 - + - -
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Residues in contact with GLY 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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179B ARG 2.9 12.2 + - - -
180B LYS 3.7 0.9 - - - -
182B TYR* 1.3 80.5 - - - +
184B GLU* 1.3 55.1 + - - +
186B CYS* 3.5 1.8 + - - -
187B SER* 2.5 36.1 + - - -
197D SER* 4.1 2.7 - - - -
205D TRP* 3.4 42.0 - - - +
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Residues in contact with GLU 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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180B LYS 2.9 19.1 + - - +
181B ALA* 3.8 6.6 - - - +
183B GLY* 1.3 76.2 - - - +
185B ALA* 1.3 60.6 + - - +
186B CYS 3.3 0.7 + - - -
187B SER* 3.4 16.4 + - - +
195D ALA* 3.8 27.1 + - - +
197D SER* 3.5 14.7 + - - +
207D THR* 4.0 13.7 - - + +
209D ASP* 4.2 7.6 - - - +
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Residues in contact with ALA 185 (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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181B ALA 3.1 9.1 + - - +
182B TYR 3.0 4.5 + - - +
184B GLU* 1.3 78.0 - - - +
186B CYS* 1.3 58.1 + - - +
187B SER 3.5 0.6 - - - +
191B CYS* 3.4 15.6 - - - -
192B GLN* 4.2 5.0 + - - +
195B VAL* 4.0 15.2 - - + +
196B CYS* 3.6 19.8 + - - +
199B GLN* 3.5 32.5 - - + -
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Residues in contact with CYS 186 (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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182B TYR* 2.7 35.4 + - + +
183B GLY* 3.7 3.8 - - - +
185B ALA* 1.3 77.4 - - - +
187B SER* 1.3 59.6 + - - +
188B GLY 4.3 0.9 + - - +
191B CYS* 3.7 6.3 - - - -
196B CYS* 2.1 56.5 - - - -
200B LEU* 4.4 3.4 - - - -
236B ALA* 3.3 26.6 - - + +
239B CYS* 3.5 14.8 - - - +
205D TRP* 4.6 3.4 - - + +
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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