Contacts of the helix formed by residues 160 - 172 (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 ASP 160 (chain B).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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159B SER* 1.3 80.3 - - - +
161B LEU* 1.3 58.1 + - - +
162B CYS* 2.9 12.3 + - - +
163B LEU* 2.8 39.4 + - - +
164B LYS* 3.1 23.0 + - - +
224B ASP* 3.4 24.4 - - - +
226B GLY 4.4 2.4 - - - -
227B CYS* 3.6 28.8 + - + -
230B ARG* 4.5 4.0 - - - -
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Residues in contact with LEU 161 (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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159B SER 4.7 2.2 - - - +
160B ASP* 1.3 73.2 - - - +
162B CYS* 1.3 60.5 + - - +
163B LEU 3.3 0.2 - - - -
164B LYS* 3.6 29.8 - - + +
165B PHE* 2.9 40.6 + - + -
218B CYS* 4.4 0.4 - - - -
219B PRO* 3.8 42.3 + - + +
352B HIS 4.1 7.4 - - - +
353B SER* 3.9 20.9 - - - +
356B PHE* 4.0 24.2 - - + -
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Residues in contact with CYS 162 (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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160B ASP* 2.9 9.3 + - - +
161B LEU* 1.3 77.7 - - - +
163B LEU* 1.3 62.2 + - - +
165B PHE* 3.9 1.9 - - - +
166B ALA* 3.0 22.9 + - - +
215B LEU* 5.0 2.8 - - - +
218B CYS* 2.0 53.3 - - - -
219B PRO 4.1 0.2 - - - -
220B CYS* 3.5 11.0 - - - -
227B CYS* 3.5 23.2 - - - +
230B ARG* 3.9 21.9 + - + -
231B ARG* 3.9 9.0 - - - -
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Residues in contact with LEU 163 (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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159B SER* 3.8 26.5 - - - +
160B ASP* 2.8 29.1 + - - +
162B CYS* 1.3 72.0 - - - +
164B LYS* 1.3 57.1 + - - +
166B ALA* 3.2 3.3 + - - +
167B MET* 3.0 42.3 + - + +
230B ARG* 3.7 34.0 - - - +
142D ASP* 3.9 34.3 - - + +
143D GLU* 3.8 18.2 - - + -
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Residues in contact with LYS 164 (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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159B SER* 3.8 30.5 + - - +
160B ASP 3.1 14.7 + - - +
161B LEU* 3.6 23.6 - - + +
162B CYS 3.3 0.2 - - - -
163B LEU* 1.3 76.8 - - - +
165B PHE* 1.3 58.8 + - - +
167B MET* 3.1 7.6 + - - +
168B LEU* 2.8 31.4 + - - +
356B PHE* 3.4 41.3 - - + -
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Residues in contact with PHE 165 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
161B LEU* 2.9 38.6 + - + +
162B CYS 4.1 2.7 - - - +
164B LYS* 1.3 73.6 - - - +
166B ALA* 1.3 65.5 + - - +
168B LEU* 3.3 21.5 + - + +
169B CYS* 3.2 20.3 + - - +
210B PRO 5.2 3.1 - - - -
211B HIS* 5.2 5.9 - + - +
214B GLY* 3.1 41.1 - - - +
215B LEU* 4.0 4.8 + - - +
218B CYS* 4.3 4.3 - - + -
219B PRO* 4.5 1.3 - - + -
352B HIS* 3.7 46.9 - + + -
355B LEU* 5.1 8.7 - - + -
356B PHE* 3.4 36.1 - + - -
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Residues in contact with ALA 166 (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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162B CYS 3.0 12.3 + - - +
163B LEU 3.2 8.0 + - - +
165B PHE* 1.3 75.2 - - - +
167B MET* 1.3 66.4 + - + +
169B CYS* 3.3 6.6 + - - +
170B THR* 3.1 26.2 + - - -
179B ARG* 4.1 7.5 - - - +
215B LEU* 3.8 24.8 - - + +
230B ARG* 3.2 31.9 - - - +
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Residues in contact with MET 167 (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 LEU* 3.0 26.4 + - + +
164B LYS* 3.1 9.2 + - - +
166B ALA* 1.3 84.6 - - + +
168B LEU* 1.3 59.8 + - - +
169B CYS 3.2 0.4 - - - -
170B THR* 3.2 24.7 + - - +
171B LEU* 2.9 36.9 + - + +
179B ARG* 4.3 1.8 - - - +
142D ASP 5.6 0.7 - - - +
143D GLU* 3.7 38.4 - - + +
144D LEU* 3.5 50.5 - - + +
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Residues in contact with LEU 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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164B LYS 2.8 15.1 + - - +
165B PHE* 3.3 29.8 + - + +
167B MET* 1.3 77.0 - - - +
169B CYS* 1.3 61.3 + - - +
171B LEU* 3.5 20.1 + - + +
172B ASN* 3.4 18.9 + - - +
211B HIS* 4.0 19.2 + - + +
356B PHE* 3.9 27.4 - - + -
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Residues in contact with CYS 169 (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 PHE 3.2 12.0 + - - +
166B ALA* 3.4 10.8 - - - +
167B MET 3.2 0.2 - - - -
168B LEU* 1.3 77.6 - - - +
170B THR* 1.3 62.2 + - - +
172B ASN 3.0 21.1 + - - +
175B CYS* 2.1 63.9 - - - +
176B ASP 3.1 8.0 + - - -
179B ARG* 3.8 24.9 - - - -
203B PHE* 4.3 4.3 - - - -
211B HIS* 4.4 11.3 - - + +
215B LEU* 5.1 4.3 - - + -
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Residues in contact with THR 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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166B ALA 3.1 14.8 + - - -
167B MET* 3.2 27.6 + - - +
169B CYS* 1.3 75.0 - - - +
171B LEU* 1.3 58.1 + - - +
176B ASP* 3.3 27.0 + - - +
179B ARG* 3.7 13.2 + - - -
129D LEU* 3.7 26.2 - - + -
144D LEU* 4.1 15.3 + - + +
145D VAL* 4.5 0.9 - - + -
146D ARG* 2.9 31.4 + - + +
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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
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167B MET* 2.9 21.9 + - + +
168B LEU* 3.7 22.9 - - + +
169B CYS 3.3 0.2 - - - -
170B THR* 1.3 76.9 - - - +
172B ASN* 1.3 57.0 + - - +
173B ASP 3.6 0.9 + - - -
129D LEU* 3.4 29.6 - - + -
144D LEU* 6.4 0.7 - - + -
146D ARG* 3.0 13.3 + - - +
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Residues in contact with ASN 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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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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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