Contacts of the helix formed by residues 160 - 171 (chain A) 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 A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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158A ASP 3.6 2.7 + - - +
159A SER* 1.3 78.5 - - - +
161A LEU* 1.3 60.1 + - - +
162A CYS* 3.0 11.3 + - - +
163A LEU* 2.8 39.5 + - - +
164A LYS* 3.1 23.2 + - - +
224A ASP* 3.7 23.6 - - - +
226A GLY 4.5 1.9 - - - +
227A CYS* 3.7 29.3 + - + +
230A ARG* 4.3 3.8 - - - +
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Residues in contact with LEU 161 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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159A SER 4.9 0.9 - - - +
160A ASP* 1.3 74.6 - - - +
162A CYS* 1.3 60.6 + - - +
164A LYS* 3.6 29.4 - - + +
165A PHE* 2.8 40.8 + - + -
218A CYS* 4.5 0.2 - - - -
219A PRO* 3.7 42.7 + - + +
352A HIS 4.2 5.6 - - - +
353A SER* 3.8 22.4 - - - +
356A PHE* 3.9 22.2 - - + -
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Residues in contact with CYS 162 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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160A ASP* 3.0 9.0 + - - +
161A LEU* 1.3 79.6 - - - +
163A LEU* 1.3 61.0 + - - +
165A PHE* 3.5 1.6 + - - +
166A ALA* 3.1 22.9 + - - +
215A LEU* 5.1 2.6 - - - +
218A CYS* 2.0 53.1 - - - -
220A CYS* 3.6 11.0 - - - -
227A CYS* 3.5 22.3 - - - +
230A ARG* 3.7 22.4 + - + -
231A ARG* 4.0 8.1 - - - -
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Residues in contact with LEU 163 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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159A SER* 3.6 26.0 - - - +
160A ASP* 2.8 29.1 + - - +
162A CYS* 1.3 72.9 - - - +
164A LYS* 1.3 64.1 + - - +
166A ALA* 3.2 2.6 + - - +
167A MET* 3.0 39.8 + - + +
230A ARG* 3.6 30.4 - - - +
142C ASP* 3.6 37.0 - - + +
143C GLU* 3.8 20.6 - - + -
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Residues in contact with LYS 164 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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159A SER* 3.7 33.0 - - - +
160A ASP 3.1 12.7 + - - +
161A LEU* 3.3 29.2 + - + +
163A LEU* 1.3 78.0 - - - +
165A PHE* 1.3 58.3 + - - +
167A MET* 3.2 8.6 + - - +
168A LEU* 2.9 27.4 + - - +
356A PHE* 3.7 42.1 + - + -
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Residues in contact with PHE 165 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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161A LEU* 2.8 44.8 + - + +
162A CYS 4.1 2.5 - - - +
164A LYS* 1.3 70.2 - - - +
166A ALA* 1.3 64.7 + - - +
168A LEU* 3.4 27.2 + - + +
169A CYS* 3.3 19.2 + - - +
211A HIS 5.3 0.9 - - - +
214A GLY* 3.1 39.0 - - - +
215A LEU* 4.4 7.3 + - - +
218A CYS* 4.3 6.1 - - + -
219A PRO* 4.2 0.4 - - + -
352A HIS* 3.6 50.5 - + + -
355A LEU* 4.3 10.5 - - + -
356A PHE* 3.4 35.4 - + - -
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Residues in contact with ALA 166 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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162A CYS 3.1 12.4 + - - +
163A LEU 3.4 8.3 - - - +
165A PHE* 1.3 75.0 - - - +
167A MET* 1.3 74.1 + - + +
169A CYS* 3.2 8.1 + - - +
170A THR* 3.1 20.3 + - - -
179A ARG* 4.0 9.5 - - - +
215A LEU* 3.7 22.0 - - + +
230A ARG* 3.4 30.1 - - - +
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Residues in contact with MET 167 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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163A LEU* 3.0 23.5 + - + +
164A LYS* 3.2 10.9 + - - +
166A ALA* 1.3 88.0 - - + +
168A LEU* 1.4 58.4 + - - +
170A THR* 3.1 27.8 + - - +
171A LEU* 2.9 37.4 + - + +
179A ARG* 4.1 2.7 - - - +
142C ASP 5.7 0.4 - - - +
143C GLU* 3.9 26.5 - - + +
144C LEU* 3.3 56.8 - - + +
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Residues in contact with LEU 168 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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164A LYS 2.9 14.0 + - - +
165A PHE* 3.4 38.8 + - + +
167A MET* 1.4 75.3 - - - +
169A CYS* 1.3 62.0 + - - +
171A LEU* 3.4 26.6 + - + +
172A ASN* 3.5 12.8 + - - +
211A HIS* 4.6 20.2 + - + +
355A LEU* 5.1 7.6 - - + -
356A PHE* 4.3 17.0 - - + -
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Residues in contact with CYS 169 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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165A PHE 3.3 8.2 + - - +
166A ALA* 3.2 13.1 + - - +
167A MET 3.2 0.6 - - - -
168A LEU* 1.3 76.9 - - - +
170A THR* 1.3 60.9 + - - +
172A ASN* 2.9 28.0 + - - +
175A CYS* 2.1 64.5 - - - +
176A ASP 3.2 6.2 + - - -
179A ARG* 3.8 24.2 - - - -
203A PHE* 4.2 4.7 - - - -
211A HIS* 5.1 10.7 - - + +
215A LEU* 4.8 4.7 - - + -
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Residues in contact with THR 170 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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166A ALA 3.1 13.0 + - - -
167A MET* 3.1 28.1 + - - +
169A CYS* 1.3 76.4 - - - +
171A LEU* 1.3 57.4 + - - +
176A ASP* 3.4 26.0 + - - +
179A ARG* 3.6 13.5 + - - -
129C LEU* 3.7 27.8 - - + +
144C LEU 3.9 13.8 + - - +
145C VAL* 4.6 0.9 - - - -
146C ARG* 2.9 33.0 + - + +
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Residues in contact with LEU 171 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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167A MET* 2.9 21.9 + - + +
168A LEU* 3.6 25.1 - - + +
169A CYS 3.1 0.4 - - - -
170A THR* 1.3 77.8 - - - +
172A ASN* 1.3 55.9 + - - +
173A ASP* 3.9 2.8 + - - +
129C LEU* 3.9 29.2 - - + -
146C ARG* 3.3 10.7 + - - +
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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