Contacts of the helix formed by residues 174 - 190 (chain A) in PDB entry 3GHG
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 174 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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151A GLU* 6.1 0.4 - - - -
172A GLU 3.8 4.7 + - - +
173A VAL* 1.3 70.1 - - - +
175A LEU* 1.3 64.1 + - - +
176A LYS* 3.2 21.1 - - - +
177A ASP* 3.1 41.4 + - + +
178A TYR* 3.7 9.4 + - - -
178B LYS* 4.5 6.2 + - - +
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Residues in contact with LEU 175 (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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148A LYS* 4.9 6.7 - - + -
152A VAL* 6.3 2.7 - - + -
173A VAL* 3.1 26.5 + - + +
174A ASP* 1.3 71.4 - - - +
176A LYS* 1.3 78.6 + - + +
177A ASP 3.0 1.8 - - - -
178A TYR* 2.8 19.7 + - + +
179A GLU* 2.8 31.2 + - + +
421B GLN 6.0 1.3 - - - +
426B MET* 3.1 36.6 - - + -
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Residues in contact with LYS 176 (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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174A ASP* 3.6 18.8 - - - +
175A LEU* 1.3 85.8 - - + +
177A ASP* 1.3 61.8 + - - +
179A GLU* 3.5 8.5 + - + +
180A ASP* 3.0 57.7 + - - +
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Residues in contact with ASP 177 (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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174A ASP* 3.1 28.3 + - + +
175A LEU 3.0 0.4 - - - -
176A LYS* 1.3 79.5 - - - +
178A TYR* 1.3 63.4 + - - +
179A GLU 3.2 0.3 + - - -
180A ASP* 3.3 10.1 + - - +
181A GLN* 3.0 39.5 + - - +
174B ASN* 3.7 14.3 + - - -
178B LYS* 2.6 31.3 + - - +
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Residues in contact with TYR 178 (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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144A LEU* 3.8 18.4 - - + +
147A MET* 3.4 25.1 - - + +
148A LYS* 3.4 47.8 - - + -
151A GLU* 3.3 38.4 + - + +
173A VAL* 5.6 0.2 - - + -
174A ASP 3.9 14.4 - - - -
175A LEU* 2.8 23.2 + - + +
177A ASP* 1.3 76.2 - - - +
179A GLU* 1.3 60.8 + - - +
181A GLN* 3.4 9.9 + - - +
182A GLN* 3.0 28.1 + - - +
175B LEU* 4.0 13.0 - - + -
178B LYS* 3.7 35.2 - - + +
182B LEU* 5.1 0.2 - - - +
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Residues in contact with GLU 179 (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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148A LYS* 2.7 36.3 + - - -
175A LEU* 2.8 28.5 + - + +
176A LYS* 3.8 7.9 - - + +
178A TYR* 1.3 69.3 - - - +
180A ASP* 1.3 58.9 + - - +
182A GLN* 2.9 13.9 + - - +
183A LYS* 2.6 39.7 + - + +
423B THR* 4.5 8.5 + - - +
425B ASP* 4.3 0.9 - - - +
426B MET* 4.1 9.5 - - - +
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Residues in contact with ASP 180 (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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176A LYS* 3.0 50.8 + - - +
177A ASP* 3.5 9.9 - - - +
179A GLU* 1.3 77.6 - - - +
181A GLN* 1.3 59.5 + - + +
183A LYS* 4.3 16.6 - - + +
184A GLN* 2.5 42.9 + - + +
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Residues in contact with GLN 181 (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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144A LEU* 3.7 7.7 - - + +
177A ASP* 3.0 37.6 + - - +
178A TYR* 3.6 9.7 - - - +
180A ASP* 1.3 75.5 - - + +
182A GLN* 1.3 56.4 + - - +
184A GLN* 4.3 13.4 + - - +
185A LEU* 3.0 23.7 + - - +
170B SER* 4.0 11.1 + - - -
171B ILE* 3.1 44.9 - - + +
174B ASN* 2.7 44.4 - - - +
175B LEU* 4.4 6.6 - - - +
178B LYS* 4.9 0.3 + - - -
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Residues in contact with GLN 182 (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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144A LEU* 3.4 29.0 - - + +
145A VAL* 3.7 16.7 + - - -
148A LYS* 3.3 23.7 - - - +
178A TYR* 3.0 14.5 + - - +
179A GLU* 2.9 19.2 + - - +
181A GLN* 1.3 75.4 - - - +
183A LYS* 1.3 55.8 + - - +
184A GLN 3.2 1.1 - - - -
185A LEU* 2.9 7.2 + - + +
186A GLU* 2.6 41.6 + - + +
425B ASP* 3.1 23.6 + - - +
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Residues in contact with LYS 183 (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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179A GLU* 2.6 21.9 + - + +
180A ASP* 4.0 14.6 - - - +
182A GLN* 1.3 72.0 - - - +
184A GLN* 1.3 63.7 + - - +
186A GLU* 4.6 4.9 - - - +
187A GLN* 3.6 29.6 + - - +
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Residues in contact with GLN 184 (chain A).
Click here for Legend to table.
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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180A ASP* 2.5 30.7 + - + +
181A GLN* 4.3 14.8 + - - +
183A LYS* 1.3 77.9 - - + +
185A LEU* 1.3 57.4 + - - +
187A GLN* 2.8 39.3 - - - +
188A VAL* 3.7 6.5 - - + +
167B VAL* 3.1 33.6 + - + +
170B SER* 5.5 5.9 + - - -
171B ILE* 5.9 2.2 - - - +
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Residues in contact with LEU 185 (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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137A GLN* 5.2 0.9 - - + +
140A VAL* 5.3 5.6 - - + -
141A ARG* 4.8 15.5 - - + -
144A LEU* 5.2 5.2 - - + -
181A GLN 3.0 22.1 + - - +
182A GLN* 2.9 10.0 + - + +
184A GLN* 1.3 80.6 - - - +
186A GLU* 1.3 68.5 + - + +
188A VAL* 2.8 31.0 + - + +
189A ILE* 3.3 40.2 + - + -
167B VAL* 5.1 10.1 - - + +
168B LEU* 4.5 20.9 - - + -
171B ILE* 4.3 12.3 - - + -
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Residues in contact with GLU 186 (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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141A ARG* 2.6 46.7 + - - +
182A GLN* 2.6 23.0 + - + +
183A LYS* 4.6 4.7 - - - +
185A LEU* 1.3 81.2 - - + +
187A GLN* 1.3 64.9 + - - +
188A VAL 3.0 1.2 + - - -
189A ILE* 3.4 15.6 + - - +
190A ALA* 3.6 21.1 + - - +
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Residues in contact with GLN 187 (chain A).
Click here for Legend to table.
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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183A LYS* 3.6 22.5 + - - +
184A GLN* 2.8 34.7 - - - +
186A GLU* 1.3 76.7 - - - +
188A VAL* 1.3 63.4 + - + +
190A ALA* 4.5 3.5 + - - +
191A LYS* 4.3 17.2 - - - +
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Residues in contact with VAL 188 (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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137A GLN* 4.0 1.1 + - - +
184A GLN 3.7 14.6 - - - +
185A LEU* 2.8 21.6 + - + +
187A GLN* 1.3 80.2 - - + +
189A ILE* 1.3 61.7 + - - +
190A ALA 3.4 2.2 + - - -
191A LYS* 4.0 9.9 + - - +
192A ASP* 3.4 17.8 - - - +
163B THR* 5.7 1.8 - - - +
164B ASN* 2.7 35.0 - - - +
167B VAL* 3.8 33.4 - - + -
168B LEU* 6.6 0.4 - - + -
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Residues in contact with ILE 189 (chain A).
Click here for Legend to table.
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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134A GLN* 5.5 1.1 - - + +
137A GLN* 3.4 63.3 + - + +
141A ARG* 4.1 20.0 - - - +
185A LEU* 3.3 47.0 + - + +
186A GLU* 3.4 16.5 + - - +
188A VAL* 1.3 73.2 - - + +
190A ALA* 1.3 57.0 + - - +
191A LYS 3.0 11.3 + - - -
192A ASP 4.0 9.4 + - - +
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Residues in contact with ALA 190 (chain A).
Click here for Legend to table.
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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186A GLU* 3.6 21.0 + - - +
187A GLN 4.5 3.1 + - - +
188A VAL 3.4 1.2 - - - -
189A ILE* 1.3 77.1 - - - +
191A LYS* 1.3 61.8 + - + +
193A LEU* 6.0 1.6 - - - +
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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