Contacts of the helix formed by residues 174 - 186 (chain G) in PDB entry 2HPC
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 G).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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151G GLU* 5.2 1.0 + - - -
173G VAL* 1.3 69.8 - - - +
175G LEU* 1.3 60.7 + - - +
176G LYS* 3.1 23.9 + - - +
177G ASP* 2.6 45.7 + - + +
178G TYR* 3.1 32.0 + - - -
178H LYS* 4.5 8.1 - - - +
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Residues in contact with LEU 175 (chain G).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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148G LYS* 4.6 24.0 - - + -
151G GLU* 5.0 3.8 - - + -
152G VAL* 4.9 8.7 - - + -
173G VAL* 3.3 35.9 + - + +
174G ASP* 1.3 74.5 - - - +
176G LYS* 1.3 56.2 + - - +
177G ASP 3.1 5.8 - - - -
178G TYR* 4.2 4.5 - - + -
179G GLU* 2.8 38.8 + - + +
425H ASP* 6.0 0.7 - - - +
426H MET* 4.2 32.1 - - + -
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Residues in contact with LYS 176 (chain G).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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174G ASP* 3.3 15.4 + - - +
175G LEU* 1.3 77.3 - - - +
177G ASP* 1.3 61.9 + - - +
179G GLU* 3.8 5.6 - - - +
180G ASP* 2.8 39.6 - - - +
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Residues in contact with ASP 177 (chain G).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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174G ASP* 2.6 30.7 + - + +
176G LYS* 1.3 81.6 - - - +
178G TYR* 1.3 65.2 + - - +
180G ASP* 3.0 20.2 + - - +
181G GLN* 3.2 25.7 + - - +
174H ASN 4.8 0.3 - - - +
178H LYS* 2.7 30.6 + - - -
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Residues in contact with TYR 178 (chain G).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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144G LEU* 4.2 15.5 - - + +
147G MET* 2.9 48.3 + - + +
148G LYS* 4.0 26.7 - - + -
151G GLU* 4.0 24.0 - - + -
174G ASP 3.1 24.5 + - - +
175G LEU* 4.2 7.9 - - + +
177G ASP* 1.3 81.1 - - - +
179G GLU* 1.3 56.6 + - - +
180G ASP 3.0 5.5 + - - -
181G GLN* 3.4 16.9 - - - +
182G GLN* 3.6 24.1 + - - +
175H LEU* 4.7 7.4 + - + +
178H LYS* 3.5 50.9 - - + +
182H LEU* 4.2 6.1 - - - +
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Residues in contact with GLU 179 (chain G).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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148G LYS* 5.0 6.7 - - + +
175G LEU* 2.8 26.7 + - + +
176G LYS* 3.8 7.6 - - - +
178G TYR* 1.3 73.0 - - - +
180G ASP* 1.3 59.4 + - - +
182G GLN* 2.9 39.4 - - - +
183G LYS* 4.7 6.0 + - - +
425H ASP* 6.0 2.9 - - - +
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Residues in contact with ASP 180 (chain G).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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176G LYS* 2.8 36.0 - - - +
177G ASP* 3.0 14.8 - - - +
178G TYR 3.0 1.2 + - - -
179G GLU* 1.3 74.3 - - - +
181G GLN* 1.3 62.1 + - + +
182G GLN 2.9 2.2 - - - +
183G LYS* 2.8 35.3 + - - +
184G GLN* 3.2 5.9 + - - +
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Residues in contact with GLN 181 (chain G).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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144G LEU* 3.4 21.0 - - + +
177G ASP* 3.2 31.9 + - - +
178G TYR* 3.4 23.5 + - - +
180G ASP* 1.3 76.3 - - + +
182G GLN* 1.3 52.7 - - - +
184G GLN* 2.8 33.1 + - - +
185G LEU* 2.8 16.3 + - - +
171H ILE* 4.2 25.6 + - + +
174H ASN* 3.2 41.8 + - + +
175H LEU* 4.5 4.9 - - - +
178H LYS* 5.2 0.5 + - - +
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Residues in contact with GLN 182 (chain G).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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141G ARG* 6.2 2.0 - - + -
144G LEU* 2.9 38.7 + - + +
145G VAL* 4.1 5.9 - - + +
148G LYS* 3.0 37.7 - - - +
178G TYR 3.6 10.1 + - - +
179G GLU* 2.9 44.5 - - - +
180G ASP 3.6 2.0 - - - +
181G GLN* 1.3 79.2 - - - +
183G LYS* 1.3 62.5 + - - +
184G GLN 3.1 0.2 + - - -
185G LEU* 3.2 0.8 + - - -
186G GLU* 2.9 37.7 + - + +
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Residues in contact with LYS 183 (chain G).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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179G GLU* 4.7 5.7 + - - +
180G ASP* 2.8 24.9 + - - +
182G GLN* 1.3 80.2 - - - +
184G GLN* 1.3 56.2 + - - +
186G GLU* 3.8 10.1 + - - +
187G GLN* 3.2 42.1 + - - +
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Residues in contact with GLN 184 (chain G).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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180G ASP 3.2 4.3 + - - +
181G GLN* 2.8 29.2 + - - +
183G LYS* 1.3 75.0 - - - +
185G LEU* 1.3 89.5 + - - +
186G GLU 2.7 5.8 + - - -
187G GLN* 2.6 39.7 + - - +
188G VAL* 3.0 15.2 + - + +
167H VAL* 2.9 31.4 - - - +
171H ILE* 3.4 31.2 - - + +
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Residues in contact with LEU 185 (chain G).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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137G GLN* 4.5 15.5 - - + +
140G VAL* 3.6 29.6 - - + -
141G ARG* 3.7 29.4 - - + -
144G LEU* 4.4 8.3 - - + -
181G GLN 2.8 12.8 + - - +
182G GLN* 3.9 1.6 - - - +
184G GLN* 1.3 96.7 - - - +
186G GLU* 1.3 66.3 + - - +
187G GLN 3.3 1.1 - - - -
188G VAL* 4.5 6.3 - - + -
189G ILE* 2.9 31.1 + - + +
167H VAL* 3.8 20.4 - - + -
168H LEU* 6.1 1.1 - - + -
171H ILE* 3.9 14.4 - - + -
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Residues in contact with GLU 186 (chain G).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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141G ARG* 3.0 41.0 + - - +
182G GLN* 2.9 26.2 + - + +
183G LYS* 3.8 6.8 + - - +
184G GLN 2.7 1.6 + - - -
185G LEU* 1.3 92.4 - - - +
187G GLN* 1.3 63.5 + - - +
189G ILE* 3.0 30.5 - - + +
190G ALA* 5.5 1.7 - - - +
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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