Contacts of the helix formed by residues 169 - 177 (chain H) 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 ARG 169 (chain H).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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165H LEU 3.7 4.3 + - - +
166H ARG* 3.1 32.9 - - - +
167H VAL 2.9 0.4 - - - -
168H LEU* 1.3 79.0 - - - +
170H SER* 1.3 71.5 + - - +
172H LEU* 3.1 5.4 + - - +
173H GLU* 2.9 44.5 + - + +
106I SER* 5.4 2.6 + - - +
109I TYR* 2.8 41.8 - - - +
110I LEU* 3.4 32.3 - - + +
113I ILE* 5.8 2.6 - - - +
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Residues in contact with SER 170 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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166H ARG* 4.2 12.8 - - - +
167H VAL* 3.2 21.8 + - - +
169H ARG* 1.3 78.4 - - - +
171H ILE* 1.3 60.7 + - - +
173H GLU* 2.6 32.5 + - - +
174H ASN* 2.9 26.8 + - - -
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Residues in contact with ILE 171 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
140G VAL* 4.8 8.7 - - + -
144G LEU* 3.8 23.8 - - + -
181G GLN* 4.2 22.6 + - + +
184G GLN* 3.4 42.8 - - + +
185G LEU* 3.9 21.8 - - + -
167H VAL* 3.2 12.8 + - + +
168H LEU* 5.1 1.3 - - - +
170H SER* 1.3 82.4 + - - +
172H LEU* 1.3 64.3 + - + +
173H GLU 2.9 6.4 + - - -
174H ASN* 3.7 13.1 - - - +
175H LEU* 3.2 30.4 + - + +
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Residues in contact with LEU 172 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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140G VAL* 4.1 11.9 - - + -
143G GLN* 4.4 9.4 - - - +
168H LEU* 2.9 26.0 - - + +
169H ARG* 3.1 4.2 + - - +
170H SER 3.0 1.6 + - - -
171H ILE* 1.3 82.5 - - + +
173H GLU* 1.3 65.2 + - - +
175H LEU* 4.1 9.2 - - - +
176H ARG* 3.3 21.0 + - - +
110I LEU* 4.4 11.0 - - + +
113I ILE* 3.1 38.6 - - + +
114I TYR* 3.9 39.5 - - + +
117I ASN* 4.3 4.2 - - - +
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Residues in contact with GLU 173 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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169H ARG* 2.9 43.3 + - + +
170H SER* 2.6 11.1 + - - +
172H LEU* 1.3 103.2 - - - +
174H ASN* 1.3 55.7 + - - +
175H LEU 2.4 17.3 + - - -
176H ARG* 2.9 41.2 + - - +
177H SER* 3.0 16.7 + - - -
110I LEU* 6.1 0.2 - - - +
113I ILE* 3.9 10.3 - - - +
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Residues in contact with ASN 174 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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177G ASP* 4.8 0.3 - - - +
181G GLN* 3.2 26.4 + - - +
170H SER* 2.9 29.8 + - - +
171H ILE* 3.7 6.8 + - + +
173H GLU* 1.3 79.0 - - - +
175H LEU* 1.3 57.4 + - - +
177H SER* 4.2 8.7 - - - -
178H LYS* 3.7 17.3 - - - +
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Residues in contact with LEU 175 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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140G VAL* 5.6 3.4 - - + +
143G GLN* 3.8 20.6 - - - +
144G LEU* 4.2 30.7 - - + +
147G MET* 3.7 23.3 - - + -
178G TYR* 5.1 7.4 - - + +
181G GLN* 4.5 5.4 - - - +
171H ILE* 3.2 22.9 - - + +
172H LEU* 4.1 9.2 - - - +
173H GLU 2.4 7.9 + - - -
174H ASN* 1.3 76.7 - - - +
176H ARG* 1.3 60.4 + - - +
177H SER 3.1 1.6 - - - -
178H LYS* 2.9 33.5 - - + +
179H ILE* 3.0 32.7 - - + +
117I ASN* 4.4 0.2 - - - +
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Residues in contact with ARG 176 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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172H LEU 3.3 14.3 + - - +
173H GLU* 2.9 36.2 + - - +
175H LEU* 1.3 78.6 - - - +
177H SER* 1.3 70.7 + - - +
179H ILE* 2.7 40.9 + - + +
180H GLN* 4.4 6.6 - - + +
113I ILE* 4.0 20.7 - - - +
116I SER* 4.6 2.2 - - - -
117I ASN* 3.3 34.1 - - - +
120I LYS* 5.8 7.2 - - + +
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Residues in contact with SER 177 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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173H GLU 3.0 14.9 + - - -
174H ASN* 4.2 4.0 - - - -
175H LEU 4.2 1.2 + - - -
176H ARG* 1.3 91.4 - - - +
178H LYS* 1.3 72.7 + - - +
180H GLN* 2.7 36.9 + - - +
181H LYS* 3.4 5.8 + - - +
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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