Contacts of the helix formed by residues 164 - 172 (chain H) in PDB entry 2GD4
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 164 (chain H).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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162H TYR 4.4 0.4 + - - -
163H VAL* 1.3 72.5 - - + +
165H ARG* 1.3 57.4 + - - +
166H ASN* 3.6 18.9 - - - +
167H SER* 2.6 61.1 + - - +
168H CYS 2.9 10.1 + - - -
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Residues in contact with ARG 165 (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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131H MET* 6.3 0.4 - - - +
163H VAL 3.1 7.9 + - - -
164H ASP* 1.3 71.0 + - - +
166H ASN* 1.3 70.2 + - - +
167H SER 2.8 6.6 + - - -
168H CYS* 2.9 26.2 + - + +
169H LYS* 3.1 31.2 + - + +
176H ILE* 5.1 6.6 + - + +
177H THR 4.2 10.9 + - - -
178H GLN* 4.3 13.5 + - - +
180H MET 2.8 32.5 + - - -
181H PHE* 4.0 12.4 - - - +
182H CYS* 6.0 1.3 - - - +
230H LYS* 4.4 13.4 - - - +
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Residues in contact with ASN 166 (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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164H ASP* 3.1 18.2 + - - +
165H ARG* 1.3 85.4 - - - +
167H SER* 1.3 58.9 + - - +
169H LYS* 4.0 11.7 - - - +
170H LEU* 3.6 23.4 + - - +
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Residues in contact with SER 167 (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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163H VAL* 4.6 8.1 - - - -
164H ASP* 2.6 42.5 + - - +
166H ASN* 1.3 70.5 - - - +
168H CYS* 1.3 68.1 + - - +
169H LYS 3.1 1.3 - - - -
170H LEU* 2.9 19.8 + - - +
171H SER* 3.1 11.9 + - - -
225H TYR* 5.2 6.7 - - - -
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Residues in contact with CYS 168 (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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163H VAL* 4.5 1.0 - - + +
164H ASP 2.9 8.6 + - - +
165H ARG* 3.0 17.0 - - - +
167H SER* 1.3 74.8 - - - +
169H LYS* 1.3 57.5 + - + +
171H SER* 2.7 25.1 + - - -
172H SER* 2.9 14.9 + - - -
176H ILE* 4.1 27.1 - - - -
181H PHE* 4.5 0.7 - - - -
182H CYS* 2.0 60.1 - - + -
225H TYR* 4.4 5.2 - - - -
227H ILE* 4.3 4.3 - - - -
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Residues in contact with LYS 169 (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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165H ARG* 3.1 34.1 + - + +
166H ASN* 4.0 11.2 - - - +
167H SER 3.1 0.6 - - - -
168H CYS* 1.3 80.0 - - - +
170H LEU* 1.3 65.9 + - + +
172H SER* 3.3 18.9 + - - +
175H ILE* 6.1 2.7 - - + -
176H ILE* 3.9 44.5 + - + +
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Residues in contact with LEU 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 ASN 3.6 15.7 - - - +
167H SER* 2.9 15.7 + - - +
169H LYS* 1.3 77.4 - - + +
171H SER* 1.3 59.9 + - - +
172H SER 4.5 2.1 - - - +
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Residues in contact with SER 171 (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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167H SER 3.1 7.5 + - - -
168H CYS* 2.7 21.1 + - - -
170H LEU* 1.3 78.3 - - - +
172H SER* 1.3 61.5 + - - +
173H SER* 4.5 0.2 + - - -
182H CYS* 5.2 0.7 - - - -
217H GLU* 4.0 0.2 - - - +
223H GLY 3.5 23.7 + - - -
224H LYS* 3.0 28.8 + - - +
225H TYR* 3.9 26.0 + - - +
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Residues in contact with SER 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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168H CYS* 2.9 16.1 + - - -
169H LYS 3.3 15.4 + - - +
170H LEU 4.5 1.9 - - - +
171H SER* 1.3 80.8 + - - +
173H SER* 1.3 63.6 + - - +
174H PHE* 2.3 29.8 + - - +
176H ILE* 3.3 22.1 - - - +
182H CYS* 6.3 0.2 - - - -
215H TRP* 3.9 8.3 - - - -
217H GLU* 3.8 7.0 + - - -
227H ILE* 5.4 2.1 - - - +
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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