Contacts of the helix formed by residues 169 - 175 (chain H) in PDB entry 1C1V
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 GLU 169 (chain H).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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132H ALA* 3.6 25.5 - - + +
167H ILE 4.6 1.2 - - - +
168H VAL* 1.3 76.1 - - - +
170H ARG* 1.3 68.8 + - - +
171H PRO* 3.3 10.5 - - + -
172H VAL* 2.9 30.7 + - + +
173H CYS 2.9 8.8 + - - -
191H LYS* 3.3 35.3 + - - -
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Residues in contact with ARG 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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168H VAL 3.2 4.4 + - - +
169H GLU* 1.3 68.4 - - - +
171H PRO* 1.3 64.4 - - + +
173H CYS* 2.6 33.8 + - - +
174H LYS* 2.7 27.0 + - + +
181H ILE* 3.5 18.4 - - - +
182H THR 2.7 29.3 + - - -
183H ASP* 4.3 16.2 + - - +
185H MET 2.9 24.8 + - - -
186H PHE* 4.2 13.0 - - - +
236H HIS* 4.7 6.7 + - - -
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Residues in contact with PRO 171 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
169H GLU* 3.5 11.4 - - + -
170H ARG* 1.3 95.8 - - + +
172H VAL* 1.3 61.8 + - + +
174H LYS* 3.5 12.6 - - + +
175H ASP* 2.8 40.8 + - - +
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Residues in contact with VAL 172 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
168H VAL* 3.7 18.6 - - + -
169H GLU* 2.9 32.5 + - + +
171H PRO* 1.3 77.8 - - + +
173H CYS* 1.3 69.6 + - - +
175H ASP* 3.4 6.6 + - - +
176H SER* 3.3 18.7 + - - -
191H LYS* 4.2 14.8 - - + +
231H TYR* 4.0 19.0 - - + +
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Residues in contact with CYS 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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168H VAL* 3.6 14.8 - - - -
169H GLU 2.9 18.1 + - - -
170H ARG* 2.6 18.7 + - - +
172H VAL* 1.3 72.9 - - - +
174H LYS* 1.3 64.7 + - + +
176H SER* 2.5 26.7 + - - -
177H THR* 3.9 6.1 + - - +
181H ILE* 5.0 4.5 - - + -
186H PHE* 4.8 1.1 - - - -
187H CYS* 2.0 60.6 - - + -
231H TYR* 4.9 0.7 - - - -
233H PHE* 4.1 11.7 - - + -
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Residues in contact with LYS 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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170H ARG* 2.7 30.5 + - + +
171H PRO* 3.5 12.1 - - + +
173H CYS* 1.3 76.7 - - - +
175H ASP* 1.3 61.9 + - - +
176H SER 3.0 5.1 + - - -
177H THR* 3.0 23.0 + - - +
179H ILE 5.4 0.3 - - - +
180H ARG* 5.9 1.6 - - - +
181H ILE* 4.0 48.0 + - + +
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Residues in contact with ASP 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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171H PRO* 2.8 28.0 + - - +
172H VAL* 3.4 6.7 + - - +
173H CYS 3.3 0.2 - - - -
174H LYS* 1.3 75.8 - - - +
176H SER* 1.3 59.9 + - - +
177H THR 3.3 2.0 - - - -
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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