Contacts of the strand formed by residues 164 - 167 (chain C) in PDB entry 1C3Q
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 VAL 164 (chain C).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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118C ALA 3.4 17.7 + - - +
119C ALA* 3.2 11.3 - - + -
120C ILE 3.0 26.5 + - - +
163C THR* 1.3 83.1 + - - +
165C ILE* 1.3 66.4 + - - +
166C ALA* 4.6 1.6 - - + +
174C ILE* 3.9 23.3 - - + -
175C ALA 3.3 7.9 - - - +
176C ASP* 4.0 18.6 - - + -
214C PRO* 3.9 12.1 - - + +
215C LEU* 3.6 33.4 - - + +
218C ALA* 4.6 3.4 - - + -
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Residues in contact with ILE 165 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
120C ILE* 3.8 22.0 - - + -
127C ILE* 4.0 23.1 - - + -
131C VAL* 5.3 0.4 - - + -
154C ALA* 3.7 20.3 - - - +
157C ALA* 3.8 13.9 - - + +
158C ALA* 3.4 31.0 - - - +
161C LEU* 4.3 4.0 - - + -
163C THR* 3.8 17.0 - - + -
164C VAL* 1.3 79.5 - - - +
166C ALA* 1.3 60.8 + - - +
167C ILE* 4.0 21.8 - - + -
173C VAL 3.6 2.3 - - - +
174C ILE* 3.3 2.8 - - - -
175C ALA* 2.8 37.7 + - - +
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Residues in contact with ALA 166 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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119C ALA* 6.1 1.3 - - + -
120C ILE 2.9 14.9 + - - +
121C ARG* 3.4 20.0 - - + +
122C GLY 3.1 24.9 + - - +
127C ILE* 4.9 0.3 - - - +
164C VAL* 4.1 4.0 - - + -
165C ILE* 1.3 72.4 - - - +
167C ILE* 1.3 63.2 + - - +
168C THR* 3.8 1.2 + - - -
173C VAL 3.5 4.7 - - - -
174C ILE* 3.3 27.1 - - + -
204C VAL* 6.1 0.4 - - + -
218C ALA* 5.1 4.5 - - + -
222C ILE* 4.2 7.2 - - + -
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Residues in contact with ILE 167 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
122C GLY 3.2 2.9 - - - -
124C ALA* 3.4 35.4 - - + +
127C ILE* 3.9 24.0 - - + -
150C ILE* 4.2 17.5 - - + -
153C LEU* 4.0 31.9 - - + -
154C ALA* 4.2 19.1 - - + -
165C ILE* 4.0 7.4 - - + -
166C ALA* 1.3 74.3 - - - +
168C THR* 1.3 65.3 + - - +
171C VAL 4.1 1.0 - - - +
172C ASP* 3.3 4.0 - - - +
173C VAL* 2.8 46.5 + - + +
174C ILE* 4.3 0.4 - - - +
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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