Contacts of the strand formed by residues 186 - 189 (chain C) in PDB entry 3N1O
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 186 (chain C).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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151C VAL 3.4 1.9 - - - +
152C ASP* 3.3 3.5 - - - -
153C ILE* 2.9 47.2 + - + +
163C TYR* 3.6 38.1 - - + +
166C LEU* 4.4 5.8 - - + -
167C ALA* 3.8 25.6 - - + +
178C VAL* 3.8 14.4 - - + -
179C TYR 3.6 13.0 - - - +
180C TYR* 4.6 8.3 - - + -
185C HIS* 1.3 80.7 - - - +
187C HIS* 1.3 63.6 + - - +
188C CYS* 4.2 6.5 - - - -
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Residues in contact with HIS 187 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
58C GLU* 2.6 33.4 + - - -
143C SER* 5.3 1.6 - - - -
144C LEU* 5.2 2.5 - - + -
145C HIS* 3.5 5.8 + + - -
150C ALA* 3.4 24.2 - - + +
151C VAL 3.6 3.1 - - - -
152C ASP* 3.3 2.8 + - - +
177C TRP* 3.5 23.3 - + - -
178C VAL* 3.4 2.6 - - - +
179C TYR* 2.7 48.8 + + + +
181C GLU* 4.2 15.9 - - + +
185C HIS* 4.1 1.8 - - + -
186C VAL* 1.3 71.2 - - - +
188C CYS* 1.3 64.5 + - - +
189C SER* 3.9 4.8 - - - -
194C ZN 2.1 37.5 - - - -
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Residues in contact with CYS 188 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
150C ALA* 3.1 4.3 - - - +
151C VAL* 2.8 40.8 + - + +
153C ILE* 3.7 35.4 - - - -
170C ALA* 3.8 18.6 - - - -
175C PHE* 3.6 30.9 - - + -
177C TRP 3.4 6.7 - - - +
178C VAL* 4.3 2.7 - - + -
186C VAL* 4.2 7.2 - - - -
187C HIS* 1.3 80.8 - - - +
189C SER* 1.3 61.8 + - - +
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Residues in contact with SER 189 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
58C GLU* 2.9 27.1 + - - -
64C SER* 2.9 20.0 + - - -
144C LEU* 3.9 7.9 - - - -
149C ARG 3.0 17.7 - - - -
150C ALA* 4.0 2.0 - - - +
175C PHE* 3.7 3.3 - - - -
176C ASP 2.9 23.2 + - - -
177C TRP* 3.0 21.5 + - - +
187C HIS* 3.9 3.1 - - - -
188C CYS* 1.3 76.8 - - - +
190C VAL* 1.3 65.2 + - - +
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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
------------------------------------------------------------
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