Contacts of the strand formed by residues 192 - 196 (chain A) in PDB entry 2I6A
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 ILE 192 (chain A).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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163A ARG* 2.9 17.6 + - + +
164A VAL* 4.3 14.1 - - + -
165A CYS* 2.8 32.9 + - - +
186A ALA* 4.4 1.1 - - - +
191A ARG* 1.3 71.6 - - - +
193A PHE* 1.3 60.0 + - - +
194A THR* 3.7 23.1 - - + -
218A ASP* 3.7 13.9 - - + -
219A ILE* 4.5 7.0 - - + -
258A ARG* 3.6 35.7 - - - +
310A LEU* 3.9 30.5 - - + +
313A ASP* 5.9 4.5 - - - +
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Residues in contact with PHE 193 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
165A CYS* 4.0 16.6 - - + -
167A ILE* 3.8 20.9 - - + -
179A VAL* 3.6 24.9 - - + -
182A VAL* 4.1 8.5 - - + -
183A ALA* 3.6 40.4 - - + -
186A ALA* 3.7 15.3 - - + -
191A ARG 3.4 0.4 + - - -
192A ILE* 1.3 71.8 - - - +
194A THR* 1.3 73.9 + - - +
195A LEU* 4.4 5.2 - - + -
213A VAL* 4.2 9.2 - - + -
216A TYR 3.4 26.5 - - - +
217A VAL* 3.5 17.3 - - + -
218A ASP* 2.7 41.1 + - - +
219A ILE 3.5 1.2 + - - -
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Residues in contact with THR 194 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
164A VAL* 4.4 7.6 - - + -
165A CYS 2.9 21.8 + - - +
166A TYR* 3.0 22.6 - - - +
167A ILE 3.2 19.6 + - - +
192A ILE* 3.7 19.7 - - + -
193A PHE* 1.3 87.8 - - - +
195A LEU* 1.3 61.0 - - - +
219A ILE* 3.4 35.2 - - + -
221A PHE* 3.7 15.5 - - + -
307A LEU* 4.1 5.5 - - + +
310A LEU* 5.5 0.4 - - + -
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Residues in contact with LEU 195 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
166A TYR* 3.8 4.9 - - - -
167A ILE* 3.1 27.8 - - + +
168A ALA 4.5 0.4 - - - +
169A GLY* 4.3 10.3 - - - +
172A LEU* 4.7 7.2 - - + -
179A VAL* 4.3 15.5 - - + -
193A PHE* 4.4 4.7 - - + -
194A THR* 1.3 75.7 - - - +
196A ASN* 1.3 76.9 + - - +
210A LEU* 3.5 32.3 - - + +
213A VAL* 4.0 20.0 - - + -
214A MET* 5.3 0.4 - - + -
217A VAL* 3.7 27.8 - - + +
219A ILE 3.3 5.6 + - - +
220A LEU* 3.8 12.2 - - + -
221A PHE* 3.1 27.5 + - - -
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Residues in contact with ASN 196 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
65A SER* 5.0 5.1 + - - -
166A TYR* 2.3 37.0 + - - +
167A ILE 3.4 3.8 + - - -
168A ALA* 3.7 5.2 - - + -
169A GLY* 3.0 23.6 + - - -
195A LEU* 1.3 84.6 - - - +
197A LEU* 1.3 65.8 + - - +
198A SER* 3.1 25.8 + - - +
210A LEU* 5.2 0.5 - - - +
220A LEU* 4.7 0.7 - - - -
221A PHE* 3.5 15.0 - - - +
222A GLY* 3.7 10.0 + - - -
226A GLU* 4.2 1.9 - - - +
299A GLY 5.6 0.8 + - - -
300A ASP* 5.3 4.2 + - - +
303A VAL* 3.7 20.4 - - - +
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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
------------------------------------------------------------
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