Contacts of the strand formed by residues 192 - 197 (chain A) in PDB entry 6JOD
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 192 (chain A).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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107A ARG 4.1 11.9 - - - +
108A TYR* 3.1 39.5 - - + +
109A ASP* 3.6 15.5 - - + +
187A ILE* 2.9 30.8 + - + +
190A LEU* 3.3 31.4 - - + +
191A GLY* 1.3 78.4 - - - +
193A ASN* 1.3 64.8 + - - +
194A ALA* 3.2 12.6 + - + +
50H TYR* 4.9 0.2 - - - +
52H SER* 4.8 2.9 - - - -
53H SER* 5.4 2.2 - - - +
57H LEU* 3.5 3.9 - - - +
102H TYR* 3.8 10.8 - - + +
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Residues in contact with ASN 193 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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109A ASP* 3.8 5.7 + - - -
110A TRP* 2.9 33.9 + - - +
184A VAL* 4.1 18.1 - - + +
185A ARG 3.7 3.6 - - - -
186A THR* 2.6 32.6 + - - -
192A VAL* 1.3 70.0 - - - +
194A ALA* 1.3 59.3 + - - +
56H SER* 3.0 45.4 + - - +
57H LEU* 3.7 13.9 - - - +
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Residues in contact with ALA 194 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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108A TYR* 3.3 16.2 - - + +
184A VAL* 3.3 4.4 - - - -
185A ARG 2.9 33.2 + - - +
187A ILE* 3.8 16.6 - - + -
190A LEU* 6.1 0.2 - - + -
192A VAL* 3.2 6.9 + - + -
193A ASN* 1.3 74.7 - - - +
195A CYS* 1.3 60.7 + - - +
196A ILE* 3.3 22.6 + - + +
5B ILE* 3.7 15.5 - - + -
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Residues in contact with CYS 195 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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100A TRP* 4.7 9.6 - - - -
103A TYR* 3.4 22.3 + - + -
110A TRP* 3.8 34.5 - - + +
117A CYS* 2.0 54.7 - - + -
182A ARG* 3.5 24.4 + - - -
183A ASP 3.7 0.7 - - - -
184A VAL* 4.2 1.8 - - - -
193A ASN 4.1 0.6 + - - -
194A ALA* 1.3 69.4 - - - +
196A ILE* 1.3 59.3 + - - +
5B ILE 3.5 5.2 - - - +
6B HIS 5.1 0.2 - - - -
7B PRO* 6.3 0.2 - - - -
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Residues in contact with ILE 196 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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181A PHE 3.4 0.3 - - - +
182A ARG* 3.4 9.6 - - - +
183A ASP 2.8 39.1 + - - +
185A ARG* 3.7 31.4 - - + -
187A ILE* 4.3 4.5 - - + -
194A ALA* 3.3 14.6 + - + +
195A CYS* 1.3 77.7 - - - +
197A MET* 1.3 72.7 + - - +
198A ALA* 4.7 1.8 - - - -
204A TYR* 5.1 1.1 - - + -
3B VAL* 3.7 36.3 - - + -
4B TYR 3.3 13.2 - - - +
5B ILE* 3.6 29.2 - - + -
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Residues in contact with MET 197 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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177A PRO 4.1 11.7 - - - +
178A THR* 4.1 15.0 - - - +
181A PHE* 3.3 25.6 - - + -
182A ARG* 3.5 50.3 - - - +
196A ILE* 1.3 76.4 - - - +
198A ALA* 1.3 57.4 + - - +
199A PHE* 3.3 35.0 - - + -
204A TYR* 2.7 36.1 + - - +
211A ILE* 4.7 12.8 - - + -
215A LYS* 5.6 5.2 - - - +
4B TYR* 3.3 21.4 + - + -
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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