Contacts of the strand formed by residues 194 - 197 (chain G) in PDB entry 6CNB
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 TYR 194 (chain G).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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38G ILE* 3.2 30.5 - - + -
42G VAL 4.0 2.9 - - - -
43G GLY* 3.8 11.2 - - - -
44G LEU* 4.7 8.7 - - + -
77G PHE* 3.1 45.0 + + - -
78G LYS* 4.3 4.6 - - + +
79G PRO* 3.7 9.5 - - - +
105G PHE* 4.3 12.1 - + - -
107G ASP* 2.9 28.2 + - - +
153G GLU* 3.0 33.8 - - + +
154G VAL 3.7 2.2 - - - -
155G PHE* 3.3 22.9 - + + -
192G PRO 4.2 0.2 - - - -
193G ALA* 1.3 79.0 - - - +
195G ALA* 1.3 60.4 + - - +
196G LEU* 3.4 21.8 - - + +
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Residues in contact with ALA 195 (chain G).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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107G ASP* 3.2 23.3 - - + +
109G PHE* 5.8 3.6 - - + -
153G GLU* 3.2 4.4 + - - +
154G VAL* 2.9 49.7 + - + +
192G PRO* 4.3 15.9 - - + +
194G TYR* 1.3 76.1 - - - +
196G LEU* 1.3 65.4 + - - +
197G LEU* 5.7 0.2 - - - +
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Residues in contact with LEU 196 (chain G).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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77G PHE* 4.2 8.7 - - + -
79G PRO* 3.6 31.2 - - + -
105G PHE* 4.9 6.7 - - + -
107G ASP 3.2 6.7 + - - +
108G ILE* 4.4 18.4 - - + -
109G PHE* 2.7 35.5 + - - +
150G ILE* 3.9 23.3 - - + -
152G ARG 3.6 2.9 - - - -
153G GLU* 3.6 16.4 - - + -
194G TYR* 3.4 39.3 - - + +
195G ALA* 1.3 80.7 - - - +
197G LEU* 1.3 60.2 + - - +
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Residues in contact with LEU 197 (chain G).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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109G PHE* 3.1 20.2 - - + +
110G ILE* 4.2 2.5 - - - -
111G PRO* 3.9 17.0 - - + -
113G ASN* 6.2 2.5 - - - +
150G ILE* 3.3 5.6 - - - +
151G GLU* 2.3 40.0 + - + -
152G ARG* 2.8 63.2 + - + +
153G GLU* 5.2 0.4 - - - -
154G VAL* 4.6 19.1 - - + +
196G LEU* 1.3 76.4 - - - +
198G GLY* 1.3 54.2 + - - +
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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
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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