Contacts of the strand formed by residues 190 - 194 (chain B) 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 THR 190 (chain B).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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186B ILE* 3.3 5.4 - - - +
187B VAL* 2.8 40.5 + - + +
188B ASN* 3.1 10.2 + - + -
189B GLY* 1.3 81.8 - - - +
191B GLU* 1.3 66.4 + - - +
192B LYS* 3.7 30.3 - - + +
438B SER* 5.5 0.9 - - - -
457B VAL* 4.2 19.6 - - - +
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Residues in contact with GLU 191 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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119B ARG* 4.7 17.9 - - - +
184B TYR* 3.0 40.9 - - + -
185B PHE 4.1 3.4 - - - +
186B ILE* 4.6 4.5 - - + +
189B GLY 5.0 2.0 - - - +
190B THR* 1.3 82.6 + - - +
192B LYS* 1.3 60.5 + - - +
457B VAL* 3.4 10.7 - - + +
458B LEU* 3.0 60.8 + - - +
460B ARG* 3.9 11.0 + - - +
720B ARG* 5.1 3.3 + - - +
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Residues in contact with LYS 192 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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184B TYR* 3.5 1.6 - - - +
185B PHE* 2.9 40.0 + - + +
186B ILE* 4.7 0.4 - - - +
187B VAL* 4.7 7.4 - - + -
190B THR* 3.7 25.5 + - + +
191B GLU* 1.3 79.7 - - - +
193B VAL* 1.3 69.8 + - - +
437B ILE* 4.2 9.4 - - + +
438B SER* 2.3 57.4 + - - +
439B THR* 4.5 1.4 - - - +
455B THR* 4.7 4.0 - - - +
456B HIS* 2.9 20.4 - - - +
457B VAL* 3.9 17.5 - - + +
458B LEU 4.1 0.4 - - - +
29Y G 5.4 5.5 + - - -
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Residues in contact with VAL 193 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
61B HIS* 4.6 2.5 - - + +
183B GLY 4.7 5.6 - - - +
184B TYR* 3.4 22.7 - - + -
185B PHE* 4.7 3.6 - - - +
192B LYS* 1.3 78.0 - - - +
194B ILE* 1.3 79.4 + - - +
195B LEU* 3.7 6.6 + - + +
437B ILE* 5.7 0.9 - - - -
455B THR* 3.1 10.8 - - - -
456B HIS* 2.9 33.5 + - + +
458B LEU* 3.5 29.6 - - + -
469B MET* 5.1 14.6 - - + +
470B MET* 4.2 20.4 - - - -
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Residues in contact with ILE 194 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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61B HIS* 3.2 18.7 + - + -
183B GLY 5.7 0.4 + - - -
185B PHE* 3.5 29.2 - - + -
193B VAL* 1.3 84.3 - - - +
195B LEU* 1.3 69.7 + - - +
196B VAL* 5.7 0.2 - - - -
379B LEU 5.3 0.4 - - - -
380B ALA* 3.8 28.9 - - + +
383B LEU* 4.2 14.4 - - + -
384B ILE* 3.6 28.5 - - + -
437B ILE* 3.6 24.0 - - + -
442B TRP* 4.5 13.0 - - + -
454B VAL* 4.7 3.4 - - + +
455B THR* 3.9 11.9 - - + -
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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