Contacts of the helix formed by residues 462 - 470 (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 SER 462 (chain B).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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460B ARG* 3.6 5.0 - - - +
461B LEU* 1.3 78.3 + - - +
463B TYR* 1.3 63.9 + - - +
464B ILE* 3.2 19.1 + - - +
465B SER* 2.6 34.8 + - - -
466B ALA* 3.2 17.5 + - - +
706B GLY 4.4 1.6 - - - -
707B LYS* 3.6 8.4 + - - -
709B ALA 3.2 19.1 - - - -
711B GLY* 5.1 3.6 - - - +
713B ILE* 3.7 13.2 - - - +
751B ALA* 5.0 2.7 - - - -
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Residues in contact with TYR 463 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
179B LEU* 3.3 33.0 + - + +
180B ASP* 5.1 1.3 - - - -
181B PRO* 4.5 10.7 - - + +
462B SER* 1.3 74.6 - - - +
464B ILE* 1.3 68.2 + - + +
466B ALA* 3.4 18.6 - - + +
467B LEU* 3.9 22.8 + - + +
711B GLY* 5.7 0.4 - - - -
712B ALA 5.6 0.8 - - - +
713B ILE* 3.7 23.9 - - - +
714B ALA* 5.9 1.8 - - + -
744B ILE* 2.9 32.8 + - + -
745B ASP* 4.4 12.8 + - + +
746B TYR* 4.4 15.7 - + - -
749B LEU* 3.4 45.2 + - + +
751B ALA* 5.8 1.0 - - - +
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Residues in contact with ILE 464 (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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462B SER* 3.1 17.8 + - - +
463B TYR* 1.3 80.3 - - + +
465B SER* 1.3 60.9 + - - +
466B ALA 3.2 0.5 + - - -
467B LEU* 3.4 14.9 + - + +
468B GLY* 2.8 21.3 + - - -
683B ALA 5.2 1.3 - - - +
684B VAL* 4.1 28.7 - - + -
687B LEU* 4.1 22.4 - - + -
706B GLY 4.1 12.3 - - - +
707B LYS* 4.8 7.9 - - - +
709B ALA* 5.3 0.9 - - + -
744B ILE* 5.6 5.2 - - + -
746B TYR* 3.2 43.1 - - + +
749B LEU 5.6 0.2 - - - +
751B ALA* 4.5 11.4 - - + -
1025B GLN* 5.7 1.3 - - - +
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Residues in contact with SER 465 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
458B LEU* 5.0 0.3 - - - +
459B SER* 2.5 36.5 + - - +
461B LEU* 4.3 2.2 + - - -
462B SER* 2.6 27.3 + - - -
464B ILE* 1.3 71.5 - - - +
466B ALA* 1.3 61.4 + - - +
468B GLY* 2.8 17.8 + - - +
469B MET* 3.0 18.0 + - - +
707B LYS* 3.7 28.9 + - - +
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Residues in contact with ALA 466 (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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180B ASP* 4.8 2.2 - - - +
181B PRO* 4.6 18.9 - - + +
458B LEU* 3.6 32.0 - - + +
459B SER 4.4 1.3 + - - -
460B ARG* 4.3 21.5 - - + +
462B SER 3.2 12.1 + - - +
463B TYR* 3.4 19.7 - - + +
464B ILE 3.1 0.6 - - - -
465B SER* 1.3 79.2 - - - +
467B LEU* 1.3 58.3 + - - +
470B MET* 3.7 8.1 + - - +
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Residues in contact with LEU 467 (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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57B LEU* 4.9 12.8 - - + -
58B VAL* 4.8 9.4 - - + -
181B PRO* 4.2 20.4 - - + -
463B TYR* 4.2 33.2 - - + +
464B ILE* 3.7 17.7 - - + +
466B ALA* 1.3 76.4 - - - +
468B GLY* 1.3 56.0 + - - +
470B MET* 2.6 32.4 - - + +
471B THR* 4.3 5.2 - - - +
683B ALA* 3.8 33.0 - - + +
684B VAL* 5.3 1.7 - - + +
744B ILE* 4.5 21.1 - - + -
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Residues in contact with GLY 468 (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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464B ILE 2.8 12.2 + - - -
465B SER* 2.8 13.9 + - - -
467B LEU* 1.3 74.5 - - - +
469B MET* 1.3 60.5 + - - +
470B MET 2.8 11.8 - - - +
471B THR 3.7 7.6 - - - +
472B ARG* 3.9 6.8 - - - +
513B ASN* 4.5 3.9 + - - +
684B VAL* 4.6 17.0 - - - -
707B LYS* 4.4 17.7 + - - -
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Residues in contact with MET 469 (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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193B VAL* 5.1 11.2 - - + +
195B LEU* 3.6 16.3 - - + +
456B HIS* 3.5 34.8 - - + +
457B VAL 4.1 5.2 - - - +
458B LEU* 4.3 15.7 - - + -
459B SER* 3.7 30.3 - - - +
465B SER* 3.0 16.4 + - - +
468B GLY* 1.3 71.5 - - - +
470B MET* 1.3 65.9 + - - +
471B THR 3.6 0.7 + - - -
472B ARG* 3.3 56.1 - - - +
707B LYS* 5.2 1.3 - - - +
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Residues in contact with MET 470 (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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58B VAL* 3.2 46.4 - - + -
61B HIS* 3.2 25.1 - - + +
181B PRO* 5.7 1.3 - - + -
182B GLY 3.4 15.5 - - - +
183B GLY* 3.2 32.1 - - - +
184B TYR 4.9 0.2 - - - -
193B VAL* 4.2 18.4 - - - +
458B LEU* 4.8 5.4 - - + +
466B ALA 3.7 7.6 + - - +
467B LEU* 2.6 42.3 - - - +
468B GLY 2.8 11.6 - - - +
469B MET* 1.3 78.1 - - - +
471B THR* 1.3 63.5 + - - +
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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