Contacts of the helix formed by residues 461 - 469 (chain B) in PDB entry 3KG2
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 ASN 461 (chain B).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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447B ASP* 3.3 12.5 + - - +
449B LYS* 4.2 15.1 - - - +
451B GLY* 3.4 17.2 - - - -
452B ALA* 2.8 43.5 + - - +
454B ASP 5.9 1.1 - - - +
459B ILE* 5.0 3.8 - - + +
460B TRP* 1.3 75.0 - - - +
462B GLY* 1.3 67.7 + - - +
464B VAL* 4.3 0.2 - - - +
465B GLY* 3.4 7.1 + - - -
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Residues in contact with GLY 462 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
445B VAL* 3.5 7.6 - - - +
447B ASP* 2.9 28.1 + - - -
449B LYS* 3.2 22.7 - - - -
461B ASN* 1.3 72.2 - - - +
463B MET* 1.3 64.2 + - - -
465B GLY* 3.2 1.6 + - - -
466B GLU* 3.1 25.5 + - - +
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Residues in contact with MET 463 (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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398B THR* 3.7 32.8 - - + +
399B THR* 3.6 16.6 - - - -
400B ILE* 3.6 9.0 - - + -
445B VAL* 3.7 16.6 - - + +
449B LYS 3.4 1.3 + - - +
450B TYR* 2.8 42.6 + - + +
462B GLY* 1.3 67.4 - - - -
464B VAL* 1.3 66.1 + - - +
465B GLY 3.0 1.3 - - - -
466B GLU* 3.0 14.7 + - - +
467B LEU* 3.1 18.9 + - - +
475B ALA* 4.4 7.9 - - + -
477B ALA* 3.5 32.3 - - + -
479B LEU* 3.9 22.2 - - + -
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Residues in contact with VAL 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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450B TYR 3.2 1.9 + - - +
451B GLY* 3.5 27.1 - - - -
460B TRP* 3.5 32.3 - - + -
463B MET* 1.3 76.5 - - - +
465B GLY* 1.3 61.2 + - - +
467B LEU* 3.5 11.1 + - - +
468B VAL* 3.2 22.4 + - + +
479B LEU* 3.6 30.3 - - + -
485B ARG* 3.9 13.5 - - + -
488B VAL* 4.3 9.9 - - + -
489B ILE* 4.1 16.4 - - + -
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Residues in contact with GLY 465 (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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460B TRP* 3.7 34.1 - - - +
461B ASN* 3.4 5.2 + - - -
462B GLY 3.2 7.7 + - - -
463B MET 3.0 1.2 - - - -
464B VAL* 1.3 75.1 - - - +
466B GLU* 1.3 57.1 + - - +
467B LEU 2.9 10.4 + - - -
468B VAL 3.0 9.2 + - - -
469B TYR* 2.9 25.7 + - - -
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Residues in contact with GLU 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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398B THR* 3.3 19.6 + - - +
443B THR* 5.1 2.9 + - - -
444B ILE 5.3 0.5 - - - +
445B VAL* 3.4 15.4 - - + +
446B GLY* 3.2 27.2 + - - -
462B GLY 3.1 11.0 + - - +
463B MET* 3.0 9.6 + - - +
465B GLY* 1.3 74.3 - - - +
467B LEU* 1.3 57.7 + - - +
469B TYR* 4.2 2.5 - - - +
471B LYS* 2.7 51.9 + - + +
472B ALA* 2.9 17.7 + - + +
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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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398B THR* 4.5 1.1 - - + -
463B MET 3.1 14.2 + - - +
464B VAL* 3.6 9.4 - - - +
465B GLY 3.0 0.4 - - - -
466B GLU* 1.3 78.5 - - - +
468B VAL* 1.3 65.4 + - - +
469B TYR 3.2 0.8 + - - -
470B GLY* 3.4 10.2 + - - -
472B ALA* 3.8 18.3 - - + +
473B ASP 4.0 2.9 - - - +
474B ILE* 3.7 37.0 - - - +
475B ALA* 3.6 25.6 - - + +
479B LEU* 5.3 0.7 - - + -
489B ILE* 4.2 33.9 - - + -
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Residues in contact with VAL 468 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
460B TRP* 4.6 13.0 - - + -
464B VAL* 3.2 18.2 - - + +
465B GLY 3.0 6.5 + - - +
467B LEU* 1.3 77.2 - - - +
469B TYR* 1.3 80.5 + - + +
470B GLY 3.4 1.2 + - - -
488B VAL* 4.3 22.9 - - + +
489B ILE* 3.8 20.4 - - + -
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Residues in contact with TYR 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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458B LYS 4.4 1.7 + - - -
459B ILE* 3.4 18.1 - - + +
460B TRP* 2.8 56.2 + + + +
465B GLY* 2.9 29.5 + - - +
466B GLU* 5.0 2.2 - - - +
468B VAL* 1.3 92.0 - - + +
470B GLY* 1.3 62.1 + - - +
471B LYS* 3.3 6.8 + - + +
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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