Contacts of the helix formed by residues 465 - 472 (chain B) in PDB entry 6RKU
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 GLN 465 (chain B).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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462B LEU* 3.3 45.2 - - + +
463B SER 4.8 1.0 - - - +
464B SER* 1.3 82.9 + - - +
466B GLU* 1.3 61.1 + - - -
467B VAL* 3.2 3.9 + - - +
468B ALA* 3.3 15.5 + - + +
469B THR* 2.9 38.9 + - - +
474B LEU* 5.2 11.8 - - + +
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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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402B GLY* 4.1 27.8 + - - +
406B LYS* 4.8 15.0 - - - +
444B LEU* 4.7 15.2 - - + +
445B PRO 5.2 2.8 - - - +
464B SER* 2.8 25.7 + - - +
465B GLN* 1.3 77.3 - - - +
467B VAL* 1.3 64.9 + - + +
469B THR* 4.2 6.3 - - - -
470B LEU* 2.9 41.5 + - + +
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Residues in contact with VAL 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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422B LEU* 5.2 11.2 - - + -
444B LEU* 4.3 21.3 - - + -
446B LEU* 4.4 19.1 - - + -
450B ILE* 5.7 6.7 - - + -
464B SER* 5.4 6.3 - - - +
465B GLN* 3.2 1.1 - - - -
466B GLU* 1.3 79.3 - - + +
468B ALA* 1.3 59.8 + - - +
470B LEU* 3.8 1.4 - - - +
471B ILE* 2.9 40.7 + - + +
510B LEU* 6.1 3.4 - - + -
513B PHE* 4.8 19.5 - - + -
514B PHE* 4.9 17.9 - - + -
518B MET* 6.5 0.4 - - + -
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Residues in contact with ALA 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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465B GLN* 3.3 18.1 + - + +
467B VAL* 1.3 80.2 - - - +
469B THR* 1.3 55.6 + - - +
471B ILE* 3.4 9.8 - - - +
472B THR* 2.7 38.3 + - - +
473B ALA 5.9 0.2 - - - -
474B LEU* 4.1 35.2 - - + -
513B PHE* 5.8 8.3 - - + -
518B MET* 6.1 2.0 - - + -
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Residues in contact with THR 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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402B GLY* 5.4 9.2 - - - -
403B LEU* 5.5 2.0 - - + +
465B GLN* 2.9 33.5 + - - +
466B GLU* 3.8 7.6 - - - -
467B VAL 3.3 0.2 - - - -
468B ALA* 1.3 77.5 - - - +
470B LEU* 1.3 69.1 + - + +
472B THR 3.5 10.1 - - - +
489B ARG* 4.3 7.8 + - - -
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Residues in contact with LEU 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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402B GLY 3.7 16.8 - - - +
403B LEU* 3.6 47.3 - - + +
407B LEU* 3.7 22.5 - - + +
420B LEU* 6.3 3.6 - - + -
444B LEU* 3.7 35.7 - - + -
466B GLU* 2.9 24.2 + - + +
467B VAL 4.0 1.8 - - - +
469B THR* 1.3 83.8 - - + +
471B ILE* 1.3 66.4 + - - +
489B ARG* 3.6 16.1 + - - +
490B TYR* 4.6 12.6 - - + -
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Residues in contact with ILE 471 (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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420B LEU* 5.6 9.2 - - + -
467B VAL* 2.9 28.9 + - + +
468B ALA* 3.4 12.8 - - - +
470B LEU* 1.3 80.9 - - - +
472B THR* 1.3 89.8 + - + +
487B LYS* 5.4 0.3 - - - +
489B ARG* 4.0 33.9 + - - +
490B TYR* 5.4 6.7 - - + +
493B ILE* 4.6 24.5 - - + -
514B PHE* 4.8 8.5 - - + -
518B MET* 4.5 17.5 - - + -
521B ILE* 4.0 25.4 - - + -
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Residues in contact with THR 472 (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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468B ALA 2.7 15.4 + - - +
469B THR* 3.5 12.1 - - - +
471B ILE* 1.3 103.8 - - + +
473B ALA* 1.3 61.4 + - - +
474B LEU* 3.3 15.3 + - - +
484B ASN* 4.8 15.3 - - + +
487B LYS* 3.3 35.7 - - - +
488B LEU* 4.8 4.7 - - + -
489B ARG* 5.0 6.7 + - - +
518B MET* 4.2 13.6 - - - -
521B ILE* 5.9 4.0 - - + -
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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