Contacts of the helix formed by residues 482 - 492 (chain A) in PDB entry 6DBU
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 HIS 482 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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480A GLY 4.3 0.2 + - - -
481A LEU* 1.3 79.9 - - + +
483A PRO* 1.3 83.7 - - + +
484A ALA* 4.1 11.7 + - + -
485A VAL* 2.9 32.3 + - + +
486A CYS* 3.2 9.2 + - - +
1020A TYR* 5.0 6.4 + - - -
1024A PHE* 3.8 25.3 - + - -
510C THR* 5.6 1.6 - - + -
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Residues in contact with PRO 483 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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481A LEU 3.3 0.2 - - - -
482A HIS* 1.3 96.8 - - + +
484A ALA* 1.3 55.8 + - - +
486A CYS* 3.1 4.7 + - + +
487A LEU* 3.0 27.0 + - - +
517A GLN* 3.3 40.8 - - + +
521A THR* 5.3 7.0 - - - +
522A LEU* 4.3 6.2 - - + +
525A ALA* 4.0 23.6 - - + +
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Residues in contact with ALA 484 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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482A HIS* 3.2 8.3 + - + +
483A PRO* 1.3 78.3 - - - +
485A VAL* 1.3 57.8 + - - +
487A LEU* 3.3 9.8 + - - +
488A ALA* 2.9 29.1 + - - +
525A ALA* 5.2 3.3 - - - +
529A LEU* 5.8 4.7 - - + -
1020A TYR* 4.2 15.9 - - + +
1021A LEU* 4.0 7.9 - - + +
1024A PHE* 3.4 28.9 - - + -
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Residues in contact with VAL 485 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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481A LEU* 3.8 28.0 - - + -
482A HIS* 2.9 18.1 + - + +
484A ALA* 1.3 77.4 - - - +
486A CYS* 1.3 58.9 + - - +
488A ALA* 3.3 6.9 + - - +
489A ILE* 2.8 29.1 + - + +
1024A PHE* 3.5 38.1 - - + +
506C THR* 4.5 14.0 - - + +
507C VAL* 5.8 0.2 - - - -
510C THR* 3.9 31.9 - - + +
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Residues in contact with CYS 486 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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481A LEU* 5.7 3.8 - - + +
482A HIS 3.2 8.7 + - - +
483A PRO* 3.1 12.2 + - + +
485A VAL* 1.3 77.1 - - - +
487A LEU* 1.3 65.8 + - - +
489A ILE* 3.2 11.6 - - - +
490A ARG* 2.9 23.0 + - - +
500A TYR* 2.5 44.9 - - - -
516A PHE* 3.7 29.4 - - + -
517A GLN* 4.0 10.5 - - + -
522A LEU* 3.5 7.0 - - + +
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Residues in contact with LEU 487 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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483A PRO 3.0 13.7 + - - +
484A ALA* 3.3 9.8 + - - +
486A CYS* 1.3 75.9 - - - +
488A ALA* 1.3 61.3 + - - +
490A ARG* 3.0 14.4 + - - +
491A VAL* 3.0 30.1 + - + +
522A LEU* 3.3 34.4 - - + +
525A ALA* 5.4 1.3 - - + -
526A GLU* 3.5 34.1 - - + +
529A LEU* 3.7 9.6 - - + -
1015A LEU* 3.5 30.7 - - + -
1021A LEU* 3.7 14.1 - - + -
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Residues in contact with ALA 488 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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484A ALA 2.9 17.5 + - - +
485A VAL* 3.6 8.3 - - - +
487A LEU* 1.3 75.8 - - - +
489A ILE* 1.3 57.2 + - - +
491A VAL* 3.1 3.0 + - - +
492A ASN* 2.5 43.0 + - + +
1021A LEU* 3.8 40.8 - - + +
1024A PHE* 5.0 5.8 - - + -
1025A MET* 5.5 5.2 - - + +
506C THR* 6.3 1.3 - - + -
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Residues in contact with ILE 489 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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485A VAL* 2.8 18.0 + - + +
486A CYS* 3.2 28.9 - - - +
488A ALA* 1.3 75.2 - - - +
490A ARG* 1.3 57.9 + - - +
493A THR* 3.0 30.2 - - + +
495A LEU* 4.0 8.1 - - + +
500A TYR* 4.9 6.5 - - + -
516A PHE* 4.9 10.3 - - + -
1025A MET* 4.5 8.3 - - + -
503C MET* 3.4 53.8 - - + +
506C THR* 3.5 32.1 - - + +
507C VAL* 6.0 1.6 - - + -
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Residues in contact with ARG 490 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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486A CYS 2.9 12.7 + - - +
487A LEU* 3.0 14.8 + - - +
489A ILE* 1.3 79.9 - - - +
491A VAL* 1.3 68.0 + - - +
494A PHE 4.0 0.3 - - - -
495A LEU* 3.1 38.7 + - + +
496A SER 3.6 21.7 + - - +
497A CYS* 3.1 28.8 - - - +
500A TYR* 4.3 24.7 - - + -
519A LEU* 4.6 11.1 - - - +
522A LEU* 4.4 24.9 - - + +
523A ARG* 4.8 12.9 - - - +
1011A LYS* 4.6 7.3 - - - +
1012A HIS* 2.9 36.3 + - - -
23E G 5.6 0.6 - - - -
24E C 5.5 3.4 + - - -
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Residues in contact with VAL 491 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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487A LEU* 3.0 22.4 + - + +
488A ALA* 4.1 2.5 - - - +
490A ARG* 1.3 88.9 - - - +
492A ASN* 1.3 60.8 + - - +
493A THR 2.9 11.6 + - - -
494A PHE* 3.0 22.0 + - - +
993A PHE* 4.7 6.8 - - + -
997A ASN* 6.0 0.4 - - - +
1012A HIS* 4.1 26.2 - - + +
1015A LEU* 4.1 22.4 - - + +
1016A TYR* 3.7 40.8 - - + +
1021A LEU* 6.1 1.3 - - + -
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Residues in contact with ASN 492 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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488A ALA* 2.5 26.9 + - + +
489A ILE* 5.0 0.4 - - - -
491A VAL* 1.3 74.6 - - + +
493A THR* 1.3 57.7 + - - +
494A PHE* 3.7 3.1 - - - -
672A LEU* 5.4 1.7 - - - +
1016A TYR* 3.2 30.8 - - - -
1021A LEU* 4.2 9.2 + - + +
1022A GLN* 5.3 7.5 - - - +
1025A MET* 2.5 50.7 - - + +
502C LYS* 4.0 13.7 + - - -
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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