Contacts of the helix formed by residues 497 - 511 (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 CYS 497 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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490A ARG* 3.1 40.4 - - - +
496A SER* 1.3 78.2 + - - +
498A SER* 1.3 64.9 + - - +
499A GLN 3.3 0.7 - - - -
500A TYR* 3.4 6.0 + - - +
501A HIS* 3.2 20.4 + - - +
519A LEU* 4.5 11.6 - - + +
1012A HIS* 4.9 1.1 - - - -
23E G 3.0 57.6 + - + +
24E C 5.5 0.9 - - - -
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Residues in contact with SER 498 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
496A SER* 3.2 2.1 + - - -
497A CYS* 1.3 76.9 - - - +
499A GLN* 1.3 76.3 + - - +
501A HIS* 3.1 10.4 + - - +
502A LYS* 2.9 28.7 + - - +
22E T 3.3 29.0 + - - +
23E G 4.2 1.8 + - - -
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Residues in contact with GLN 499 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
495A LEU* 3.5 24.8 - - + +
496A SER* 2.8 36.8 + - - +
498A SER* 1.3 79.2 + - - +
500A TYR* 1.3 62.2 + - - +
502A LYS* 3.2 7.8 + - - +
503A MET* 2.9 26.4 + - - +
493C THR* 3.2 38.3 + - - +
494C PHE* 4.7 6.6 + - + +
495C LEU* 4.7 6.4 - - - +
499C GLN* 5.4 1.4 - - - +
992C ARG* 3.5 26.4 - - - +
996C MET* 4.8 7.3 - - - +
22E T 4.1 5.3 + - - -
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Residues in contact with TYR 500 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
486A CYS* 2.5 46.6 - - - -
489A ILE* 4.9 4.0 - - + -
490A ARG* 4.3 20.9 - - + -
495A LEU* 4.7 18.1 - - + +
496A SER 3.6 16.2 + - - +
497A CYS 3.4 8.3 + - - +
498A SER 3.2 0.6 - - - -
499A GLN* 1.3 78.7 - - - +
501A HIS* 1.3 57.0 + - - +
503A MET* 3.2 12.8 - - + +
504A TYR* 2.9 31.8 + - + +
516A PHE* 3.8 16.8 - + + +
517A GLN 2.9 20.2 + - - -
519A LEU* 3.4 38.1 - - + -
522A LEU* 3.5 16.5 - - + +
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Residues in contact with HIS 501 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
497A CYS 3.2 7.3 + - - +
498A SER* 3.1 12.2 + - - +
500A TYR* 1.3 79.2 - - - +
502A LYS* 1.3 61.3 + - + +
504A TYR* 3.3 22.0 + + - +
505A ARG* 2.9 40.4 + - + +
519A LEU* 3.7 29.3 - - + +
8F G 4.7 11.9 - - + -
9F T 3.5 49.6 + - + +
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Residues in contact with LYS 502 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
498A SER* 2.9 16.5 + - - +
499A GLN* 3.2 10.7 + - - +
501A HIS* 1.3 80.8 - - + +
503A MET* 1.3 57.4 + - - +
505A ARG* 3.3 25.8 + - - +
506A THR* 3.0 30.2 + - - -
492C ASN* 4.1 20.3 + - - -
493C THR* 4.3 14.4 - - - +
494C PHE* 5.1 9.7 - - - -
1025C MET* 3.4 23.0 - - + +
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Residues in contact with MET 503 (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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495A LEU* 5.2 5.8 - - + -
499A GLN 2.9 15.4 + - - +
500A TYR* 3.2 22.7 - - + +
502A LYS* 1.3 77.1 - - - +
504A TYR* 1.3 60.8 + - - +
506A THR* 3.3 2.4 + - - -
507A VAL* 3.0 31.2 + - - +
516A PHE* 3.3 31.9 - - - -
489C ILE* 3.4 37.2 - - + +
493C THR* 4.3 7.6 - - + +
495C LEU* 4.4 16.4 - - + -
503C MET* 3.6 26.7 - - + -
516C PHE* 4.1 17.9 - - + -
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Residues in contact with TYR 504 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
500A TYR* 2.9 26.6 + + + +
501A HIS* 3.6 25.1 - + - +
503A MET* 1.3 76.1 - - - +
505A ARG* 1.3 77.6 + - + +
507A VAL* 3.3 10.7 - - + +
508A LYS* 2.9 59.0 + - + +
514A GLN* 4.1 10.2 + - + -
515A ILE 5.9 0.4 - - - -
516A PHE* 2.9 46.0 - - + -
517A GLN 4.0 4.3 - - - -
518A PRO* 3.7 25.2 - - + +
519A LEU* 5.1 2.2 - - + -
7F T 5.1 0.7 - - - -
8F G 2.5 30.6 + - - -
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Residues in contact with ARG 505 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
501A HIS* 2.9 28.5 + - + +
502A LYS* 3.7 31.7 + - - +
504A TYR* 1.3 86.8 - - + +
506A THR* 1.3 62.8 + - - +
508A LYS* 3.5 6.9 - - + +
509A ALA* 2.9 26.1 + - + +
1025C MET* 5.2 4.2 - - - +
1027C ALA* 3.4 38.5 - - + +
8F G 5.1 4.5 - - - +
9F T 2.9 44.9 + - - -
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Residues in contact with THR 506 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
502A LYS 3.0 6.4 + - - -
503A MET 3.4 8.1 - - - -
504A TYR 3.2 0.2 - - - -
505A ARG* 1.3 79.0 + - - +
507A VAL* 1.3 62.1 + - - +
509A ALA* 3.8 3.1 - - - +
510A THR* 2.9 42.1 + - - +
485C VAL* 4.5 12.3 - - + +
488C ALA* 6.3 1.3 - - + -
489C ILE* 3.5 27.6 - - + +
1024C PHE 4.7 8.5 - - - +
1025C MET* 3.1 45.3 - - - +
1027C ALA* 6.1 2.2 - - - +
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Residues in contact with VAL 507 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
503A MET* 3.0 18.6 + - - +
504A TYR* 3.3 17.3 - - + +
506A THR* 1.3 79.8 - - + +
508A LYS* 1.3 66.7 + - - +
510A THR* 4.6 4.3 - - - -
511A SER* 3.5 17.6 + - - +
513A ARG 4.0 6.4 - - - +
515A ILE* 4.4 29.3 - - + +
516A PHE* 4.6 18.8 - - + +
481C LEU* 3.9 28.3 - - + -
489C ILE* 6.0 1.6 - - + -
515C ILE* 5.3 1.3 - - + -
516C PHE* 4.4 15.3 - - + -
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Residues in contact with LYS 508 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
504A TYR* 2.9 48.5 + - + +
505A ARG* 3.5 9.4 - - + +
507A VAL* 1.3 81.5 - - - +
509A ALA* 1.3 68.6 + - + +
510A THR 3.2 0.3 + - - -
511A SER 3.7 5.2 + - - -
512A GLY* 3.9 9.9 + - - -
513A ARG 3.7 21.4 + - - +
514A GLN* 4.1 24.8 - - + +
515A ILE 5.7 0.4 - - - +
7F T 5.1 4.9 + - - -
8F G 4.3 10.5 + - - -
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Residues in contact with ALA 509 (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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505A ARG* 2.9 17.7 + - + +
506A THR* 4.1 2.7 - - - +
508A LYS* 1.3 82.2 - - + +
510A THR* 1.3 63.7 + - - +
512A GLY 4.9 1.0 + - - -
1026C GLU* 5.0 13.7 - - + +
1027C ALA* 4.3 24.5 - - - +
1028C HIS* 5.0 7.2 - - + +
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Residues in contact with THR 510 (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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506A THR* 2.9 20.6 + - - +
507A VAL* 4.3 3.1 - - - -
508A LYS 3.2 0.4 - - - -
509A ALA* 1.3 80.8 - - - +
511A SER* 1.3 61.7 + - - +
512A GLY 3.8 1.7 + - - -
481C LEU* 3.7 26.0 - - + -
482C HIS* 5.6 2.2 - - + -
485C VAL* 3.8 25.9 - - + +
1024C PHE* 3.5 22.7 + - + -
1026C GLU* 6.0 2.7 - - - -
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Residues in contact with SER 511 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
507A VAL* 3.5 10.8 + - - +
508A LYS 4.0 2.7 - - - -
510A THR* 1.3 78.0 - - - +
512A GLY* 1.3 52.0 + - - +
513A ARG* 2.4 32.1 + - - +
515A ILE* 5.6 1.9 - - - +
479C PHE* 3.5 36.5 + - - +
480C GLY 5.4 0.4 - - - -
481C LEU* 3.6 27.1 - - - -
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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