Contacts of the helix formed by residues 492 - 505 (chain A) in PDB entry 3W6R
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 ASP 492 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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484A ALA* 4.2 12.1 - - - +
490A LYS 4.0 1.2 - - - -
491A MET* 1.3 76.3 - - - +
493A VAL* 1.3 64.6 + - - +
494A ALA* 3.3 11.9 + - - +
495A ASN* 2.8 44.8 + - - +
496A LEU* 3.0 21.9 + - - +
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Residues in contact with VAL 493 (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 GLN* 6.0 2.5 - - + -
484A ALA* 4.1 19.4 - - + +
492A ASP* 1.3 74.7 - - - +
494A ALA* 1.3 62.5 + - - +
496A LEU* 3.5 2.1 + - - +
497A ALA* 3.0 23.7 + - - +
529A GLU* 3.9 25.8 - - + +
532A LEU* 3.8 42.6 - - + +
533A SER* 4.4 7.0 - - - +
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Residues in contact with ALA 494 (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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492A ASP* 3.2 13.1 + - - +
493A VAL* 1.3 80.3 - - - +
495A ASN* 1.3 65.8 + - - +
497A ALA* 3.4 4.2 + - - +
498A LYS* 3.2 29.4 + - + +
525A PRO* 5.6 0.2 - - - +
529A GLU* 3.7 24.0 - - - +
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Residues in contact with ASN 495 (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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490A LYS 3.6 21.4 + - - -
491A MET* 3.8 19.7 - - + -
492A ASP* 2.8 36.1 + - - +
494A ALA* 1.3 73.6 - - - +
496A LEU* 1.3 65.1 + - - +
498A LYS* 3.3 33.7 + - - +
499A VAL* 3.3 16.3 + - - +
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Residues in contact with LEU 496 (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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384A TYR* 4.2 22.2 - - + -
480A LEU* 3.5 33.7 - - + +
483A VAL* 4.0 22.0 - - + -
484A ALA* 4.0 7.9 - - + -
491A MET* 3.7 38.1 - - + +
492A ASP 3.0 15.3 + - - +
493A VAL* 4.0 4.9 - - - +
495A ASN* 1.3 76.5 - - - +
497A ALA* 1.3 52.2 + - - +
499A VAL* 3.3 2.9 + - + +
500A PHE* 2.8 50.5 + - + +
528A VAL* 4.7 1.3 - - - -
532A LEU* 4.3 10.5 - - + -
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Residues in contact with ALA 497 (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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493A VAL 3.0 18.2 + - - +
494A ALA 3.6 6.7 - - - +
495A ASN 3.2 0.2 - - - -
496A LEU* 1.3 76.4 - - - +
498A LYS* 1.3 57.1 + - - +
501A GLY* 2.9 29.1 + - - -
525A PRO* 3.3 35.8 - - + +
528A VAL* 3.7 12.5 - - + +
529A GLU* 3.7 19.5 - - + +
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Residues in contact with LYS 498 (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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494A ALA* 3.2 25.0 + - + +
495A ASN* 3.3 22.6 + - - +
497A ALA* 1.3 77.3 - - - +
499A VAL* 1.3 63.4 + - + +
502A PRO* 3.7 16.1 - - - +
525A PRO* 4.3 23.0 - - + +
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Residues in contact with VAL 499 (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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384A TYR* 3.2 30.3 - - + +
385A ARG* 4.3 11.2 - - + -
423A LYS* 3.7 25.5 - - + +
491A MET* 4.3 13.0 - - + -
495A ASN 3.3 11.6 + - - +
496A LEU* 3.3 9.2 + - - +
498A LYS* 1.3 80.8 - - + +
500A PHE* 1.3 69.8 + - + +
501A GLY 3.5 0.5 + - - -
502A PRO* 3.7 8.8 - - - +
503A THR* 3.5 11.1 + - - -
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Residues in contact with PHE 500 (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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384A TYR* 3.7 42.6 - + + -
422A LEU* 5.6 1.6 - - + -
423A LYS* 4.1 14.4 - - + -
426A LEU* 4.8 4.0 - - + -
476A LEU* 4.1 16.6 - - + -
480A LEU* 3.6 44.4 - - + -
496A LEU* 2.8 32.7 + - + +
497A ALA 3.8 0.2 - - - -
499A VAL* 1.3 80.5 - - + +
501A GLY* 1.3 65.2 + - - +
502A PRO 3.5 0.7 - - - -
503A THR* 3.6 21.5 - - + -
504A ILE* 2.9 39.6 + - + +
528A VAL* 4.0 18.6 - - + -
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Residues in contact with GLY 501 (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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497A ALA 2.9 18.1 + - - -
498A LYS 4.6 0.2 - - - -
500A PHE* 1.3 79.0 - - - +
502A PRO* 1.3 68.1 - - - +
505A VAL* 3.1 26.3 + - - +
506A ALA 3.3 1.6 + - - -
524A GLN* 3.3 23.7 - - - +
525A PRO* 4.5 1.3 - - - -
528A VAL* 4.0 8.7 - - - -
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Residues in contact with PRO 502 (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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427A ARG* 3.8 20.2 - - - +
498A LYS 3.7 16.4 - - - +
499A VAL 3.7 8.1 - - - +
501A GLY* 1.3 88.3 - - - +
503A THR* 1.3 61.4 + - - +
506A ALA* 3.7 19.0 - - - +
521A ILE* 5.1 9.2 - - + -
524A GLN* 3.5 21.5 - - - +
525A PRO* 6.2 0.9 - - + -
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Residues in contact with THR 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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423A LYS* 3.5 44.6 - - - +
426A LEU* 3.8 21.7 - - + +
427A ARG* 3.5 30.7 + - - +
432A PRO* 4.9 5.7 - - - +
433A LEU 5.0 0.9 + - - -
499A VAL 3.5 13.0 + - - -
500A PHE* 3.1 25.0 + - + -
502A PRO* 1.3 80.8 - - - +
504A ILE* 1.3 66.8 + - + +
506A ALA* 5.2 0.2 - - - +
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Residues in contact with ILE 504 (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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426A LEU* 4.2 5.4 - - + -
432A PRO* 3.6 6.7 - - - +
433A LEU* 3.8 28.5 - - + +
434A LEU* 3.1 35.4 + - + +
473A LEU* 4.0 25.6 - - + -
476A LEU* 3.8 17.5 - - + -
477A MET* 4.4 13.2 - - + -
500A PHE* 2.9 23.5 + - + +
503A THR* 1.3 91.3 - - + +
505A VAL* 1.3 65.3 + - + +
528A VAL* 4.1 21.1 - - + -
531A LEU* 4.3 11.7 - - + -
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Residues in contact with VAL 505 (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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432A PRO* 3.4 12.6 - - - +
434A LEU* 3.8 27.3 - - + +
439A ASN* 3.1 30.5 + - - +
442A PHE* 5.5 0.9 - - + -
443A MET* 4.2 9.2 - - + -
501A GLY 3.1 12.8 + - - +
504A ILE* 1.3 78.2 - - - +
506A ALA* 1.3 71.4 + - - +
524A GLN* 3.8 29.4 - - + +
527A VAL* 4.1 13.7 - - + -
528A VAL* 3.8 25.4 - - + -
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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