Contacts of the helix formed by residues 496 - 513 (chain A) in PDB entry 4WTM
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 PRO 496 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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489A LEU* 4.5 7.4 - - + -
490A ARG* 6.6 0.2 - - + -
494A ALA 4.1 2.7 - - - +
495A PRO* 1.3 89.9 - - + +
497A LEU* 1.3 69.3 + - - +
498A ARG* 3.2 37.0 - - + +
499A VAL* 2.9 25.2 + - + +
500A TRP* 3.2 9.3 + - - -
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Residues in contact with LEU 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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419A ILE* 4.3 24.2 - - + +
423A MET* 3.4 43.9 - - + +
424A VAL* 4.1 9.6 - - + -
482A LEU* 4.8 12.8 - - + +
485A VAL* 4.2 19.7 - - + -
486A ALA* 5.2 9.2 - - + +
489A LEU* 3.9 22.5 - - + +
496A PRO* 1.3 74.0 - - - +
498A ARG* 1.3 58.3 + - - +
500A TRP* 3.1 4.9 + - + +
501A LYS 2.9 24.1 + - - -
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Residues in contact with ARG 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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423A MET* 5.4 0.2 - - - -
496A PRO* 3.7 26.9 - - + +
497A LEU* 1.3 77.9 - - - +
499A VAL* 1.3 71.9 + - - +
501A LYS* 3.3 10.7 + - - +
502A SER* 3.2 20.4 + - - -
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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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495A PRO* 3.7 22.2 - - + -
496A PRO* 2.9 28.5 + - + +
498A ARG* 1.3 87.6 - - - +
500A TRP* 1.3 66.0 + - - +
502A SER* 3.1 13.2 + - - +
503A ARG* 2.9 41.6 + - + +
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Residues in contact with TRP 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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29A SER 4.0 3.8 - - - -
30A LEU* 3.7 44.9 - - + -
423A MET* 3.3 31.4 - - + +
424A VAL* 3.7 35.5 - - + +
427A THR* 3.8 15.7 - - + +
428A HIS* 4.1 17.7 - - + -
489A LEU* 4.6 3.2 - - + +
494A ALA* 5.1 0.2 - - + -
495A PRO* 3.0 42.9 + - + +
496A PRO 3.2 16.3 + - - -
497A LEU* 3.1 10.1 + - - +
499A VAL* 1.3 77.0 - - - +
501A LYS* 1.3 58.2 + - - +
503A ARG* 3.5 33.0 - - - +
504A ALA* 2.8 30.4 + - - +
528A TRP* 4.1 1.2 - - - -
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Residues in contact with LYS 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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423A MET* 4.2 6.3 - - + +
497A LEU 2.9 12.7 + - - +
498A ARG* 3.4 13.9 - - + +
499A VAL 3.1 0.4 - - - -
500A TRP* 1.3 76.5 - - - +
502A SER* 1.3 63.2 + - - +
504A ALA* 3.1 11.3 + - - +
505A ARG* 3.1 42.3 + - - +
528A TRP* 3.9 34.9 + - + +
529A ALA* 4.1 11.8 + - - +
530A VAL 5.9 1.6 - - - -
531A LYS* 6.0 0.6 - - - +
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Residues in contact with SER 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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498A ARG 3.2 7.8 + - - -
499A VAL* 3.1 19.0 + - - +
501A LYS* 1.3 75.3 - - - +
503A ARG* 1.3 67.6 + - - +
504A ALA 3.3 0.2 + - - -
505A ARG* 3.4 23.4 + - - +
506A ALA* 3.5 10.6 + - - +
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Residues in contact with ARG 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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29A SER* 2.8 36.3 + - - +
427A THR* 3.8 10.8 - - + -
428A HIS* 5.2 1.6 + - - -
495A PRO* 3.7 22.2 - - - +
499A VAL* 2.9 32.2 + - + +
500A TRP* 3.5 36.3 - - - +
502A SER* 1.3 77.5 + - - +
504A ALA* 1.3 63.8 + - - +
506A ALA* 3.2 7.8 + - - +
507A VAL* 3.0 26.6 + - + +
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Residues in contact with ALA 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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427A THR* 3.7 16.6 - - - +
500A TRP 2.8 13.9 + - - +
501A LYS 3.1 3.1 + - - +
503A ARG* 1.3 75.3 - - - +
505A ARG* 1.3 51.5 + - - +
507A VAL* 3.3 3.6 + - - +
508A ARG* 2.7 37.1 + - - +
526A PHE* 4.0 7.4 - - + -
528A TRP* 3.3 42.4 - - + -
529A ALA* 3.9 7.6 - - + -
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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
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501A LYS* 3.1 36.1 + - - +
502A SER* 3.6 16.2 - - - +
504A ALA* 1.3 74.0 - - - +
506A ALA* 1.3 57.8 + - - +
508A ARG* 3.3 8.3 + - - +
509A ALA* 2.9 30.3 + - - +
529A ALA* 3.4 32.1 + - - +
530A VAL* 4.3 16.0 - - + +
531A LYS* 4.1 19.2 - - - +
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Residues in contact with ALA 506 (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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502A SER 3.5 6.8 + - - +
503A ARG* 3.2 10.8 + - - +
505A ARG* 1.3 76.5 - - - +
507A VAL* 1.3 65.6 + - + +
509A ALA* 3.5 5.0 + - - +
510A SER* 3.0 26.2 + - - -
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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
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427A THR* 3.8 12.8 - - + +
430A PHE* 3.9 23.8 - - + -
431A SER* 3.7 28.7 - - - -
434A MET* 3.8 21.8 - - + +
503A ARG* 3.0 18.0 + - + +
504A ALA* 3.7 9.4 - - - +
506A ALA* 1.3 75.9 - - + +
508A ARG* 1.3 63.3 + - - +
510A SER 3.5 0.2 + - - -
511A LEU* 3.0 30.9 + - + +
526A PHE* 4.0 12.1 - - + -
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Residues in contact with ARG 508 (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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504A ALA 2.7 21.8 + - - +
505A ARG* 3.4 5.6 - - - +
506A ALA 3.2 0.2 - - - -
507A VAL* 1.3 72.3 - - - +
509A ALA* 1.3 69.8 + - - +
511A LEU* 3.0 20.1 + - - +
512A ILE* 3.0 43.1 + - + +
522A GLY* 3.5 19.1 + - - +
523A ARG* 4.6 4.0 - - - +
526A PHE* 3.2 37.0 + - + -
527A ASN* 4.5 3.4 + - - +
529A ALA* 4.7 1.8 - - - -
530A VAL* 3.5 39.4 - - - +
534A LEU* 4.1 31.3 - - - +
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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 17.6 + - - +
506A ALA* 3.9 6.5 - - - +
508A ARG* 1.3 80.1 - - - +
510A SER* 1.3 63.4 + - - +
512A ILE* 3.3 10.2 + - - +
513A SER* 3.0 24.2 + - - -
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Residues in contact with SER 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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434A MET* 3.3 23.4 - - - +
506A ALA 3.0 18.7 + - - -
507A VAL 3.9 2.9 - - - -
509A ALA* 1.3 78.7 - - - +
511A LEU* 1.3 60.4 + - - +
513A SER* 2.9 20.7 + - - -
514A ARG* 3.6 20.8 + - - +
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Residues in contact with LEU 511 (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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430A PHE* 4.0 20.6 - - + -
434A MET* 3.7 20.4 - - + -
439A LEU* 3.8 23.1 - - + -
507A VAL* 3.0 26.3 + - + +
508A ARG 3.0 5.3 + - - +
510A SER* 1.3 73.5 - - - +
512A ILE* 1.3 66.9 + - - +
514A ARG* 3.1 17.4 + - - +
518A ALA* 3.5 19.9 - - + +
519A ALA* 3.4 16.8 + - - -
521A CYS 4.3 1.6 - - - -
522A GLY* 3.7 24.7 - - - +
526A PHE* 3.8 23.6 - - + -
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Residues in contact with ILE 512 (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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508A ARG* 3.0 56.7 + - + +
509A ALA* 3.5 11.9 - - - +
511A LEU* 1.3 76.5 - - - +
513A SER* 1.3 57.9 + - - +
515A GLY* 3.0 20.1 + - - -
519A ALA* 3.6 27.5 - - - +
522A GLY* 4.4 4.7 - - - -
523A ARG* 4.0 33.7 + - + +
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Residues in contact with SER 513 (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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509A ALA 3.0 11.9 + - - -
510A SER* 2.9 23.1 + - - -
512A ILE* 1.3 76.9 - - - +
514A ARG* 1.3 59.5 + - - +
515A GLY 3.4 0.2 - - - -
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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