Contacts of the helix formed by residues 496 - 513 (chain A) in PDB entry 2AX1
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* 4.6 5.6 - - + -
494A VAL 3.5 3.3 - - - +
495A PRO* 1.3 90.9 - - + +
497A LEU* 1.3 56.9 + - - +
498A ARG* 3.1 46.4 - - + +
499A ALA* 2.7 36.4 + - + +
500A TRP* 3.3 4.0 - - - -
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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 LEU* 3.7 30.5 - - + -
423A MET* 3.6 38.6 - - + +
424A ILE* 4.0 33.2 - - + -
482A ILE* 5.8 7.4 - - + +
485A VAL* 4.3 7.9 - - + -
486A ALA* 5.6 5.4 - - + +
489A LEU* 3.9 12.4 - - + +
495A PRO 3.7 1.0 + - - -
496A PRO* 1.3 71.1 - - - +
498A ARG* 1.3 60.8 + - - +
500A TRP* 3.1 16.2 + - + +
501A ARG* 3.1 9.5 + - - +
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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* 5.6 0.4 - - - -
496A PRO* 3.0 33.3 + - + +
497A LEU* 1.3 78.3 - - - +
499A ALA* 1.3 65.7 + - + +
501A ARG* 3.3 22.9 + - - +
502A HIS* 3.5 7.3 + - - +
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Residues in contact with ALA 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* 4.0 20.0 - - + -
496A PRO* 2.7 27.7 + - + +
498A ARG* 1.3 78.0 - - + +
500A TRP* 1.3 60.8 + - - +
502A HIS* 3.5 8.7 + - - +
503A ARG* 3.4 30.7 + - - +
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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 4.1 0.2 - - - -
30A LEU* 3.7 36.1 - - + -
423A MET* 3.3 31.4 - - + +
424A ILE* 3.9 22.8 - - + +
427A THR* 3.8 15.2 + - + +
428A HIS* 3.8 29.2 - - + -
494A VAL* 3.7 7.2 - - + +
495A PRO* 2.8 50.0 + - + -
496A PRO 3.3 15.2 + - - -
497A LEU* 3.1 11.5 + - - +
499A ALA* 1.3 76.9 - - - +
501A ARG* 1.3 58.6 + - - +
503A ARG* 3.2 34.9 + - - +
504A ALA* 2.8 31.6 + - - +
528A TRP* 4.5 1.6 - - - -
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Residues in contact with ARG 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* 4.8 3.6 - - + -
497A LEU 3.1 11.0 + - - +
498A ARG* 3.4 15.9 - - - +
499A ALA 3.2 0.2 - - - -
500A TRP* 1.3 78.2 - - - +
502A HIS* 1.3 62.6 + - - +
504A ALA* 3.2 2.4 + - - +
505A ARG* 3.0 60.2 + - - +
528A TRP* 4.0 27.0 + - + -
529A ALA* 3.2 28.5 + - - +
530A VAL 4.7 0.4 - - - -
531A LYS* 4.1 29.7 - - - +
1103A SO4 4.1 0.6 + - - -
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Residues in contact with HIS 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 3.5 7.4 + - - +
499A ALA* 3.7 9.9 - - - +
500A TRP 3.3 0.2 - - - -
501A ARG* 1.3 80.9 - - - +
503A ARG* 1.3 69.1 + - + +
505A ARG* 3.5 12.7 + - - +
506A ASN* 3.4 21.3 + - + +
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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* 3.1 42.5 + - - +
427A THR* 3.6 15.5 - - + -
428A HIS* 5.4 0.8 + - - -
431A SER* 6.4 0.4 - - - -
495A PRO* 3.8 18.5 - - - +
499A ALA* 3.4 16.8 + - - +
500A TRP* 3.2 41.2 + - - +
501A ARG 3.3 0.2 - - - -
502A HIS* 1.3 81.2 - - + +
504A ALA* 1.3 61.0 + - - +
506A ASN* 3.1 10.0 + - - +
507A VAL* 2.9 32.2 + - + +
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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* 3.5 15.7 - - - +
500A TRP 2.8 17.9 + - - +
501A ARG 3.2 3.8 + - - +
503A ARG* 1.3 78.5 - - - +
505A ARG* 1.3 51.8 + - - +
507A VAL* 3.6 2.9 - - - +
508A ARG* 2.7 37.0 + - - +
526A PHE* 3.8 11.3 - - + -
528A TRP* 3.4 32.8 - - + -
529A ALA* 3.9 6.3 - - + -
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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 ARG* 3.0 48.6 + - - +
502A HIS* 3.8 10.9 + - - +
503A ARG 3.3 0.2 - - - -
504A ALA* 1.3 75.2 - - - +
506A ASN* 1.3 61.6 + - - +
508A ARG* 3.5 8.9 + - - +
509A ALA* 3.0 24.4 + - - +
529A ALA* 3.1 31.9 + - + +
530A VAL* 3.6 11.1 - - + +
1103A SO4 2.9 41.4 + - - -
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Residues in contact with ASN 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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431A SER* 5.5 0.6 + - - -
502A HIS* 3.4 12.8 + - + +
503A ARG* 3.1 11.7 + - - +
505A ARG* 1.3 77.3 - - - +
507A VAL* 1.3 70.7 + - - +
509A ALA* 3.3 6.1 + - - +
510A ARG* 3.1 58.4 + - - +
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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* 4.0 8.1 - - + +
430A PHE* 3.8 28.0 - - + -
431A SER* 3.6 32.8 - - - +
434A LEU* 4.0 12.8 - - + -
503A ARG* 2.9 21.7 + - + +
504A ALA* 3.7 6.3 - - - +
506A ASN* 1.3 83.7 - - - +
508A ARG* 1.3 64.0 + - - +
510A ARG* 3.3 4.9 + - - +
511A LEU* 3.0 31.8 + - + +
526A PHE* 3.9 11.0 - - + -
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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 22.1 + - - +
505A ARG* 3.5 6.8 + - - +
507A VAL* 1.3 73.7 - - - +
509A ALA* 1.3 67.3 + - - +
511A LEU* 3.2 3.5 + - - +
512A LEU* 3.0 42.4 + - + +
522A GLY* 3.3 26.8 + - - +
523A LYS* 5.0 0.8 - - - +
526A PHE* 3.5 40.7 + - + -
527A ASN* 4.7 2.4 + - - +
529A ALA* 5.0 1.8 - - - -
530A VAL* 3.7 39.2 - - - +
532A THR 4.9 1.6 + - - -
534A LEU* 3.3 38.0 - - - +
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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 3.0 16.4 + - - +
506A ASN* 3.3 6.7 + - - +
508A ARG* 1.3 80.7 - - - +
510A ARG* 1.3 63.6 + - + +
512A LEU* 3.2 10.8 + - - +
513A SER* 3.1 22.9 + - - -
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Residues in contact with ARG 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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431A SER* 4.5 14.6 + - - -
434A LEU* 3.7 34.1 - - + +
435A ALA* 4.3 11.5 - - - +
506A ASN* 3.1 44.2 + - - +
507A VAL* 3.7 6.9 - - - +
509A ALA* 1.3 78.1 - - + +
511A LEU* 1.3 61.7 + - - +
513A SER* 2.8 24.1 + - - -
514A ARG* 3.6 13.2 - - - +
1102A SO4 3.1 43.3 + - - +
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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* 4.1 26.2 - - + -
434A LEU* 3.9 24.9 - - + -
439A LEU* 4.2 14.1 - - + -
457A LEU* 5.4 0.2 - - + -
507A VAL* 3.0 23.5 + - + +
508A ARG 3.2 3.8 + - - +
510A ARG* 1.3 74.1 - - - +
512A LEU* 1.3 66.8 + - - +
514A ARG* 3.1 15.4 + - - +
518A ALA* 3.2 38.1 - - + +
519A ALA 3.4 1.6 + - - -
521A CYS* 4.2 2.7 - - + -
522A GLY* 3.8 17.3 - - - +
526A PHE* 3.6 31.6 - - + -
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Residues in contact with LEU 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 53.4 + - - +
509A ALA* 3.2 9.8 + - - +
511A LEU* 1.3 77.3 - - - +
513A SER* 1.3 59.9 + - - +
514A ARG 3.1 7.7 + - - +
519A ALA* 3.3 36.5 - - + +
522A GLY 4.4 4.0 - - - -
523A LYS* 3.7 17.9 - - + +
534A LEU* 4.9 6.3 - - + -
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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 3.1 11.2 + - - -
510A ARG* 2.8 20.8 + - - -
511A LEU 3.1 0.2 - - - -
512A LEU* 1.3 77.0 - - - +
514A ARG* 1.3 61.5 + - - +
1102A SO4 4.8 3.8 + - - -
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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