Contacts of the helix formed by residues 496 - 514 (chain B) 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 B).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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489B LEU* 4.3 7.4 - - + -
494B VAL 3.5 3.3 - - - +
495B PRO* 1.3 91.5 - - + +
497B LEU* 1.3 66.1 + - - +
498B ARG* 3.6 47.8 - - + +
499B ALA* 2.9 20.8 + - + +
500B TRP* 3.1 6.9 - - - -
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Residues in contact with LEU 497 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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419B LEU* 3.6 34.8 - - + -
423B MET* 3.7 32.7 - - + +
424B ILE* 4.2 21.8 - - + -
482B ILE* 5.2 12.6 - - + +
485B VAL* 4.4 7.4 - - + -
486B ALA* 5.6 5.4 - - + +
489B LEU* 3.9 21.6 - - + +
496B PRO* 1.3 72.2 - - - +
498B ARG* 1.3 57.1 + - - +
500B TRP* 2.9 23.8 + - + +
501B ARG* 3.3 10.6 + - - +
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Residues in contact with ARG 498 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
496B PRO* 3.6 34.1 - - + +
497B LEU* 1.3 77.6 - - - +
499B ALA* 1.3 64.3 + - + +
501B ARG* 3.3 44.9 + - - +
502B HIS* 3.7 6.8 + - - +
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Residues in contact with ALA 499 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
495B PRO* 3.9 20.2 - - + -
496B PRO* 2.9 22.9 + - + +
498B ARG* 1.3 81.2 - - + +
500B TRP* 1.3 60.7 + - - +
502B HIS* 3.6 8.5 + - - +
503B ARG* 3.3 30.9 + - - +
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Residues in contact with TRP 500 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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29B SER 4.1 2.5 - - - -
30B LEU* 3.8 31.6 - - + -
423B MET* 3.4 32.1 - - + +
424B ILE* 3.9 20.7 - - + +
427B THR* 3.8 14.3 - - + +
428B HIS* 4.0 26.7 - - + -
494B VAL* 3.8 13.2 - - + +
495B PRO* 2.8 33.7 + - + +
496B PRO 3.1 25.4 - - - -
497B LEU* 2.9 13.5 + - + +
499B ALA* 1.3 77.9 - - - +
501B ARG* 1.3 59.9 + - - +
503B ARG* 3.3 37.0 - - - +
504B ALA* 2.8 32.1 + - - +
528B TRP* 3.9 2.4 - - - -
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Residues in contact with ARG 501 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
423B MET* 3.6 20.6 - - + +
497B LEU* 3.3 7.3 + - - +
498B ARG* 3.3 42.5 + - - +
500B TRP* 1.3 77.0 - - - +
502B HIS* 1.3 63.0 + - - +
504B ALA* 3.2 3.1 + - - +
505B ARG* 2.9 32.1 + - - +
528B TRP* 3.5 33.8 - - + -
529B ALA* 4.0 13.3 - - - +
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Residues in contact with HIS 502 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
498B ARG 3.7 6.3 + - - +
499B ALA* 3.6 10.5 + - - +
500B TRP 3.3 0.2 - - - -
501B ARG* 1.3 79.3 - - - +
503B ARG* 1.3 64.3 + - + +
505B ARG* 3.2 20.7 + - - +
506B ASN* 2.7 44.9 + - - +
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Residues in contact with ARG 503 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
29B SER* 2.7 46.6 + - - +
427B THR* 3.9 11.7 - - + -
428B HIS* 5.6 0.4 + - - -
495B PRO* 3.8 18.4 - - - +
499B ALA* 3.3 19.5 + - - +
500B TRP* 3.3 38.6 - - - +
501B ARG 3.3 0.2 - - - -
502B HIS* 1.3 82.9 - - + +
504B ALA* 1.3 61.8 + - - +
506B ASN* 3.3 9.4 + - - +
507B VAL* 3.1 26.9 + - + +
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Residues in contact with ALA 504 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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427B THR* 3.5 19.7 - - - +
500B TRP 2.8 19.2 + - - +
501B ARG 3.6 3.1 - - - +
503B ARG* 1.3 73.9 - - - +
505B ARG* 1.3 60.2 + - - +
507B VAL* 3.7 4.1 - - - +
508B ARG* 2.8 33.7 + - - +
526B PHE* 3.8 9.8 - - + -
528B TRP* 3.5 28.3 - - + -
529B ALA* 3.9 6.1 - - + -
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Residues in contact with ARG 505 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
501B ARG* 2.9 24.6 + - - +
502B HIS* 3.2 19.9 + - - +
504B ALA* 1.3 75.0 - - - +
506B ASN* 1.3 59.6 + - - +
508B ARG* 3.5 9.7 + - - +
509B ALA* 3.0 28.5 + - - +
529B ALA* 2.8 42.5 + - + +
530B VAL* 3.4 12.7 - - + +
531B LYS 4.5 0.2 - - - +
1106B SO4 2.8 43.6 + - - -
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Residues in contact with ASN 506 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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502B HIS* 2.7 43.6 + - - +
503B ARG* 3.3 8.2 + - - +
504B ALA 3.2 0.4 - - - -
505B ARG* 1.3 78.1 - - - +
507B VAL* 1.3 65.5 + - + +
509B ALA* 3.4 6.1 + - - +
510B ARG* 3.1 34.4 + - + +
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Residues in contact with VAL 507 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
427B THR* 3.9 19.1 - - + +
430B PHE* 3.8 28.7 - - + -
431B SER* 4.0 18.4 - - - +
434B LEU* 4.0 13.4 - - + +
503B ARG* 3.1 19.8 + - + +
504B ALA* 3.3 7.4 + - - +
506B ASN* 1.3 76.1 - - + +
508B ARG* 1.3 64.2 + - - +
510B ARG* 3.2 13.2 + - - +
511B LEU* 2.9 29.3 + - + +
526B PHE* 4.3 10.3 - - + -
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Residues in contact with ARG 508 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
504B ALA 2.8 18.4 + - - +
505B ARG* 3.5 8.0 + - - +
507B VAL* 1.3 76.6 - - - +
509B ALA* 1.3 58.8 + - - +
511B LEU* 3.3 7.7 + - - +
512B LEU* 2.9 55.5 + - + +
522B GLY* 3.4 27.8 + - - +
523B LYS* 4.9 1.2 + - - +
526B PHE* 3.6 34.0 + - + -
527B ASN* 4.6 3.0 + - - +
529B ALA* 5.2 0.4 - - - -
530B VAL* 3.6 37.2 - - - +
532B THR 5.2 0.8 + - - -
534B LEU* 3.4 38.4 - - - +
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Residues in contact with ALA 509 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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505B ARG 3.0 18.1 + - - +
506B ASN* 3.7 7.9 - - - +
508B ARG* 1.3 78.1 - - - +
510B ARG* 1.3 58.3 + - + +
512B LEU* 3.2 11.6 + - - +
513B SER* 2.9 28.8 + - - -
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Residues in contact with ARG 510 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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431B SER* 4.5 15.0 + - - +
434B LEU* 3.6 42.7 + - + +
435B ALA* 4.3 6.3 - - - +
506B ASN* 3.1 21.8 + - - +
507B VAL* 3.6 8.7 - - - +
509B ALA* 1.3 77.0 - - + +
511B LEU* 1.3 62.5 + - - +
513B SER* 2.6 26.0 + - - -
514B ARG* 3.3 13.2 + - - +
1105B SO4 2.9 43.1 + - - +
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Residues in contact with LEU 511 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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430B PHE* 3.9 27.4 - - + -
434B LEU* 4.0 22.7 - - + -
439B LEU* 4.3 5.6 - - + -
507B VAL* 2.9 23.6 + - + +
508B ARG 3.5 7.0 - - - +
510B ARG* 1.3 75.7 - - - +
512B LEU* 1.3 63.7 + - - +
514B ARG* 3.2 15.4 + - - +
518B ALA* 3.5 28.0 - - + +
519B ALA* 3.3 19.2 + - - -
521B CYS* 4.0 3.1 - - + -
522B GLY* 3.6 26.2 - - - +
526B PHE* 3.7 23.1 - - + -
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Residues in contact with LEU 512 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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508B ARG* 2.9 61.0 + - + +
509B ALA* 3.5 8.5 - - - +
511B LEU* 1.3 76.8 - - - +
513B SER* 1.3 62.1 + - - +
515B GLY* 3.0 15.2 + - - -
519B ALA* 3.7 31.3 - - + +
522B GLY* 4.8 0.9 - - - -
523B LYS* 4.3 13.5 - - + +
534B LEU* 5.5 4.7 - - + -
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Residues in contact with SER 513 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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509B ALA 2.9 12.5 + - - -
510B ARG* 2.6 26.5 + - - -
512B LEU* 1.3 75.6 - - - +
514B ARG* 1.3 62.6 + - - +
515B GLY 3.2 1.1 + - - -
1105B SO4 4.3 6.1 + - - -
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Residues in contact with ARG 514 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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434B LEU* 3.4 32.2 + - - +
437B GLU* 3.0 42.3 + - - -
439B LEU* 3.7 23.6 - - - +
440B GLU* 5.0 5.7 + - - -
510B ARG 3.4 11.0 - - - +
511B LEU* 3.2 9.1 + - - +
512B LEU 3.1 1.2 - - - -
513B SER* 1.3 77.1 - - - +
515B GLY* 1.3 64.5 + - - +
518B ALA* 3.9 11.7 - - + -
1105B SO4 2.8 40.8 + - - +
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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
------------------------------------------------------------
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