Contacts of the helix formed by residues 491 - 506 (chain Y) in PDB entry 5A31
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 LYS 491 (chain Y).
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
486Y LEU* 3.4 13.6 + - - +
489Y GLU* 3.1 15.0 - - + +
490Y GLN* 1.3 74.2 - - - +
492Y TYR* 1.3 56.6 + - - +
493Y GLU* 3.4 2.7 - - + +
494Y ASP* 1.9 70.4 - - - +
495Y GLY 3.6 2.9 + - - -
----------------------------------------------------------
Back to top of page
Residues in contact with TYR 492 (chain Y).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
486Y LEU 4.9 2.9 - - - -
487Y SER* 4.1 24.2 + - - -
490Y GLN* 3.3 42.1 + - + +
491Y LYS* 1.3 74.0 - - - +
493Y GLU* 1.3 79.7 + - - +
495Y GLY 3.2 9.2 + - - -
496Y ILE* 3.2 15.1 + - - +
518Y PHE* 3.4 32.5 - + + +
521Y ALA* 3.4 37.0 - - + -
522Y VAL* 5.3 0.4 - - + +
----------------------------------------------------------
Back to top of page
Residues in contact with GLU 493 (chain Y).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
491Y LYS* 3.4 1.9 - - + +
492Y TYR* 1.3 87.7 - - - +
494Y ASP* 1.3 64.5 + - - +
495Y GLY 3.2 0.2 - - - -
496Y ILE* 3.6 5.2 + - - +
497Y ALA* 3.4 20.6 + - - +
521Y ALA 4.5 2.9 - - - +
522Y VAL* 3.3 39.6 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with ASP 494 (chain Y).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
486Y LEU* 3.4 18.8 - - + +
489Y GLU* 5.5 1.2 - - - +
491Y LYS* 1.9 81.4 - - - +
493Y GLU* 1.3 71.5 - - - +
495Y GLY* 1.3 58.2 + - - -
497Y ALA* 3.6 6.7 + - - +
498Y LEU* 3.2 23.6 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with GLY 495 (chain Y).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
483Y ALA* 6.1 1.0 - - - +
486Y LEU* 3.2 20.3 - - - +
492Y TYR 3.2 2.0 + - - -
493Y GLU 3.2 1.0 - - - -
494Y ASP* 1.3 82.6 + - - +
496Y ILE* 1.3 59.1 + - - +
498Y LEU* 3.3 4.6 + - - +
499Y LEU* 2.8 33.1 + - - +
518Y PHE* 3.5 24.7 - - - -
----------------------------------------------------------
Back to top of page
Residues in contact with ILE 496 (chain Y).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
492Y TYR 3.2 11.5 + - - +
493Y GLU* 3.6 7.6 + - - +
494Y ASP 3.5 0.2 - - - -
495Y GLY* 1.3 72.4 - - - +
497Y ALA* 1.3 66.5 + - - +
499Y LEU* 4.1 4.8 - - - +
500Y ARG* 2.9 52.6 + - + +
515Y LEU* 4.2 7.6 - - + -
518Y PHE* 3.6 29.2 - - + +
519Y LEU* 3.4 22.9 - - + -
522Y VAL* 3.1 36.1 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with ALA 497 (chain Y).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
493Y GLU 3.4 12.6 + - - +
494Y ASP* 3.8 10.8 - - - +
495Y GLY 3.3 0.4 - - - -
496Y ILE* 1.3 79.3 - - - +
498Y LEU* 1.3 61.2 + - - +
500Y ARG* 3.6 6.1 + - - +
501Y ASN* 3.5 16.3 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with LEU 498 (chain Y).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
469Y LEU* 4.2 15.7 - - + -
479Y VAL* 4.2 19.3 - - + -
482Y LYS* 3.6 52.3 - - + +
483Y ALA* 4.6 9.0 - - + +
486Y LEU* 4.2 14.4 - - + -
494Y ASP 3.2 15.1 + - - +
495Y GLY* 3.6 3.6 - - - +
497Y ALA* 1.3 75.2 - - - +
499Y LEU* 1.3 65.9 - - + +
501Y ASN* 3.2 23.8 + - + +
502Y ALA* 3.2 9.0 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with LEU 499 (chain Y).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
479Y VAL* 3.4 25.8 - - + -
483Y ALA* 4.1 18.8 - - + -
495Y GLY 2.8 21.6 + - - +
496Y ILE 4.1 1.1 - - - +
498Y LEU* 1.3 75.1 - - + +
500Y ARG* 1.3 56.2 + - - +
502Y ALA* 3.2 6.5 + - + +
503Y LEU* 2.8 31.7 + - + +
511Y LEU* 4.1 21.1 - - + +
514Y ILE* 3.5 17.3 - - + +
515Y LEU* 3.3 52.0 - - + +
518Y PHE* 4.9 8.1 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with ARG 500 (chain Y).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
496Y ILE* 2.9 34.8 + - + +
497Y ALA* 3.8 7.0 - - - +
498Y LEU 3.2 0.2 - - - -
499Y LEU* 1.3 72.4 - - - +
501Y ASN* 1.3 55.1 + - - +
503Y LEU* 3.5 9.9 - - - +
504Y ALA* 2.7 33.6 + - - +
515Y LEU* 3.5 21.9 - - + +
519Y LEU* 3.9 19.4 - - - +
524Y GLU* 4.9 0.6 + - - -
527Y GLU* 3.2 26.1 + - - -
531Y GLN* 5.3 5.5 + - - -
----------------------------------------------------------
Back to top of page
Residues in contact with ASN 501 (chain Y).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
474Y ASP* 2.9 22.7 + - - +
497Y ALA 3.5 8.4 + - - +
498Y LEU* 3.2 18.0 + - - +
500Y ARG* 1.3 75.7 - - - +
502Y ALA* 1.3 63.0 + - - +
504Y ALA* 3.1 22.4 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with ALA 502 (chain Y).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
474Y ASP* 2.8 20.0 + - + +
479Y VAL* 3.8 29.8 - - + -
498Y LEU 3.2 3.1 + - - +
499Y LEU* 3.2 11.3 + - - +
501Y ASN* 1.3 77.2 - - - +
503Y LEU* 1.3 61.3 + - - +
505Y ASN* 3.1 17.8 + - - +
506Y GLN 3.4 6.9 + - - -
507Y SER* 4.2 5.0 + - - -
511Y LEU* 3.4 27.1 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with LEU 503 (chain Y).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
129F ASP* 5.4 1.1 - - - +
499Y LEU* 2.8 22.4 + - + +
500Y ARG* 3.7 12.1 - - - +
502Y ALA* 1.3 70.9 - - - +
504Y ALA* 1.3 53.1 - - - +
506Y GLN* 2.1 48.7 + - - +
508Y ASP* 4.8 5.6 - - - +
511Y LEU* 3.6 40.6 - - + +
512Y HIS* 3.8 22.4 - - + +
515Y LEU* 3.3 29.8 - - + -
531Y GLN* 3.8 20.9 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with ALA 504 (chain Y).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
130F ARG* 3.6 10.4 - - - +
132F ALA* 6.3 3.4 - - + -
133F LYS* 4.0 13.1 - - + +
500Y ARG 2.7 16.3 + - - +
501Y ASN* 3.1 20.1 + - - +
503Y LEU* 1.3 70.9 - - - +
505Y ASN* 1.3 62.8 + - - +
506Y GLN* 3.0 14.1 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with ASN 505 (chain Y).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
89F GLU* 5.4 0.5 - - - +
96F VAL* 5.3 18.6 - - + +
100F GLN* 3.0 32.1 + - - +
130F ARG* 3.3 15.3 + - - +
133F LYS* 4.5 9.4 + - - +
473Y PRO* 4.1 11.5 + - - +
474Y ASP* 2.5 40.6 + - + +
501Y ASN 3.7 0.6 + - - -
502Y ALA 3.1 7.7 + - - +
504Y ALA* 1.3 80.3 - - - +
506Y GLN* 1.3 68.0 + - - +
507Y SER* 3.6 3.1 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with GLN 506 (chain Y).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
128F THR 3.9 7.4 - - - +
129F ASP* 2.7 36.5 + - + +
130F ARG* 2.9 64.1 + - + +
502Y ALA 3.4 3.4 + - - -
503Y LEU* 2.1 43.2 + - - +
504Y ALA* 3.0 9.9 + - - +
505Y ASN* 1.3 74.2 - - - +
507Y SER* 1.3 60.9 + - - +
508Y ASP* 2.8 41.8 - - - +
512Y HIS* 4.2 4.5 - - - -
----------------------------------------------------------
Back to top of page
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
------------------------------------------------------------
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) + - + + + + + -
------------------------------------------------------------
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