Contacts of the helix formed by residues 499 - 503 (chain A) in PDB entry 4AY6
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 HIS 499 (chain A).
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
430A LYS* 5.0 3.8 - - - -
458A ASN* 5.9 2.7 - - - -
461A HIS* 3.3 51.9 - + + +
495A VAL* 4.5 2.4 - - + +
496A HIS* 2.7 30.3 + - + +
498A HIS* 1.3 85.1 - + - +
500A SER* 1.3 63.5 + - - +
501A MET 3.0 6.5 - - - -
502A LEU* 2.8 31.4 + - + +
503A TYR* 3.8 23.2 - - + +
841A TYR* 6.3 0.9 - + - -
1397E ALA* 3.4 30.1 + - + +
----------------------------------------------------------
Back to top of page
Residues in contact with SER 500 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
495A VAL* 4.0 14.6 - - - -
496A HIS 3.1 7.8 + - - -
497A PRO* 2.8 25.2 + - - +
499A HIS* 1.3 77.5 - - - +
501A MET* 1.3 62.8 + - - +
502A LEU 3.1 1.4 + - - -
503A TYR* 3.4 9.7 + - - -
505A LEU* 3.4 15.9 - - - +
510A ARG* 3.0 42.5 + - - +
513A ILE* 4.4 9.9 - - - -
----------------------------------------------------------
Back to top of page
Residues in contact with MET 501 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
497A PRO 4.9 2.2 - - - +
498A HIS* 3.3 37.0 - - + +
499A HIS 2.9 1.6 + - - -
500A SER* 1.3 82.2 + - - +
502A LEU* 1.3 76.3 - - + +
503A TYR 3.4 4.2 - - - +
510A ARG* 3.8 12.1 + - - +
655A TYR* 5.8 1.8 - - + +
656A PRO* 3.8 33.4 - - + +
841A TYR* 5.8 2.0 - - - -
916A LEU* 4.1 15.4 - - - +
917A CYS* 4.3 21.3 - - + -
940A THR* 4.5 24.0 - - + +
942A ALA* 4.1 19.5 - - + -
1200A 12V 5.0 4.7 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with LEU 502 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
461A HIS* 4.2 18.2 - - + +
464A GLN* 4.2 19.7 - - + +
472A TYR* 4.7 7.4 + - - -
476A MET* 4.9 0.2 - - - +
499A HIS* 2.8 23.1 + - + +
501A MET* 1.3 88.3 - - - +
503A TYR* 1.3 73.1 + - + +
504A PRO* 4.6 0.7 - - - +
841A TYR* 3.8 40.4 - - + +
842A LYS* 5.2 0.4 - - - -
916A LEU* 3.3 41.0 - - + +
917A CYS* 4.2 18.2 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with TYR 503 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
457A CYS 4.5 2.9 + - - -
460A ALA* 4.2 3.5 - - + -
461A HIS* 3.7 39.0 + - - +
464A GLN* 4.4 12.8 - - + -
476A MET* 3.8 19.7 - - + -
479A LEU* 3.5 35.8 - - + +
495A VAL* 3.7 32.1 - - + -
499A HIS* 3.8 19.8 - - + +
500A SER 3.4 4.8 + - - +
501A MET 4.2 1.2 - - - +
502A LEU* 1.3 97.6 - - + +
504A PRO* 1.4 70.4 - - + +
505A LEU* 3.1 20.7 + - + -
510A ARG* 3.0 23.6 + - - -
916A LEU* 5.7 1.1 - - - +
----------------------------------------------------------
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