Contacts of the helix formed by residues 495 - 502 (chain A) in PDB entry 1S2S
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 ASN 495 (chain A).
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
483A ASN* 4.1 15.3 - - - +
485A LYS* 4.8 9.5 - - - +
487A GLY* 3.6 3.1 - - - -
488A LYS* 2.7 46.2 + - - +
490A ILE* 3.7 28.2 - - + +
494A TRP* 1.4 77.1 - - - +
496A GLY* 1.3 64.5 + - - +
498A ILE* 3.4 7.4 - - - +
499A GLY* 2.7 25.0 + - - -
505A ARG* 5.4 2.0 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with GLY 496 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
481A VAL* 4.1 5.2 - - - -
483A ASN* 2.6 35.9 + - - +
485A LYS* 3.2 15.7 - - - -
486A HIS 4.2 0.2 - - - -
495A ASN* 1.3 72.1 - - - +
497A MET* 1.3 54.1 + - - -
499A GLY* 2.8 4.6 + - - -
500A GLU* 2.6 40.0 + - - +
505A ARG* 5.3 0.6 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with MET 497 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
409A VAL* 2.8 45.8 - - + +
410A THR* 3.0 25.6 - - - +
411A LEU* 3.6 9.4 - - + +
481A VAL* 3.5 19.5 - - + +
485A LYS 2.7 15.4 + - - +
486A HIS* 2.8 57.8 + - + +
496A GLY* 1.3 66.9 - - - -
498A ILE* 1.4 62.4 + - - +
500A GLU* 3.0 7.1 + - - +
501A VAL* 2.7 29.0 + - - +
509A ALA* 4.0 8.1 - - + -
510A VAL 4.3 8.1 - - - +
511A GLY 4.3 0.4 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with ILE 498 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
486A HIS 2.7 13.6 + - - +
487A GLY* 3.4 19.3 - - - -
494A TRP* 3.5 24.0 - - + -
495A ASN 3.4 10.3 - - - +
496A GLY 3.3 0.2 - - - -
497A MET* 1.4 71.0 - - - +
499A GLY* 1.4 58.7 + - - +
501A VAL* 3.1 4.8 + - - +
502A VAL* 2.6 43.3 + - + +
509A ALA* 5.6 0.2 - - - -
513A LEU* 4.1 13.0 - - + +
519A ARG* 3.8 26.5 - - + -
522A VAL* 3.8 20.4 - - + -
523A VAL* 3.8 39.0 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with GLY 499 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
494A TRP* 4.1 5.2 - - - -
495A ASN* 2.7 36.1 + - - -
496A GLY 2.8 4.3 + - - -
498A ILE* 1.4 72.3 - - - +
500A GLU* 1.3 54.4 + - - -
502A VAL* 4.0 9.9 - - - -
503A MET* 3.3 20.6 + - - +
505A ARG* 2.5 25.0 + - - -
----------------------------------------------------------
Back to top of page
Residues in contact with GLU 500 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
409A VAL* 3.6 6.2 - - + +
479A TYR* 2.5 40.3 + - - +
481A VAL* 3.1 14.8 - - - +
482A THR* 2.6 44.2 + - - -
483A ASN* 3.3 4.7 + - - +
496A GLY* 2.6 21.4 + - - +
497A MET* 3.7 4.9 - - - +
499A GLY* 1.3 69.9 - - - +
501A VAL* 1.4 59.9 + - - +
503A MET 3.6 0.5 - - - -
504A LYS 3.5 1.4 + - - -
505A ARG* 3.3 41.6 + - + +
506A ALA* 2.7 27.8 + - + -
----------------------------------------------------------
Back to top of page
Residues in contact with VAL 501 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
409A VAL* 3.9 3.1 - - + -
497A MET 2.7 21.8 + - - +
498A ILE* 3.5 10.8 - - - +
500A GLU* 1.4 67.3 - - - +
502A VAL* 1.4 60.5 + - - +
503A MET 3.0 4.0 - - - -
504A LYS* 2.8 21.3 + - - +
506A ALA* 3.5 17.6 - - + +
507A TYR 3.6 6.3 - - - +
508A MET* 3.4 40.8 - - - +
509A ALA* 4.2 6.3 - - + +
523A VAL* 3.7 18.2 - - + -
765B ALA* 5.3 0.9 - - + +
767B GLN* 3.0 37.3 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with VAL 502 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
494A TRP* 4.1 12.3 - - + -
498A ILE* 2.6 33.6 + - + +
499A GLY* 4.0 7.2 - - - -
501A VAL* 1.4 70.5 - - + +
503A MET* 1.4 79.5 + - + +
504A LYS* 3.6 2.3 - - - +
522A VAL* 3.1 53.6 - - + +
523A VAL* 3.7 22.0 - - + -
767B GLN* 4.7 7.6 - - + -
----------------------------------------------------------
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