Contacts of the strand formed by residues 502 - 505 (chain B) in PDB entry 5IWI
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 502 (chain B).
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
427B GLU 6.1 0.9 - - - +
429B CYS 3.6 3.8 + - - +
430B GLU* 3.4 32.1 + - + +
431B ILE 2.9 26.3 + - - -
500B TYR* 3.8 4.3 - - - +
501B HIS* 1.3 86.8 - - + +
503B ILE* 1.3 63.7 + - - +
504B VAL* 3.8 7.0 - - + -
536B TYR 3.4 3.8 - - - -
538B TYR* 3.5 37.7 + - + -
601B ARG* 3.6 20.4 - - - +
603B LEU* 4.4 9.6 - - + +
----------------------------------------------------------
Back to top of page
Residues in contact with ILE 503 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
431B ILE* 3.7 15.9 - - + -
433B LEU* 3.9 17.7 - - + -
485B PHE* 3.7 41.1 - - + -
498B ALA* 5.9 0.2 - - + -
500B TYR* 3.6 28.7 - - + +
502B LYS* 1.3 73.2 - - - +
504B VAL* 1.3 62.0 + - - +
505B ILE* 3.9 0.6 + - + +
524B PHE* 4.2 13.9 - - + -
531B LEU* 4.2 23.8 - - + -
536B TYR* 2.7 20.4 + - + +
537B VAL* 3.5 8.9 - - + +
538B TYR 2.8 26.7 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with VAL 504 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
430B GLU* 4.7 2.9 - - + +
431B ILE 2.8 17.4 + - - +
432B PHE* 3.4 41.4 - - + -
433B LEU* 2.8 31.0 + - - -
502B LYS* 4.2 20.6 - - + +
503B ILE* 1.3 75.0 - - - +
505B ILE* 1.3 62.7 + - - +
506B MET 3.4 0.9 + - - -
538B TYR* 3.6 12.6 - - + +
540B ALA* 3.8 27.6 - - + +
603B LEU* 4.0 17.3 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with ILE 505 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
433B LEU* 4.1 8.3 - - + +
503B ILE 5.1 0.9 - - - +
504B VAL* 1.3 71.2 - - - +
506B MET* 1.3 61.8 + - - +
507B THR* 3.7 26.1 + - + +
517B ARG* 4.1 19.2 + - + +
520B LEU* 3.8 24.9 - - + -
521B LEU* 3.8 34.5 - - + -
524B PHE* 3.9 24.9 - - + -
537B VAL* 4.3 5.4 - - + -
538B TYR 2.9 19.4 + - - +
539B ILE* 3.7 10.4 - - + +
540B ALA* 2.9 27.3 + - - +
----------------------------------------------------------
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