Contacts of the strand formed by residues 756 - 761 (chain A) in PDB entry 1EGI
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 756 (chain A).
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
645A TYR 3.2 11.7 - - - +
646A ALA* 3.2 26.1 - - + +
648A GLY 4.8 3.1 - - - +
652A LYS* 3.8 30.3 - - - +
693A LYS* 3.6 26.1 + - - +
694A LEU 3.0 23.6 + - - +
695A PHE* 3.5 11.4 - - + -
696A TRP* 3.0 20.0 + - - -
755A ASN* 1.3 85.2 + - - +
757A TRP* 1.3 67.2 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with TRP 757 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
645A TYR* 2.9 66.2 + + + +
651A GLU* 3.7 20.0 - - + -
652A LYS* 4.5 1.3 - - - -
653A LYS* 3.4 33.0 - - + -
658A SER* 3.5 32.3 + - - +
661A PHE* 3.4 42.6 - + + -
662A CYS* 3.7 22.4 - - - -
669A LEU* 4.1 1.8 - - + -
695A PHE* 3.9 2.0 - - - -
696A TRP* 3.6 15.0 - - + +
755A ASN 3.6 13.2 - - - -
756A ASN* 1.3 78.8 - - - +
758A ILE* 1.3 69.1 + - - +
759A CYS* 3.6 3.1 - - - -
----------------------------------------------------------
Back to top of page
Residues in contact with ILE 758 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
642A PHE* 4.3 9.2 - - + -
643A LYS 3.5 18.8 - - - +
644A LEU* 3.4 29.6 - - + -
662A CYS* 4.2 1.1 - - - -
669A LEU* 3.5 9.4 - - - +
670A ALA* 2.8 41.7 + - + +
681A ILE* 3.5 23.1 - - + -
695A PHE* 3.7 21.1 - - + -
696A TRP 3.3 9.5 + - - +
697A LEU* 4.2 9.4 - - + -
738A LEU* 3.9 11.7 - - + -
757A TRP* 1.3 82.9 - - - +
759A CYS* 1.3 67.9 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with CYS 759 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
632A TRP* 4.1 14.1 - - + -
642A PHE* 3.3 4.9 - - - -
643A LYS 3.0 28.7 + - - +
645A TYR* 3.7 19.3 - - + -
661A PHE* 4.1 4.0 - - - -
662A CYS* 2.0 57.4 - - + +
665A LEU* 4.1 4.3 - - + -
668A ASP 3.5 2.2 - - - +
670A ALA* 4.1 1.1 - - - -
757A TRP* 3.6 16.8 - - - -
758A ILE* 1.3 79.4 - - - +
760A GLN* 1.3 62.9 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with GLN 760 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
632A TRP* 4.3 1.1 - - - -
640A LEU* 3.5 29.0 - - + +
641A CYS 2.9 11.0 - - - +
642A PHE* 3.6 13.2 - - + -
667A GLY* 3.4 4.7 - - - -
668A ASP* 2.8 45.1 + - - +
669A LEU 3.7 8.7 + - - +
670A ALA* 3.5 1.3 - - - -
671A SER* 2.9 42.5 + - - -
759A CYS* 1.3 77.7 - - - +
761A ILE* 1.3 61.1 + - - +
762A GLN* 5.2 1.8 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with ILE 761 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
629A PRO* 3.5 35.9 - - + -
632A TRP* 3.2 38.1 - - + -
641A CYS* 2.9 41.0 + - + +
665A LEU* 4.6 13.2 - - + +
666A GLY* 4.8 13.7 - - - +
667A GLY* 4.6 6.1 - - - +
760A GLN* 1.3 73.6 - - - +
762A GLN* 1.3 80.4 + - + +
----------------------------------------------------------
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