Contacts of the strand formed by residues 673 - 683 (chain A) in PDB entry 1EX0
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 THR 673 (chain A).
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
231A GLU* 4.5 2.8 - - - +
667A LEU* 4.4 15.9 - - + +
668A ASP* 3.8 28.8 - - - +
669A GLY 2.9 21.3 + - - +
670A PRO* 4.6 0.3 - - - +
672A VAL* 1.3 80.8 - - - +
674A ARG* 1.3 82.8 + - - +
675A PRO* 4.2 0.7 - - - +
676A MET* 3.7 18.9 - - - -
695A CYS* 3.9 14.6 - - - -
698A TRP* 3.7 14.5 - - - -
705A LEU* 4.4 8.1 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with ARG 674 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
231A GLU* 5.8 0.4 - - - -
300A LEU* 5.1 13.3 - - - +
667A LEU 3.9 0.3 - - - +
668A ASP* 4.5 0.2 - - - -
673A THR* 1.3 94.4 + - - +
675A PRO* 1.3 82.3 - - + +
676A MET* 3.3 9.3 + - + +
698A TRP* 3.7 15.1 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with PRO 675 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
293A THR* 4.8 2.2 - - - +
296A VAL* 4.0 34.1 - - + -
297A ASP* 3.7 34.2 - - + +
666A HIS* 6.3 0.2 - - - +
667A LEU 3.5 9.0 - - - +
668A ASP* 3.5 29.8 - - - +
673A THR 4.2 0.7 - - - +
674A ARG* 1.3 95.3 - - + +
676A MET* 1.3 60.5 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with MET 676 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
666A HIS* 3.3 7.5 + - - +
667A LEU* 2.8 37.7 + - + +
673A THR* 3.7 14.6 - - + +
674A ARG* 3.3 20.2 - - + +
675A PRO* 1.3 74.6 - - - +
677A LYS* 1.3 62.6 + - - +
691A TRP* 3.8 13.9 - - + -
693A GLU* 3.4 42.2 - - - +
694A VAL 6.1 0.2 - - - +
695A CYS* 5.9 1.3 - - - -
----------------------------------------------------------
Back to top of page
Residues in contact with LYS 677 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
287A VAL* 6.0 6.1 - - - -
664A TRP* 3.5 38.4 - - + -
665A VAL 3.2 11.7 - - - +
666A HIS* 3.8 30.7 - - + +
676A MET* 1.3 78.0 - - - +
678A LYS* 1.3 63.2 + - - +
691A TRP* 3.9 5.6 - - - -
----------------------------------------------------------
Back to top of page
Residues in contact with LYS 678 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
663A VAL 3.5 2.1 - - - +
664A TRP* 3.6 5.2 - - - -
665A VAL* 2.6 37.3 + - - +
677A LYS* 1.3 76.9 - - - +
679A MET* 1.3 62.6 + - - +
680A PHE* 3.8 23.9 - - + -
691A TRP* 3.6 48.9 - - + +
693A GLU* 5.1 2.2 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with MET 679 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
662A ASN* 3.8 29.6 - - - +
663A VAL 3.2 17.0 - - - +
664A TRP* 3.5 51.3 - - + +
678A LYS* 1.3 80.9 - - - +
680A PHE* 1.3 67.2 + - - +
681A ARG* 4.2 26.4 + - + +
----------------------------------------------------------
Back to top of page
Residues in contact with PHE 680 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
663A VAL* 2.8 49.5 + - + +
665A VAL* 4.1 16.8 - - + -
678A LYS* 3.8 31.9 - - + -
679A MET* 1.3 81.3 - - - +
681A ARG* 1.3 63.0 + - - +
682A GLU 3.2 10.1 + - - +
683A ILE* 4.6 4.0 - - + -
689A VAL* 3.5 39.0 - - + -
690A GLN 3.9 20.4 - - - -
691A TRP* 4.1 14.4 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with ARG 681 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
661A ARG* 2.9 45.2 + - - +
662A ASN 2.9 19.0 + - - +
679A MET* 4.2 17.7 - - + +
680A PHE* 1.3 70.6 - - - +
682A GLU* 1.3 98.9 + - + +
684A ARG* 5.6 0.6 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with GLU 682 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
659A THR* 3.9 7.6 + - - +
660A LEU 3.2 11.0 - - - +
661A ARG* 3.1 20.1 + - + +
663A VAL* 4.8 0.2 - - - -
680A PHE* 3.2 6.9 + - - +
681A ARG* 1.3 113.9 + - + +
683A ILE* 1.3 70.0 - - - +
684A ARG* 2.8 57.5 + - - +
689A VAL* 5.2 1.0 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with ILE 683 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
652A PHE* 4.3 12.1 - - + +
654A ASN* 3.0 40.5 + - + +
659A THR* 3.3 4.0 + - - -
660A LEU* 2.7 27.8 + - + +
663A VAL* 4.0 29.8 - - + -
680A PHE* 4.6 3.1 - - + -
682A GLU* 1.3 80.1 - - - +
684A ARG* 1.3 70.3 + - - +
687A SER* 3.7 17.7 - - - +
689A VAL* 3.6 43.5 - - + -
----------------------------------------------------------
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