Contacts of the strand formed by residues 688 - 692 (chain B) in PDB entry 4XUF
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 TYR 688 (chain B).
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
607B ARG* 3.1 36.1 + - + -
610B LEU* 4.0 13.2 - - + -
612B PHE* 3.6 30.5 - + - -
643B VAL* 3.7 13.2 - - + -
644B LYS 3.7 1.8 - - - -
645B MET* 3.7 30.5 - - + -
680B ALA* 3.3 8.7 - - - +
681B CYS* 2.8 57.2 + - + +
686B PRO* 3.6 16.7 - - + +
687B ILE* 1.3 80.8 - - - +
689B LEU* 1.3 66.2 + - - +
690B ILE* 4.0 2.9 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with LEU 689 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
642B ALA 3.1 6.9 - - - +
643B VAL* 3.3 1.7 - - - -
644B LYS* 2.9 46.5 + - + +
658B LEU* 4.3 26.7 - - + +
661B GLU* 4.3 20.9 - - + +
662B LEU* 3.7 33.4 - - + -
665B MET* 5.3 0.2 - - + -
677B LEU* 4.8 0.4 - - + -
679B GLY 4.2 3.4 - - - -
687B ILE* 3.7 20.9 - - + -
688B TYR* 1.3 80.5 - - - +
690B ILE* 1.3 62.8 + - - +
691B PHE* 3.5 31.4 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with ILE 690 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
605B PHE* 3.6 39.0 - - + -
610B LEU* 3.9 16.8 - - + -
632B ILE* 3.3 28.7 - - + -
641B VAL* 3.7 27.1 - - + -
642B ALA 3.5 3.8 - - - +
643B VAL* 4.4 13.7 - - + +
677B LEU* 3.3 5.7 - - - +
678B LEU* 2.9 23.1 + - + -
679B GLY 2.9 25.5 + - - +
680B ALA* 4.3 2.9 - - - +
681B CYS* 4.3 10.3 - - - -
688B TYR* 5.1 0.2 - - + -
689B LEU* 1.3 72.4 - - - +
691B PHE* 1.3 63.0 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with PHE 691 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
641B VAL* 3.5 12.0 - - - +
642B ALA* 2.7 40.2 + - + +
644B LYS* 4.6 7.4 - - + -
661B GLU* 4.9 0.2 - - - -
665B MET* 3.7 42.6 - - + -
675B VAL* 3.6 24.7 - - + -
676B ASN 3.3 17.7 - - - -
677B LEU* 3.6 25.1 - - + -
678B LEU* 3.6 8.0 - - - +
689B LEU* 3.5 44.0 - - + -
690B ILE* 1.3 72.4 - - - +
692B GLU* 1.3 63.0 + - - +
1001B P30 4.1 26.9 - + + -
----------------------------------------------------------
Back to top of page
Residues in contact with GLU 692 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
642B ALA* 4.6 1.0 - - - +
675B VAL* 4.2 9.8 - - + +
676B ASN* 3.2 39.0 + - + +
678B LEU* 3.8 17.9 - - + +
691B PHE* 1.3 76.8 - - - +
693B TYR* 1.3 72.4 + - - +
694B CYS* 3.6 11.9 + - - -
820B THR* 5.7 4.2 - - - +
821B HIS* 6.0 1.7 - - - -
826B LYS* 2.7 31.4 + - - +
1001B P30 4.5 5.4 + - - -
----------------------------------------------------------
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