Contacts of the strand formed by residues 724 - 730 (chain B) in PDB entry 1L8A
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 GLY 724 (chain B).
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
721B GLY 3.3 8.5 - - - +
722B SER 3.3 3.4 + - - -
723B LYS* 1.3 81.2 - - - +
725B LYS* 1.3 57.3 + - - +
750B GLY 3.6 2.2 + - - -
751B VAL* 3.9 10.5 - - - +
752B GLY 2.7 29.7 + - - -
856B LEU* 4.5 5.2 - - - -
861B GLU* 4.2 12.3 - - - -
----------------------------------------------------------
Back to top of page
Residues in contact with LYS 725 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
718B THR* 4.0 11.7 - - - +
719B ILE 4.9 0.6 + - - -
720B GLU* 5.5 2.4 + - - -
721B GLY 5.5 1.1 - - - +
724B GLY* 1.3 74.6 - - - +
726B VAL* 1.3 74.3 + - - +
751B VAL* 4.1 1.4 - - - +
752B GLY* 3.3 13.5 - - - +
753B SER* 3.9 11.7 - - - +
754B ASP* 2.9 37.3 + - - -
793B ASN* 4.4 7.4 - - - +
795B ALA* 3.6 20.8 - - + +
796B PRO* 3.5 19.8 - - - +
856B LEU* 4.0 7.0 - - - +
859B ARG* 4.8 0.9 + - - -
861B GLU* 4.6 2.4 + - - -
----------------------------------------------------------
Back to top of page
Residues in contact with VAL 726 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
725B LYS* 1.3 85.3 - - - +
727B GLN* 1.3 68.2 + - - +
728B LEU* 4.0 14.8 - - + -
745B LEU* 4.1 17.3 - - + -
751B VAL* 4.1 2.7 - - + -
752B GLY 3.1 12.5 + - - +
753B SER* 3.0 16.1 - - - -
754B ASP 3.0 21.5 + - - -
795B ALA* 4.2 2.7 - - - -
796B PRO* 3.2 18.6 - - + +
798B VAL* 5.8 0.2 - - + -
852B ALA* 4.2 17.7 - - + +
855B GLU* 4.5 2.5 - - - +
856B LEU* 4.1 28.3 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with GLN 727 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
726B VAL* 1.3 78.9 - - - +
728B LEU* 1.3 65.9 - - - +
729B LEU* 4.3 1.1 - - - -
754B ASP* 3.4 8.7 - - - +
756B TYR* 2.6 42.7 + - + +
792B MET* 3.4 17.9 - - + +
793B ASN* 2.9 56.2 - - - +
795B ALA* 3.0 21.1 - - + +
796B PRO 2.9 6.3 + - - +
797B ALA* 3.3 13.8 - - + +
798B VAL 2.9 25.6 + - - -
817B ALA* 4.1 0.9 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with LEU 728 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
726B VAL* 4.0 13.0 - - + -
727B GLN* 1.3 83.8 - - - +
729B LEU* 1.3 61.7 + - - +
738B VAL* 3.5 18.8 - - + +
741B ALA 4.7 0.2 - - - -
742B ALA* 3.7 35.7 - - + +
745B LEU* 3.9 15.5 - - + -
753B SER* 3.7 18.2 - - - +
754B ASP 2.8 11.9 + - - +
755B VAL* 3.4 6.3 - - + +
756B TYR* 2.8 28.8 + - - +
798B VAL* 3.4 24.0 - - + +
848B VAL* 3.9 16.6 - - + -
852B ALA* 4.5 1.1 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with LEU 729 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
713B ILE* 4.1 8.5 - - + -
727B GLN 4.3 0.4 - - - -
728B LEU* 1.3 84.4 - - - +
730B GLY* 1.3 58.9 + - - +
738B VAL* 3.6 11.4 - - - +
756B TYR* 3.5 19.3 - - + -
758B VAL* 3.8 20.6 - - + -
761B PHE* 4.3 15.9 - - + -
788B ILE* 4.8 2.9 - - + -
792B MET* 3.6 41.5 - - + -
797B ALA* 4.3 8.5 - - + -
798B VAL 2.8 21.3 + - - +
799B ALA* 3.2 9.2 - - + -
800B SER 3.0 25.1 + - - -
820B TYR* 4.6 9.9 - - + +
----------------------------------------------------------
Back to top of page
Residues in contact with GLY 730 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
729B LEU* 1.3 76.3 - - - +
731B SER* 1.3 60.6 + - - -
735B LEU* 3.9 19.2 - - - +
738B VAL* 4.1 6.5 - - - -
756B TYR 3.2 7.3 + - - -
757B SER* 3.6 6.2 + - - -
758B VAL* 2.9 27.8 + - - +
761B PHE* 5.5 0.2 - - - -
800B SER 3.3 12.8 - - - -
801B THR* 4.9 2.2 - - - -
----------------------------------------------------------
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