Contacts of the strand formed by residues 743 - 749 (chain B) in PDB entry 1RL3
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 LEU 743 (chain B).
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
673B GLN* 3.2 2.9 - - - +
674B PHE* 2.6 45.7 + - + +
680B ILE* 4.3 11.0 - - + -
693B ILE* 3.4 36.3 - - + -
695B GLU 3.5 8.5 - - - +
696B GLY 3.6 15.5 - - - +
697B SER 4.0 4.5 - - - +
698B ALA* 3.4 28.9 - - + -
722B PHE* 5.5 3.4 - - + -
739B ALA* 3.5 25.6 - - + -
741B GLY 3.2 1.9 + - - +
742B PRO* 1.3 73.2 - - - +
744B LYS* 1.3 61.5 + - - +
745B CYS* 3.7 19.1 - - - -
----------------------------------------------------------
Back to top of page
Residues in contact with LYS 744 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
672B VAL 3.8 3.4 - - - -
673B GLN* 2.9 38.6 + - + +
693B ILE* 3.7 2.6 - - - +
694B LEU* 2.9 34.6 + - + -
695B GLU* 3.0 50.1 + - + +
742B PRO* 5.6 3.6 - - + -
743B LEU* 1.3 75.2 - - - +
745B CYS* 1.3 66.7 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with CYS 745 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
671B PRO* 3.5 1.4 - - - +
672B VAL* 2.7 51.7 + - + +
674B PHE* 4.1 17.3 - - + -
691B PHE* 4.7 12.1 - - + -
692B ILE 3.2 16.6 - - - +
693B ILE* 4.4 8.3 - - - -
694B LEU* 3.5 9.8 - - - +
722B PHE* 5.1 5.4 - - - -
743B LEU* 3.7 27.1 - - - -
744B LYS* 1.3 81.1 - - - +
746B VAL* 1.3 65.0 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with VAL 746 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
644B TYR* 3.2 35.4 - - + +
647B PHE* 4.8 2.2 - - + -
669B LEU* 3.7 32.1 - - + +
670B GLU 3.1 6.7 - - - +
671B PRO* 4.1 9.6 - - + -
690B PHE 4.0 1.4 - - - +
691B PHE 4.1 0.2 - - - -
692B ILE* 3.1 42.4 + - + +
694B LEU* 3.5 22.2 - - + -
745B CYS* 1.3 80.6 - - - +
747B LYS* 1.3 61.9 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with LYS 747 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
670B GLU* 2.9 64.6 + - - +
672B VAL* 3.8 25.1 - - + +
674B PHE* 6.3 0.2 - - + -
689B GLU* 2.8 40.5 + - + +
690B PHE 3.2 11.7 - - - +
691B PHE* 4.1 22.4 - - + +
746B VAL* 1.3 73.3 - - - +
748B LEU* 1.3 81.9 + - - +
752B ARG* 3.4 3.2 + - - -
----------------------------------------------------------
Back to top of page
Residues in contact with LEU 748 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
665B VAL* 4.9 2.2 - - + +
668B ALA* 3.9 15.5 - - + +
669B LEU* 3.6 23.6 - - + -
689B GLU* 3.1 11.4 - - - +
690B PHE* 2.9 41.5 + - + +
692B ILE* 6.2 0.9 - - + -
747B LYS* 1.3 98.6 - - - +
749B ASP* 1.3 60.7 + - - +
752B ARG* 3.8 10.8 - - + +
753B PHE* 3.8 18.8 - - + +
756B VAL* 3.5 23.3 - - + -
757B LEU* 3.4 34.8 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with ASP 749 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
532B LYS* 5.6 1.2 - - - +
688B ASP* 3.8 9.9 - - - +
689B GLU* 4.5 7.9 - - + +
727B LEU* 4.8 0.9 - - - -
748B LEU* 1.3 75.6 - - - +
750B ARG* 1.3 67.0 + - - +
751B PRO* 3.2 20.0 - - + +
752B ARG* 3.0 50.6 + - - +
753B PHE* 2.8 19.8 + - - +
----------------------------------------------------------
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