Contacts of the strand formed by residues 689 - 695 (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 GLU 689 (chain B).
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
681B VAL* 5.4 0.5 - - - +
688B ASP* 1.3 86.8 - - - +
690B PHE* 1.3 60.0 + - - +
691B PHE* 3.0 41.6 - - + -
723B GLY* 3.8 13.7 + - - +
727B LEU* 3.4 7.6 - - - +
747B LYS* 2.8 35.9 + - + +
748B LEU 3.1 12.9 - - - +
749B ASP* 4.9 7.0 - - + +
----------------------------------------------------------
Back to top of page
Residues in contact with PHE 690 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
654B LEU* 6.0 2.0 - - + -
689B GLU* 1.3 69.7 - - - +
691B PHE* 1.3 80.2 + - - +
692B ILE* 3.9 20.4 - - + +
721B TYR* 3.3 46.2 - + + -
722B PHE 3.5 8.5 - - - -
724B GLU* 4.0 17.3 - - + +
727B LEU* 3.3 19.7 - - + +
746B VAL 4.0 0.5 - - - +
747B LYS* 3.2 4.7 - - - -
748B LEU* 2.9 45.5 + - + +
753B PHE* 3.7 13.0 - + + -
757B LEU* 3.2 36.6 - - + -
764B LEU* 4.9 6.3 - - + -
----------------------------------------------------------
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
----------------------------------------------------------
672B VAL* 5.2 0.7 - - + -
674B PHE* 4.3 14.6 - + - -
680B ILE* 3.3 29.8 - - + -
681B VAL* 4.1 14.6 - - + -
689B GLU* 3.0 53.2 - - + -
690B PHE* 1.3 75.1 - - - +
692B ILE* 1.3 67.6 + - - +
721B TYR* 3.0 26.4 - - - +
722B PHE* 2.7 52.6 + + + +
723B GLY* 4.7 0.4 - - - -
745B CYS* 4.7 13.2 - - + -
746B VAL 4.0 3.1 - - - -
747B LYS* 4.1 19.7 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with ILE 692 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
647B PHE* 3.4 33.0 - - + -
648B LEU* 5.0 15.3 - - + -
651B VAL* 6.0 3.6 - - + -
654B LEU* 5.4 10.1 - - + -
665B VAL* 5.7 4.5 - - + -
669B LEU* 5.1 7.4 - - + -
690B PHE* 3.9 20.9 - - + -
691B PHE* 1.3 82.7 - - - +
693B ILE* 1.3 63.5 + - - +
719B SER 4.6 6.7 - - - +
720B ASP 3.0 10.8 - - - +
721B TYR* 3.8 11.9 - - + +
745B CYS* 3.2 7.5 - - - +
746B VAL* 3.1 43.0 + - + +
748B LEU* 6.2 1.3 - - + -
757B LEU* 5.7 0.4 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with ILE 693 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
647B PHE* 2.9 14.4 - - - -
692B ILE* 1.3 75.3 - - - +
694B LEU* 1.3 64.3 + - - +
695B GLU 3.9 2.7 - - - +
696B GLY 3.3 23.1 - - - +
698B ALA* 4.7 5.8 - - + +
716B LEU* 3.2 35.4 - - + +
717B GLY 3.2 26.5 - - - +
718B PRO* 3.8 3.8 - - + -
719B SER 2.9 19.5 + - - -
720B ASP* 2.8 16.5 + - + +
722B PHE* 4.4 19.3 - - + -
743B LEU* 3.4 24.7 - - + -
744B LYS 3.7 3.6 - - - +
745B CYS* 4.4 3.8 - - - -
----------------------------------------------------------
Back to top of page
Residues in contact with LEU 694 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
643B MET* 6.5 0.2 - - + -
644B TYR* 3.9 23.8 - - + +
647B PHE* 3.7 39.8 - - + -
671B PRO* 5.7 1.3 - - + -
693B ILE* 1.3 75.8 - - - +
695B GLU* 1.3 71.2 + - + +
718B PRO* 3.4 18.3 - - - +
744B LYS* 2.9 17.2 + - + +
745B CYS* 3.5 37.5 - - - +
746B VAL* 3.5 15.9 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with GLU 695 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
694B LEU* 1.3 88.9 - - + +
696B GLY* 1.3 63.3 + - - +
718B PRO* 4.1 3.4 - - + -
742B PRO 3.6 4.7 - - - +
743B LEU* 3.5 3.4 - - - +
744B LYS* 3.0 56.8 + - + +
----------------------------------------------------------
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