Contacts of the helix formed by residues 694 - 707 (chain B) in PDB entry 1SOJ
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 ARG 694 (chain B).
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
688B MET* 4.0 4.7 - - + -
691B LYS* 3.2 25.2 + - + +
692B SER 3.0 1.8 - - - -
693B GLY* 1.3 82.3 - - - +
695B ILE* 1.3 59.7 + - - +
697B SER* 3.6 8.1 - - - +
698B GLN* 3.0 35.6 + - + +
725B ARG* 3.5 52.6 - - - +
728B GLU* 2.8 16.4 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with ILE 695 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
681B ILE* 5.1 5.4 - - + -
684B LEU* 4.7 13.2 - - + -
685B VAL* 3.4 43.5 - - + +
688B MET* 3.8 18.8 - - - -
692B SER* 2.9 20.4 + - - +
693B GLY 3.5 1.4 + - - -
694B ARG* 1.3 76.4 - - - +
696B LEU* 1.3 54.1 + - - +
698B GLN* 3.1 2.7 + - - +
699B VAL* 2.8 41.6 + - + +
728B GLU* 3.2 0.6 + - - -
739B ARG* 5.4 6.0 - - - +
740B ILE* 3.9 20.0 - - + -
743B THR* 3.7 26.5 - - + +
----------------------------------------------------------
Back to top of page
Residues in contact with LEU 696 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
695B ILE* 1.3 79.2 - - - +
697B SER* 1.3 58.2 + - - +
699B VAL* 3.2 0.3 + - - -
700B MET* 2.8 39.3 + - + +
724B PHE* 5.2 2.5 - - + +
727B LEU* 4.3 11.0 - - + -
728B GLU* 3.0 24.8 + - + +
731B TYR* 4.1 17.5 - - + -
739B ARG* 4.5 8.6 - - + +
742B ALA* 4.2 8.1 - - + -
743B THR* 3.4 36.7 + - - +
746B LEU* 4.2 17.0 - - + -
819B ALA* 3.5 32.3 - - + +
----------------------------------------------------------
Back to top of page
Residues in contact with SER 697 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
694B ARG* 3.4 12.8 + - - +
696B LEU* 1.3 73.1 - - - +
698B GLN* 1.3 63.9 + - - +
700B MET* 3.9 1.9 - - - +
701B TYR* 3.2 23.7 + - - +
720B PHE* 4.8 0.2 - - - -
721B MET* 3.6 18.9 - - - +
724B PHE* 4.0 30.3 - - - -
725B ARG* 3.6 13.9 + - - -
728B GLU* 2.6 36.0 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with GLN 698 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
670B LEU* 5.0 7.6 - - + -
688B MET* 3.9 20.4 - - + -
694B ARG* 3.0 31.4 + - + +
695B ILE* 3.7 2.9 - - - +
697B SER* 1.3 80.0 + - - +
699B VAL* 1.3 67.3 + - + +
701B TYR* 3.5 7.2 + - - +
702B THR* 2.9 28.1 + - - -
721B MET* 3.5 28.1 - - - +
725B ARG* 4.2 10.7 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with VAL 699 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
670B LEU* 4.6 7.4 - - + -
674B MET* 3.3 32.8 - - + -
679B PHE* 5.3 0.7 - - + -
684B LEU* 4.5 16.4 - - + -
695B ILE* 2.8 30.4 + - + +
696B LEU 3.9 2.2 - - - +
698B GLN* 1.3 72.6 - - + +
700B MET* 1.3 56.0 + - - +
702B THR* 3.0 6.7 + - - -
703B LEU* 2.7 46.8 + - + +
743B THR* 3.6 25.6 - - + +
746B LEU* 4.0 10.5 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with MET 700 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
696B LEU* 2.8 23.5 + - + +
697B SER* 3.9 6.5 - - - +
699B VAL* 1.3 74.5 - - - +
701B TYR* 1.3 58.8 + - - +
703B LEU* 3.3 2.8 + - + -
704B PHE* 2.9 64.2 + - + -
720B PHE* 4.0 12.1 - - + -
724B PHE* 3.9 28.0 - - + -
746B LEU* 3.0 46.9 - - + -
815B TYR* 4.0 8.5 - - + +
816B VAL* 4.9 0.9 - - - -
819B ALA* 3.6 23.6 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with TYR 701 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
663B LEU* 6.0 5.6 - - + -
667B TYR* 6.0 0.2 - + - -
697B SER 3.2 15.7 + - - +
698B GLN* 3.8 7.9 - - - +
700B MET* 1.3 79.8 - - - +
702B THR* 1.3 67.6 + - - +
704B PHE* 3.4 2.8 + - - +
705B GLN* 3.0 59.0 + - - +
710B LEU* 3.8 17.2 - - + +
717B THR* 3.6 33.1 + - + +
720B PHE* 3.7 17.4 - + - -
721B MET* 3.9 25.6 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with THR 702 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
667B TYR* 3.6 24.4 - - + -
670B LEU* 3.5 28.5 - - + +
671B ILE* 3.4 29.8 - - + -
674B MET* 4.8 5.6 - - - -
698B GLN* 2.9 16.5 + - - +
699B VAL* 3.0 8.3 + - - -
701B TYR* 1.3 82.7 - - - +
703B LEU* 1.3 63.4 + - - +
705B GLN* 3.0 14.4 + - - +
706B ASP* 3.1 10.6 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with LEU 703 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
671B ILE* 5.0 2.9 - - + -
674B MET* 4.0 21.3 - - + -
699B VAL* 2.7 32.7 + - + +
700B MET* 3.9 4.9 - - + +
702B THR* 1.3 74.6 - - - +
704B PHE* 1.3 63.5 + - + +
705B GLN 3.0 0.4 - - - -
706B ASP* 3.3 4.5 + - + +
707B THR* 2.9 35.8 + - + +
746B LEU* 3.7 33.0 - - + +
747B HIS* 4.5 1.6 - - - -
750B TRP* 3.4 61.0 - - + -
815B TYR* 6.0 2.2 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with PHE 704 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
700B MET* 2.9 47.1 + - + +
701B TYR 3.9 3.8 - - - +
702B THR 3.2 0.6 - - - -
703B LEU* 1.3 79.8 - - + +
705B GLN* 1.3 58.7 + - - +
707B THR* 3.5 5.6 - - - -
708B GLY 3.5 0.9 + - - -
709B LEU* 3.3 32.7 + - + -
710B LEU* 3.2 37.3 + - + +
715B ILE* 4.2 11.4 - - + -
720B PHE* 3.5 28.9 - + + -
812B MET* 4.0 28.7 - - + -
815B TYR* 4.1 12.8 - + + -
816B VAL* 3.8 26.2 - - + -
870B PHE* 4.9 2.0 - + - -
----------------------------------------------------------
Back to top of page
Residues in contact with GLN 705 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
663B LEU* 6.2 0.3 - - - +
667B TYR* 3.5 31.8 - - + +
701B TYR* 3.0 51.6 + - - +
702B THR 3.0 6.7 + - - +
704B PHE* 1.3 75.7 - - - +
706B ASP* 1.3 68.3 + - - +
707B THR 3.0 2.5 + - - -
708B GLY* 3.3 4.0 + - - -
710B LEU* 3.5 17.9 - - + +
790B LYS* 2.9 29.2 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with ASP 706 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
667B TYR* 3.4 15.8 + - - +
671B ILE* 3.8 12.7 - - + +
702B THR 3.1 10.4 + - - +
703B LEU* 3.3 10.1 + - - +
705B GLN* 1.3 79.3 - - - +
707B THR* 1.3 55.1 + - - +
750B TRP* 3.3 21.8 + - + -
788B SER 3.4 0.3 - - - +
789B SER* 2.5 24.5 + - - -
790B LYS* 2.9 38.5 + - - +
791B SER* 2.8 38.9 + - - -
----------------------------------------------------------
Back to top of page
Residues in contact with THR 707 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
703B LEU 2.9 18.8 + - - +
704B PHE 3.5 2.3 + - - -
706B ASP* 1.3 81.7 - - - +
708B GLY* 1.3 59.5 + - - +
709B LEU* 3.3 25.7 + - - +
712B ILE* 4.8 1.0 - - - +
750B TRP* 3.7 29.8 - - + +
754B THR* 5.2 2.2 - - - +
787B ILE* 3.4 47.0 - - + +
788B SER 3.6 16.8 + - - +
789B SER* 5.2 2.0 - - - -
790B LYS* 5.0 1.1 - - - -
815B TYR* 4.1 7.4 - - + -
----------------------------------------------------------
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