Contacts of the helix formed by residues 671 - 681 (chain B) in PDB entry 3F7F
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 ASP 671 (chain B).
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
723A PHE* 3.8 10.4 - - + -
727A TYR* 3.9 20.5 - - + -
413B SER* 5.3 1.8 - - - -
667B LEU 3.1 8.9 + - - -
669B ARG 3.4 0.8 - - - -
670B GLN* 1.3 82.6 - - - +
672B LYS* 1.3 61.9 + - - +
673B CYS* 3.4 8.5 + - - +
674B LEU* 3.0 30.3 + - - +
675B LEU* 3.0 19.1 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with LYS 672 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
13B GLN* 3.4 41.7 - - + +
14B TYR* 3.9 15.5 - - + -
413B SER* 3.2 34.3 + - - +
414B ARG* 4.2 9.0 - - - +
613B ILE* 5.1 0.9 - - + -
616B LEU* 3.6 8.4 - - + +
617B GLU* 3.9 6.1 - - - +
668B TYR* 3.3 59.4 + - + +
669B ARG* 4.5 3.0 - - - +
671B ASP* 1.3 71.2 + - - +
673B CYS* 1.3 63.0 + - - +
675B LEU* 3.2 5.7 + - - +
676B ALA* 2.9 24.4 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with CYS 673 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
14B TYR* 3.6 49.0 - - + +
15B TYR* 6.0 2.9 - - - -
671B ASP* 3.3 6.5 + - - +
672B LYS* 1.3 79.6 - - - +
674B LEU* 1.3 68.0 + - - +
676B ALA* 3.0 2.8 + - - +
677B GLU* 2.9 26.9 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with LEU 674 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
723A PHE* 3.4 47.3 - - + +
726A SER* 3.8 16.2 - - - -
727A TYR* 3.9 18.4 - - + +
671B ASP* 3.0 30.2 + - - +
673B CYS* 1.3 77.8 - - - +
675B LEU* 1.3 64.2 + - - +
677B GLU* 3.2 25.5 + - - +
678B VAL* 3.0 32.0 + - + +
----------------------------------------------------------
Back to top of page
Residues in contact with LEU 675 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
719A PHE* 4.4 2.9 - - + -
723A PHE* 3.7 8.0 - - + -
616B LEU* 3.7 25.1 - - + -
664B LEU* 4.0 31.9 - - + -
667B LEU* 4.2 19.7 - - + +
668B TYR* 3.6 34.3 - - + +
671B ASP 3.0 13.3 + - - +
672B LYS* 3.5 8.5 - - - +
674B LEU* 1.3 75.2 - - - +
676B ALA* 1.3 64.7 + - - +
678B VAL* 3.2 17.1 - - + +
679B LEU* 2.8 35.1 + - + +
----------------------------------------------------------
Back to top of page
Residues in contact with ALA 676 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
14B TYR* 3.6 31.9 - - + +
612B SER* 4.2 9.4 - - - +
616B LEU* 4.1 11.4 - - + +
672B LYS 2.9 11.8 + - - +
673B CYS* 3.5 7.4 - - - +
675B LEU* 1.3 75.7 - - - +
677B GLU* 1.3 54.1 + - - +
679B LEU* 4.3 2.7 - - - -
680B LEU* 2.7 50.7 + - + +
----------------------------------------------------------
Back to top of page
Residues in contact with GLU 677 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
726A SER* 5.2 1.9 + - - -
673B CYS* 2.9 18.9 + - - +
674B LEU* 3.3 29.8 - - - +
675B LEU 3.1 0.2 - - - -
676B ALA* 1.3 77.5 - - - +
678B VAL* 1.3 61.0 + - - +
680B LEU* 3.4 2.4 + - - +
681B LYS* 2.9 44.4 + - + +
----------------------------------------------------------
Back to top of page
Residues in contact with VAL 678 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
719A PHE* 3.7 39.9 - - + +
722A THR* 3.7 29.2 - - + -
723A PHE* 4.0 13.5 - - + +
726A SER* 5.1 0.2 - - - +
674B LEU* 3.0 31.8 + - + +
675B LEU* 3.2 18.4 - - + +
677B GLU* 1.3 80.2 - - - +
679B LEU* 1.3 63.7 + - - +
681B LYS* 3.9 5.3 - - - -
682B ASP* 3.3 22.3 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with LEU 679 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
719A PHE* 3.7 40.8 - - + -
616B LEU* 4.5 7.9 - - + -
619B LEU* 3.5 32.1 - - + -
664B LEU* 4.4 4.0 - - + -
675B LEU* 2.8 36.7 + - + +
676B ALA* 3.7 4.7 - - - +
678B VAL* 1.3 81.5 - - + +
680B LEU* 1.3 63.6 + - + +
682B ASP* 3.5 18.3 - - - +
683B SER* 4.3 3.1 + - - -
705B LEU* 4.4 22.3 - - + +
708B ASN* 4.8 8.4 + - + -
709B VAL* 4.5 6.7 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with LEU 680 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
607B PHE* 4.5 13.2 - - + -
612B SER* 4.1 27.4 - - - +
615B SER* 6.0 3.1 - - - -
616B LEU* 6.3 2.2 - - + +
676B ALA* 2.7 41.0 + - + +
677B GLU* 4.4 2.7 - - - +
679B LEU* 1.3 79.7 - - + +
681B LYS* 1.3 58.9 + - - +
682B ASP 3.1 6.1 + - - -
683B SER* 3.5 14.3 + - - +
686B PHE 3.5 20.5 - - - +
687B SER* 3.6 9.0 - - - +
688B PHE 4.7 1.1 - - - +
689B GLY* 4.2 25.6 - - - +
701B TYR* 4.0 19.1 - - - +
705B LEU* 5.1 7.9 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with LYS 681 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
537A THR 5.9 1.2 + - - -
538A GLY 5.4 7.5 + - - -
539A GLU* 6.3 0.6 - - - +
677B GLU* 2.9 29.5 + - + +
678B VAL* 3.7 6.3 + - - +
680B LEU* 1.3 76.2 - - - +
682B ASP* 1.3 60.4 - - - +
683B SER 4.3 4.5 - - - +
684B SER* 5.9 0.2 - - - -
687B SER* 5.1 9.6 - - - +
----------------------------------------------------------
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