Contacts of the helix formed by residues 657 - 669 (chain B) in PDB entry 3KN5
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 SER 657 (chain B).
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
518B GLU* 2.7 36.6 + - - -
655B ASN 3.2 5.2 + - - -
656B VAL* 1.3 76.2 - - - +
658B GLN* 1.3 64.5 + - - +
659B GLU* 3.3 14.2 + - - -
660B ALA* 3.3 16.6 + - - +
661B LYS* 3.4 17.8 + - - +
686B TRP* 3.9 4.4 + - - -
693B LEU* 6.5 0.2 - - - -
694B SER* 5.8 4.3 - - - -
----------------------------------------------------------
Back to top of page
Residues in contact with GLN 658 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
656B VAL 3.6 0.6 + - - -
657B SER* 1.3 72.6 - - - +
659B GLU* 1.3 66.4 + - - +
661B LYS* 3.4 23.3 + - - +
662B ASP* 2.6 67.3 + - - +
665B GLN* 5.5 1.0 + - - -
----------------------------------------------------------
Back to top of page
Residues in contact with GLU 659 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
657B SER* 3.3 12.1 - - - +
658B GLN* 1.3 86.9 + - - +
660B ALA* 1.3 65.1 + - - +
662B ASP* 3.3 8.5 + - - +
663B LEU* 3.1 22.9 + - - +
684B ASN* 5.0 1.4 + - - +
685B GLU* 3.2 29.6 - - + +
686B TRP* 4.1 26.7 - - + +
693B LEU* 6.1 0.9 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with ALA 660 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
518B GLU* 4.2 1.3 - - - +
612B LEU* 4.6 1.2 - - - +
616B LEU* 3.5 28.7 - - + -
656B VAL* 3.9 7.2 - - + -
657B SER* 3.3 20.9 + - - +
659B GLU* 1.3 78.7 - - - +
661B LYS* 1.3 62.1 + - - +
663B LEU* 3.1 5.4 + - - +
664B ILE* 3.0 29.0 + - - +
686B TRP* 3.9 23.6 - - + +
----------------------------------------------------------
Back to top of page
Residues in contact with LYS 661 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
648B PHE* 3.6 53.8 + - + +
653B TRP* 2.7 41.0 + - + +
654B LYS 4.4 4.4 + - - -
656B VAL* 3.1 30.9 + - + +
657B SER 3.4 12.5 + - - +
658B GLN* 3.4 29.6 + - - +
659B GLU 3.3 0.6 - - - -
660B ALA* 1.3 76.7 - - - +
662B ASP* 1.3 58.5 + - - +
664B ILE* 3.8 2.9 - - - +
665B GLN* 3.0 27.8 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with ASP 662 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
658B GLN* 2.6 52.6 + - - +
659B GLU* 3.7 7.8 - - - +
660B ALA 3.1 0.4 - - - -
661B LYS* 1.3 74.6 - - - +
663B LEU* 1.3 66.8 + - - +
665B GLN* 3.3 17.6 + - - +
666B GLY* 3.0 18.5 + - - -
676B LEU* 5.3 0.7 - - - +
684B ASN* 5.4 0.7 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with LEU 663 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
525B MET* 5.1 2.7 - - + -
612B LEU* 3.8 15.7 - - + -
659B GLU 3.1 12.6 + - - +
660B ALA* 3.1 8.5 + - - +
662B ASP* 1.3 74.2 - - - +
664B ILE* 1.3 67.1 + - - +
666B GLY* 2.9 13.0 + - - -
667B LEU* 3.3 17.7 + - + +
676B LEU* 3.9 18.2 - - + -
681B LEU* 4.2 12.6 - - + -
684B ASN* 3.2 42.8 + - + +
686B TRP* 3.6 30.1 - - + -
687B LEU* 4.0 13.2 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with ILE 664 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
609B GLY* 4.3 4.9 - - - +
612B LEU* 3.6 21.8 - - + -
613B TYR* 3.9 17.7 - - + +
616B LEU* 4.3 11.0 - - + -
646B PHE* 4.7 0.9 - - + -
648B PHE* 4.0 18.4 - - + -
653B TRP* 3.6 36.1 - - + -
660B ALA 3.0 18.0 + - - +
661B LYS 3.8 4.3 - - - +
663B LEU* 1.3 75.2 - - - +
665B GLN* 1.3 63.9 + - - +
667B LEU* 3.0 9.3 + - - +
668B LEU* 3.0 47.5 + - + +
----------------------------------------------------------
Back to top of page
Residues in contact with GLN 665 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
646B PHE* 3.8 27.6 - - + -
648B PHE* 4.8 7.6 - - + -
658B GLN* 5.5 1.0 + - - -
661B LYS 3.0 19.5 + - - +
662B ASP* 3.5 19.2 - - - +
663B LEU 3.1 0.4 - - - -
664B ILE* 1.3 77.1 - - - +
666B GLY* 1.3 57.3 + - - +
669B THR* 2.8 40.7 + - - -
674B LYS* 4.0 32.6 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with GLY 666 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
662B ASP 3.0 9.2 + - - -
663B LEU 2.9 9.4 + - - -
665B GLN* 1.3 77.2 - - - +
667B LEU* 1.3 58.1 + - - +
669B THR* 4.0 3.5 - - - +
674B LYS* 4.0 16.6 - - - -
675B ARG* 3.5 7.8 + - - +
676B LEU* 2.8 41.5 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with LEU 667 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
525B MET* 5.6 3.4 - - - -
529B VAL* 6.4 0.7 - - + -
605B LEU* 3.7 28.5 - - + +
606B TRP* 3.9 12.3 - - - -
608B LEU* 3.9 10.5 - - + +
609B GLY* 3.3 37.7 - - - +
612B LEU* 5.2 5.2 - - + -
663B LEU* 3.7 26.7 - - + +
664B ILE* 3.0 5.8 + - - +
666B GLY* 1.3 81.7 - - - +
668B LEU* 1.3 60.0 + - - +
669B THR 3.5 0.2 - - - -
675B ARG* 3.4 24.3 + - - +
676B LEU* 4.4 11.4 - - + +
681B LEU* 4.2 28.0 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with LEU 668 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
606B TRP* 3.5 41.9 + - + +
609B GLY* 3.8 11.2 - - - +
610B VAL* 3.6 20.2 - - + +
613B TYR* 4.3 11.4 - - + -
621B PRO* 4.4 4.5 - - + -
622B PHE* 4.3 17.8 - - + -
644B GLY* 4.3 1.4 - - - -
646B PHE* 3.5 37.8 - - + -
664B ILE* 3.0 33.1 + - + +
667B LEU* 1.3 77.4 - - - +
669B THR* 1.3 62.5 + - - +
670B VAL* 3.5 13.5 + - - +
675B ARG* 4.3 1.6 - - - -
----------------------------------------------------------
Back to top of page
Residues in contact with THR 669 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
644B GLY* 5.1 0.4 - - - -
646B PHE* 4.0 11.1 - - - -
665B GLN* 2.8 27.9 + - - +
666B GLY* 4.0 2.2 - - - +
667B LEU 3.5 0.4 - - - -
668B LEU* 1.3 76.0 - - - +
670B VAL* 1.3 57.9 + - - +
671B ASP* 2.6 21.4 + - - +
674B LYS* 3.8 21.3 - - + +
675B ARG* 2.8 65.3 + - + +
----------------------------------------------------------
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