Contacts of the helix formed by residues 662 - 673 (chain B) in PDB entry 3T6A
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 662 (chain B).
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
613B ILE* 4.4 11.2 - - + -
614B LEU* 3.4 27.4 - - + -
623B ARG* 4.5 4.9 - - - +
658B GLN 3.5 11.9 - - - +
659B ILE* 3.1 24.9 + - + +
660B THR 3.2 0.4 - - - -
661B ARG* 1.3 72.6 - - + +
663B GLU* 1.3 62.9 + - - +
665B THR* 3.0 26.2 + - + +
666B TRP* 3.1 16.2 + - + -
812B SER* 3.4 30.3 - - - +
815B LEU* 4.5 5.8 - - + -
816B GLU* 2.9 37.0 - - + +
----------------------------------------------------------
Back to top of page
Residues in contact with GLU 663 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
660B THR 4.9 2.0 - - - +
661B ARG 2.6 16.7 + - - +
662B LEU* 1.3 70.8 - - - +
664B LYS* 1.3 67.2 + - + +
666B TRP* 3.7 10.1 + - - +
667B THR* 3.0 27.2 + - - -
816B GLU* 3.0 4.9 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with LYS 664 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
620B LEU* 3.8 22.7 - - + +
623B ARG* 5.7 0.7 - - - +
663B GLU* 1.3 81.8 - - + +
665B THR* 1.3 55.7 + - - +
667B THR* 3.1 6.4 + - - -
668B ALA* 2.7 36.7 + - - +
815B LEU 5.2 1.6 + - - -
816B GLU* 3.1 35.8 + - + +
817B PRO* 5.0 7.3 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with THR 665 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
613B ILE* 5.5 2.2 - - + -
620B LEU* 3.4 8.7 - - - +
623B ARG* 2.8 46.4 + - + +
624B ALA* 4.1 11.7 - - - +
627B LEU* 4.1 19.9 - - + +
662B LEU* 3.0 21.3 + - + +
664B LYS* 1.3 79.1 - - - +
666B TRP* 1.3 57.9 + - + +
668B ALA* 3.6 2.6 + - - +
669B LEU* 3.0 25.8 + - - +
816B GLU* 2.7 18.5 + - - -
----------------------------------------------------------
Back to top of page
Residues in contact with TRP 666 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
627B LEU* 3.9 26.8 - - + +
631B ILE* 4.6 0.9 - - + -
654B LEU* 3.8 23.8 - - + -
659B ILE* 3.0 32.0 + - + +
660B THR* 3.7 17.5 - - - +
662B LEU* 3.1 26.2 + - + +
663B GLU* 4.0 7.0 - - - +
664B LYS 3.2 0.2 - - - -
665B THR* 1.3 77.7 - - + +
667B THR* 1.3 57.8 + - - +
669B LEU* 3.4 30.7 + - + +
670B ARG* 3.1 25.8 + - - +
677B ALA* 5.5 0.4 - - + +
680B TYR* 3.5 43.5 - + - -
681B GLU* 6.2 1.3 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with THR 667 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
663B GLU* 3.0 15.8 + - - +
664B LYS* 3.1 11.4 + - - -
666B TRP* 1.3 72.8 - - - +
668B ALA* 1.3 68.2 + - - +
670B ARG* 3.2 9.6 + - + +
671B HIS* 2.9 48.7 + - + +
----------------------------------------------------------
Back to top of page
Residues in contact with ALA 668 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
620B LEU* 4.1 22.9 - - + -
621B GLU* 5.8 1.1 - - - -
624B ALA* 4.0 17.0 - - + -
664B LYS 2.7 20.3 + - - +
665B THR 3.8 4.7 - - - +
667B THR* 1.3 76.1 - - - +
669B LEU* 1.3 55.8 + - - +
671B HIS* 3.2 8.3 + - - +
672B GLN* 2.9 34.6 + - + +
----------------------------------------------------------
Back to top of page
Residues in contact with LEU 669 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
624B ALA* 3.9 12.5 - - + +
627B LEU* 4.1 8.1 - - + -
628B SER* 3.8 30.7 - - - +
631B ILE* 3.8 19.3 - - + -
665B THR 3.0 16.2 + - - +
666B TRP* 3.5 31.2 - - + +
667B THR 3.1 0.4 - - - -
668B ALA* 1.3 75.7 - - - +
670B ARG* 1.3 57.5 + - - +
673B TYR* 2.7 61.1 + - + +
676B THR* 4.9 1.6 - - + -
677B ALA* 3.5 28.5 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with ARG 670 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
666B TRP 3.1 10.4 + - - +
667B THR* 3.4 11.7 - - + +
669B LEU* 1.3 77.9 - - - +
671B HIS* 1.3 60.4 + - + +
674B THR* 2.6 40.2 + - - +
677B ALA* 3.9 16.9 - - + +
678B ILE* 2.9 45.5 - - - +
681B GLU* 6.0 2.6 - - - +
682B LYS* 6.0 4.2 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with HIS 671 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
667B THR* 2.9 40.9 + - + +
668B ALA* 3.6 8.3 - - - +
670B ARG* 1.3 84.0 + - + +
672B GLN* 1.3 63.0 + - + +
674B THR* 3.6 8.5 + - - -
----------------------------------------------------------
Back to top of page
Residues in contact with GLN 672 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
621B GLU* 5.9 8.7 + - + +
624B ALA* 5.7 1.1 - - + -
668B ALA* 2.9 15.4 + - + +
671B HIS* 1.3 81.5 + - + +
673B TYR* 1.3 94.0 + - + +
674B THR* 3.6 2.4 + - - -
----------------------------------------------------------
Back to top of page
Residues in contact with TYR 673 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
621B GLU* 4.9 2.1 + - - +
624B ALA* 3.9 8.1 - - + -
625B ALA* 3.3 41.9 - - - +
628B SER* 3.3 28.5 - - - +
669B LEU* 2.7 40.2 + - + +
672B GLN* 1.3 101.3 - - + +
674B THR* 1.3 52.8 + - - +
675B GLN* 3.4 3.4 - - - -
676B THR* 3.1 9.8 + - - +
677B ALA 2.8 30.5 + - - -
----------------------------------------------------------
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