Contacts of the helix formed by residues 632 - 646 (chain D) in PDB entry 2BT4
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 THR 632 (chain D).
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
620D LEU* 3.4 19.5 - - - +
621D GLY* 4.8 4.3 - - - -
622D GLN* 5.9 2.7 - - + -
630D SER 4.6 5.8 - - - +
631D ASP* 1.3 76.4 - - - +
633D LEU* 1.3 65.0 + - - +
634D ALA* 3.5 9.5 + - - +
635D ASP* 3.1 30.3 + - - +
636D VAL* 3.0 21.3 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with LEU 633 (chain D).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
613D ASN* 4.1 14.1 - - + +
617D LEU* 3.5 33.2 - - + +
618D ASN* 4.1 11.5 + - + +
620D LEU* 3.9 22.4 + - + +
632D THR* 1.3 75.9 - - - +
634D ALA* 1.3 58.2 + - - +
636D VAL* 3.1 10.1 + - + +
637D GLU* 2.9 27.3 + - - +
653D PHE* 3.8 27.5 - - + -
655D GLN* 3.7 34.8 - - + -
738D TYR* 4.7 2.5 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with ALA 634 (chain D).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
632D THR* 3.1 8.9 - - - +
633D LEU* 1.3 80.8 - - - +
635D ASP* 1.3 58.2 + - - +
637D GLU* 3.4 12.1 + - - +
638D ALA* 3.0 26.9 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with ASP 635 (chain D).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
630D SER 4.6 1.2 - - - +
631D ASP* 3.6 24.8 - - + +
632D THR* 3.1 38.4 + - - +
634D ALA* 1.3 78.6 - - - +
636D VAL* 1.3 63.3 + - - +
638D ALA* 3.3 7.3 + - - +
639D LEU* 3.1 24.9 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with VAL 636 (chain D).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
620D LEU* 3.6 15.5 - - + -
631D ASP* 4.6 3.6 - - + -
632D THR 3.0 14.7 + - - +
633D LEU* 3.1 11.0 + - + +
635D ASP* 1.3 72.9 - - - +
637D GLU* 1.3 66.3 + - - +
639D LEU* 3.1 10.8 + - + +
640D CYS* 2.9 22.4 + - - -
653D PHE* 3.9 15.7 - - + -
735D VAL* 3.6 31.6 - - + -
738D TYR* 3.8 37.5 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with GLU 637 (chain D).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
633D LEU 2.9 11.4 + - - +
634D ALA* 3.6 13.2 - - - +
635D ASP 3.3 0.2 - - - -
636D VAL* 1.3 75.7 - - - +
638D ALA* 1.3 64.2 + - - +
640D CYS* 3.1 3.3 + - - +
641D VAL* 2.9 35.0 + - + +
651D VAL* 5.4 0.7 - - + +
653D PHE* 3.7 57.0 + - + +
----------------------------------------------------------
Back to top of page
Residues in contact with ALA 638 (chain D).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
634D ALA 3.0 13.6 + - - +
635D ASP* 3.6 10.3 - - - +
636D VAL 3.1 0.2 - - - -
637D GLU* 1.3 78.1 - - - +
639D LEU* 1.3 62.2 + - - +
641D VAL* 3.3 10.8 + - - +
642D LYS* 3.2 36.0 + - + +
----------------------------------------------------------
Back to top of page
Residues in contact with LEU 639 (chain D).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
631D ASP* 5.2 3.6 - - - +
635D ASP 3.1 13.8 + - - +
636D VAL* 3.1 12.5 + - + +
638D ALA* 1.3 77.4 - - - +
640D CYS* 1.4 57.6 + - - +
642D LYS* 3.4 9.3 + - + +
643D ALA* 2.9 28.8 + - - +
735D VAL* 3.8 36.6 - - + +
736D GLN* 4.9 1.3 - - - +
738D TYR* 5.8 0.7 - - + -
739D VAL* 4.3 24.7 - - + +
----------------------------------------------------------
Back to top of page
Residues in contact with CYS 640 (chain D).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
611D ILE* 3.5 32.1 - - + -
636D VAL 2.9 16.8 + - - -
637D GLU 3.5 7.4 - - - +
639D LEU* 1.4 73.5 - - - +
641D VAL* 1.3 67.3 + - - +
643D ALA* 3.8 6.8 - - - +
644D ALA* 2.9 27.0 + - - +
651D VAL* 3.8 4.6 - - + +
653D PHE* 4.0 16.6 - - + -
738D TYR* 3.8 32.1 - - - -
739D VAL* 5.6 0.9 - - - -
742D VAL* 4.7 7.0 - - + +
----------------------------------------------------------
Back to top of page
Residues in contact with VAL 641 (chain D).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
637D GLU* 2.9 30.4 + - + +
638D ALA* 3.5 11.2 - - - +
639D LEU 3.3 0.2 - - - -
640D CYS* 1.3 76.3 - - - +
642D LYS* 1.3 63.3 + - + +
644D ALA* 3.5 2.4 + - - +
645D ALA* 3.0 30.0 + - + +
649D GLY 5.0 0.7 - - - +
650D THR* 5.8 0.7 - - - +
651D VAL* 3.8 23.1 - - + +
----------------------------------------------------------
Back to top of page
Residues in contact with LYS 642 (chain D).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
638D ALA* 3.2 25.2 + - - +
639D LEU* 3.9 9.6 - - + +
641D VAL* 1.3 82.2 - - + +
643D ALA* 1.3 61.9 + - - +
645D ALA* 3.2 7.2 + - + +
646D ALA* 2.9 30.2 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with ALA 643 (chain D).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
639D LEU 2.9 18.1 + - - +
640D CYS* 3.8 5.6 - - - +
642D LYS* 1.3 78.7 - - - +
644D ALA* 1.3 60.7 + - - +
646D ALA* 3.3 8.5 + - - +
647D HIS* 2.8 31.8 - - + +
739D VAL* 4.0 31.0 - - + +
742D VAL* 3.9 17.3 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with ALA 644 (chain D).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
604D LEU* 5.7 1.3 - - - -
609D ILE* 4.4 5.4 - - + -
640D CYS 2.9 16.6 + - - +
641D VAL* 3.9 2.7 - - - +
643D ALA* 1.3 78.5 - - - +
645D ALA* 1.3 57.9 + - - +
647D HIS* 2.9 20.6 + - - +
648D GLY 3.0 0.2 + - - -
649D GLY* 2.9 35.8 + - - +
650D THR* 4.0 3.8 - - - +
651D VAL* 3.6 21.5 - - + -
742D VAL* 3.7 15.0 - - + +
----------------------------------------------------------
Back to top of page
Residues in contact with ALA 645 (chain D).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
641D VAL* 3.0 21.0 + - + +
642D LYS* 3.6 8.3 - - + +
644D ALA* 1.3 76.4 - - - +
646D ALA* 1.3 61.7 + - - +
647D HIS 3.1 1.7 + - - -
648D GLY* 3.2 12.2 + - - +
649D GLY 3.5 11.8 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with ALA 646 (chain D).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
642D LYS 2.9 17.3 + - - +
643D ALA* 3.4 11.0 - - - +
645D ALA* 1.3 75.0 - - - +
647D HIS* 1.4 74.5 + - + +
----------------------------------------------------------
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