Contacts of the helix formed by residues 685 - 697 (chain A) in PDB entry 3BWT
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 ASN 685 (chain A).
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
644A SER 3.2 16.4 - - - +
645A LEU* 2.6 26.2 + - - +
646A ASN 3.9 4.5 - - - +
647A PRO* 3.5 33.2 - - - +
650A THR* 2.7 31.6 + - + +
683A ASP* 3.2 4.2 + - - -
684A LEU* 1.3 93.4 - - - +
686A GLY* 1.3 63.5 + - - +
687A ASN 3.3 2.7 + - - -
688A HIS* 3.5 12.5 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with GLY 686 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
644A SER* 3.2 25.8 + - - -
680A LEU* 3.0 19.7 - - - +
683A ASP* 3.2 13.6 + - - +
685A ASN* 1.3 77.0 - - - +
687A ASN* 1.3 63.3 + - - +
689A VAL* 3.0 16.5 + - - +
690A ILE* 3.3 12.8 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with ASN 687 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
680A LEU 2.8 11.6 + - - -
681A SER* 3.3 24.2 - - - +
683A ASP 2.8 22.2 + - - +
684A LEU* 3.0 21.8 + - - +
686A GLY* 1.3 75.3 - - - +
688A HIS* 1.3 73.8 + - - +
690A ILE* 3.4 4.2 + - - +
691A GLN* 2.8 59.3 + - - +
721A HIS* 3.9 20.8 + - + +
724A CYS* 4.6 2.8 - - - +
725A VAL* 3.6 11.1 - - + +
----------------------------------------------------------
Back to top of page
Residues in contact with HIS 688 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
650A THR* 5.0 2.9 - - + -
654A GLN* 3.3 31.5 - - - +
684A LEU* 3.6 22.0 + - - +
685A ASN* 3.5 10.3 + - - +
686A GLY 3.1 0.4 - - - -
687A ASN* 1.3 96.4 + - - +
689A VAL* 1.3 66.0 + - - +
691A GLN* 3.4 16.3 + - - +
692A LYS* 3.0 23.6 + - - +
695A GLN* 5.4 0.2 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with VAL 689 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
644A SER* 3.5 25.1 - - - +
650A THR* 3.6 27.6 + - - +
653A LEU* 3.8 25.4 - - + -
654A GLN* 4.2 7.6 - - + +
657A ILE* 3.8 17.9 - - + +
673A LEU* 3.9 23.1 - - + -
680A LEU* 5.2 0.7 - - + -
686A GLY 3.0 9.5 + - - +
688A HIS* 1.3 76.2 - - - +
690A ILE* 1.3 66.0 + - + +
692A LYS* 3.2 13.8 + - - +
693A CYS* 3.2 13.0 + - - -
----------------------------------------------------------
Back to top of page
Residues in contact with ILE 690 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
673A LEU* 4.4 22.7 - - + -
677A THR* 4.4 13.9 - - + +
680A LEU* 3.8 38.8 - - + -
681A SER* 3.7 24.9 - - - +
686A GLY 3.3 3.1 + - - +
687A ASN* 3.5 8.7 - - - +
688A HIS 3.2 0.2 - - - -
689A VAL* 1.3 80.4 - - + +
691A GLN* 1.3 60.9 + - - +
693A CYS* 3.2 18.9 + - - +
694A LEU* 3.5 5.8 + - + +
704A PHE* 4.9 6.3 - - + -
705A ILE* 3.7 23.3 - - + +
725A VAL* 3.8 19.7 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with GLN 691 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
687A ASN* 2.8 43.9 + - - +
688A HIS* 3.8 18.7 + - - +
689A VAL 3.3 0.2 - - - -
690A ILE* 1.3 72.8 - - - +
692A LYS* 1.3 67.6 + - - +
694A LEU* 3.0 12.9 + - - +
695A GLN* 2.9 30.2 + - - +
724A CYS* 3.8 26.8 - - - +
725A VAL* 3.8 12.7 - - + +
728A ARG* 2.9 48.6 + - + +
----------------------------------------------------------
Back to top of page
Residues in contact with LYS 692 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
654A GLN* 3.6 43.7 + - + +
657A ILE* 3.7 18.6 - - + -
658A GLU* 2.7 31.0 + - + +
688A HIS 3.0 12.7 + - - +
689A VAL 3.2 10.7 + - - +
691A GLN* 1.3 76.2 - - - +
693A CYS* 1.3 62.8 - - - +
695A GLN* 3.0 25.9 + - + +
696A ARG* 2.9 52.1 + - + +
----------------------------------------------------------
Back to top of page
Residues in contact with CYS 693 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
657A ILE* 3.8 14.1 - - - +
669A VAL* 4.5 3.4 - - - -
673A LEU* 3.6 30.7 - - - -
689A VAL 3.2 13.3 + - - -
690A ILE* 3.3 12.3 - - - +
691A GLN 3.1 0.6 - - - -
692A LYS* 1.3 79.5 - - - +
694A LEU* 1.3 56.7 + - - +
697A LEU* 2.9 58.0 + - + +
702A PHE* 4.0 4.4 - - + +
704A PHE* 4.5 7.4 - - + -
705A ILE* 3.7 13.9 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with LEU 694 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
690A ILE 3.8 15.7 - - - +
691A GLN* 3.0 8.4 + - - +
693A CYS* 1.3 77.0 - - - +
695A GLN* 1.3 62.4 + - - +
696A ARG 3.3 0.3 + - - -
697A LEU 4.2 8.5 - - - +
702A PHE* 3.1 45.0 - - + -
705A ILE* 4.0 16.6 - - + -
706A PHE* 4.1 13.5 - - + -
725A VAL* 4.0 6.5 - - + +
728A ARG* 3.7 32.3 - - + +
729A CYS* 4.0 24.5 - - - +
732A HIS* 3.5 24.9 + - + +
----------------------------------------------------------
Back to top of page
Residues in contact with GLN 695 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
691A GLN* 2.9 16.1 + - - +
692A LYS* 3.0 37.5 + - + +
694A LEU* 1.3 76.3 - - - +
696A ARG* 1.3 72.6 + - + +
728A ARG* 3.2 31.0 + - - +
732A HIS* 3.7 30.5 + - + +
----------------------------------------------------------
Back to top of page
Residues in contact with ARG 696 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
657A ILE* 4.0 17.3 - - + +
658A GLU* 3.4 59.9 + - + +
692A LYS* 2.9 38.3 + - + +
695A GLN* 1.3 88.7 + - - +
697A LEU* 1.3 69.0 + - + +
----------------------------------------------------------
Back to top of page
Residues in contact with LEU 697 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
657A ILE* 4.2 13.0 - - + -
660A ILE* 4.1 28.0 - - + -
666A ALA* 4.8 9.9 - - + -
669A VAL* 5.0 5.8 - - + -
670A VAL* 4.2 12.6 - - + -
693A CYS* 2.9 46.5 + - + +
694A LEU 4.2 2.6 - - - +
695A GLN 5.2 0.2 - - - -
696A ARG* 1.3 82.2 - - + +
698A LYS* 1.3 63.5 + - - +
699A PRO* 4.1 0.9 - - - +
701A ASN* 3.9 33.7 - - + +
702A PHE* 3.0 21.8 - - + +
704A PHE* 4.9 1.1 - - + -
----------------------------------------------------------
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