Contacts of the helix formed by residues 670 - 679 (chain A) in PDB entry 4OT9
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 670 (chain A).
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
639A HIS* 4.2 0.7 - - - -
662A ASN* 4.1 19.3 + - + +
663A ALA 3.2 15.0 - - - +
664A ARG* 3.5 27.6 - - + +
669A ASN* 1.3 74.1 - - - +
671A PRO* 1.3 71.2 - - - +
672A LEU* 3.5 17.2 + - - +
673A HIS* 2.7 42.4 + - + +
674A LEU* 3.0 8.5 - - - +
693A ASP 5.1 0.7 + - - -
696A ALA* 4.6 10.5 - - + +
733A PRO* 5.3 0.2 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with PRO 671 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
638A LEU* 4.6 18.4 - - + +
639A HIS* 4.1 6.6 - - + +
642A THR* 3.8 26.9 + - + +
661A VAL* 2.9 31.2 - - + +
662A ASN* 5.3 0.4 - - - +
663A ALA* 3.8 10.1 - - + +
670A THR* 1.3 87.6 - - - +
672A LEU* 1.3 62.5 + - + +
673A HIS 3.0 1.0 + - - -
674A LEU* 3.5 10.5 + - + +
675A ALA* 3.2 25.1 + - - +
687A LEU* 3.4 20.3 - - + +
692A ALA* 5.9 0.4 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with LEU 672 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
662A ASN* 4.9 1.1 - - - +
670A THR* 3.1 11.6 - - - +
671A PRO* 1.3 81.8 - - - +
673A HIS* 1.3 63.2 + - - +
675A ALA 4.3 0.2 - - - -
676A ALA* 3.5 16.9 + - - +
684A THR* 3.6 16.8 - - + +
687A LEU* 4.0 9.0 - - + -
688A LEU* 3.5 32.5 - - + -
692A ALA* 3.8 25.8 - - + +
693A ASP 3.3 28.9 - - - +
694A ILE* 3.7 17.9 - - + -
733A PRO* 4.0 18.7 - - + +
----------------------------------------------------------
Back to top of page
Residues in contact with HIS 673 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
664A ARG* 5.0 0.6 + - - -
668A GLY 4.6 0.6 + - - -
669A ASN* 3.1 27.0 + - + +
670A THR* 2.7 43.9 + - + +
672A LEU* 1.3 75.7 - - - +
674A LEU* 1.3 67.5 + - - +
675A ALA 3.1 1.3 - - - -
676A ALA* 3.0 15.1 + - - +
677A GLY* 3.0 11.8 + - - -
696A ALA* 3.2 29.1 - - + +
697A GLU 4.1 2.2 + - - -
698A ASN* 3.6 26.1 + - - -
731A HIS 3.9 1.6 - - - -
732A THR 3.9 0.6 - - - -
733A PRO* 3.4 38.4 - - + +
736A LEU* 4.4 9.3 - - + +
----------------------------------------------------------
Back to top of page
Residues in contact with LEU 674 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
635A ARG* 4.0 5.2 - - - +
639A HIS* 3.8 32.1 - - + +
642A THR* 4.2 9.2 - - - +
643A GLU* 3.3 28.5 - - - +
669A ASN* 4.5 9.6 - - + -
670A THR 3.0 26.5 - - - +
671A PRO* 3.8 8.1 - - + +
673A HIS* 1.3 80.2 - - + +
675A ALA* 1.3 62.5 + - - +
677A GLY* 3.4 1.5 + - - +
678A LEU* 2.9 41.4 + - + +
680A TYR* 5.2 0.9 - - - -
802A SO4 4.0 18.4 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with ALA 675 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
642A THR* 5.0 2.1 - - - -
671A PRO 3.2 16.3 + - - +
672A LEU 4.2 3.4 - - - +
673A HIS 3.0 0.4 + - - -
674A LEU* 1.3 79.9 - - - +
676A ALA* 1.3 63.6 + - - +
678A LEU* 3.7 1.2 - - - +
679A GLY 2.9 18.9 + - - -
680A TYR* 3.1 22.7 + - + -
683A LEU* 4.0 16.8 - - + -
684A THR* 4.1 15.3 - - - +
687A LEU* 3.8 19.5 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with ALA 676 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
672A LEU* 3.5 13.3 + - + +
673A HIS 3.0 7.9 + - - +
675A ALA* 1.3 78.2 - - - +
677A GLY* 1.3 66.0 + - - +
679A GLY* 3.0 14.6 + - - -
684A THR* 4.3 7.1 + - + -
733A PRO* 3.6 28.0 - - + +
736A LEU* 3.5 6.2 - - + +
737A THR* 3.8 17.0 - - - +
742A VAL* 3.8 18.4 - - + -
746A LEU* 6.4 1.3 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with GLY 677 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
673A HIS 3.0 12.1 + - - -
674A LEU* 3.8 3.1 - - - -
676A ALA* 1.3 78.9 - - - +
678A LEU* 1.3 64.6 + - - +
679A GLY* 4.3 0.3 - - - -
736A LEU* 3.1 28.1 + - - +
737A THR* 4.7 5.0 - - - -
738A CYS* 4.7 5.7 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with LEU 678 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
642A THR 5.4 0.7 - - - +
643A GLU* 4.7 12.6 - - - +
674A LEU* 2.9 36.5 + - + +
677A GLY* 1.3 77.9 - - - +
679A GLY* 1.3 61.4 + - - +
680A TYR* 3.2 47.0 - - + +
----------------------------------------------------------
Back to top of page
Residues in contact with GLY 679 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
675A ALA 2.9 5.1 + - - -
676A ALA 3.0 13.4 + - - -
677A GLY 4.3 0.7 - - - -
678A LEU* 1.3 80.2 - - - +
680A TYR* 1.3 66.6 + - - +
681A PRO* 3.0 15.0 - - - +
738A CYS 5.9 0.4 - - - -
739A SER* 4.2 14.6 + - - -
742A VAL* 3.6 15.0 - - - +
----------------------------------------------------------
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