Contacts of the helix formed by residues 683 - 692 (chain M) in PDB entry 6G0L
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 ARG 683 (chain M).
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
263M THR* 5.9 4.8 - - - +
265M GLU* 5.5 4.8 + - - -
681M MET 4.0 1.5 + - - +
682M THR* 1.3 80.1 + - - +
684M GLU* 1.3 65.1 + - - +
685M ASN 3.3 1.3 - - - -
686M VAL* 3.6 6.6 + - - +
687M LEU* 3.5 20.1 + - - +
733M ILE* 4.3 33.7 - - + +
----------------------------------------------------------
Back to top of page
Residues in contact with GLU 684 (chain M).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
682M THR* 3.8 1.8 + - - +
683M ARG* 1.3 77.2 - - - +
685M ASN* 1.3 65.5 + - - +
687M LEU* 3.6 17.0 + - - +
688M ARG* 2.9 36.4 + - + +
733M ILE* 6.1 1.4 - - - +
734M LYS* 5.4 5.2 + - - -
----------------------------------------------------------
Back to top of page
Residues in contact with ASN 685 (chain M).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
673M LEU* 4.0 11.8 - - + +
675M LYS* 3.5 39.2 + - + +
676M PHE 5.4 2.2 - - - -
682M THR* 3.0 31.7 + - + +
683M ARG 3.3 0.4 - - - -
684M GLU* 1.3 81.3 - - - +
686M VAL* 1.3 59.8 + - - +
688M ARG* 3.8 14.4 + - - +
689M GLY* 2.9 25.3 + - - -
----------------------------------------------------------
Back to top of page
Residues in contact with VAL 686 (chain M).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
669M GLU* 6.0 3.6 - - + +
673M LEU* 4.3 26.4 - - + +
681M MET* 5.2 5.6 - - - -
682M THR* 3.8 34.8 - - + +
683M ARG* 3.9 5.8 - - - +
684M GLU 3.3 0.8 - - - -
685M ASN* 1.3 77.5 - - - +
687M LEU* 1.3 57.3 + - - +
689M GLY 3.4 2.1 + - - -
690M LEU* 2.9 33.5 + - + +
733M ILE* 6.3 3.1 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with LEU 687 (chain M).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
683M ARG 3.5 13.0 + - - +
684M GLU* 4.1 16.8 - - - +
685M ASN 3.4 0.2 - - - -
686M VAL* 1.3 75.4 - - - +
688M ARG* 1.3 62.5 + - - +
690M LEU* 3.1 8.9 + - + +
691M ILE* 2.9 38.8 + - + +
730M TYR* 3.6 37.5 - - + +
733M ILE* 3.8 38.3 - - + +
734M LYS* 3.8 34.1 - - + +
----------------------------------------------------------
Back to top of page
Residues in contact with ARG 688 (chain M).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
675M LYS* 3.1 30.5 - - - +
684M GLU* 2.9 27.3 + - + +
685M ASN* 3.8 13.3 + - - +
686M VAL 3.3 0.2 - - - -
687M LEU* 1.3 79.9 - - - +
689M GLY* 1.3 68.5 + - - +
690M LEU 3.4 0.7 + - - -
691M ILE* 3.4 9.4 - - + +
692M MET* 3.4 62.7 + - + +
----------------------------------------------------------
Back to top of page
Residues in contact with GLY 689 (chain M).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
663M TYR* 3.1 18.7 + - - -
672M VAL* 4.2 19.0 - - - +
673M LEU* 5.3 5.2 - - - -
685M ASN 2.9 18.3 + - - -
686M VAL* 3.6 3.6 - - - -
688M ARG* 1.3 84.5 - - - +
690M LEU* 1.3 58.8 + - - +
692M MET* 4.4 4.2 - - - +
693M SER* 3.8 12.6 + - - -
----------------------------------------------------------
Back to top of page
Residues in contact with LEU 690 (chain M).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
661M HIS* 4.3 11.3 - - + +
663M TYR* 3.6 35.0 - - + +
686M VAL* 2.9 21.2 + - + +
687M LEU* 3.1 10.5 + - + +
689M GLY* 1.3 78.7 - - - +
691M ILE* 1.3 60.2 + - - +
693M SER* 2.8 21.5 + - - -
697M MET* 4.2 10.2 - - + +
726M ILE* 4.4 15.3 - - + +
729M ASP* 5.4 3.8 - - + -
730M TYR* 4.0 37.0 - - + +
733M ILE* 6.5 1.3 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with ILE 691 (chain M).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
687M LEU* 2.9 24.1 + - + +
688M ARG* 3.4 14.4 - - + +
690M LEU* 1.3 75.0 - - - +
692M MET* 1.3 68.8 + - + +
693M SER 3.2 2.8 + - - -
694M SER 3.1 21.8 + - - +
697M MET* 3.3 28.8 - - + +
698M VAL* 3.3 15.6 - - + +
701M ASP* 3.8 23.6 - - + +
730M TYR* 3.3 30.7 - - + +
----------------------------------------------------------
Back to top of page
Residues in contact with MET 692 (chain M).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
619M SER* 4.9 6.8 + - - -
620M ASP* 5.6 1.0 - - - +
621M VAL* 5.8 0.5 - - - +
688M ARG* 3.4 53.0 + - + +
689M GLY* 4.4 3.1 - - - -
691M ILE* 1.3 82.6 - - + +
693M SER* 1.3 62.2 + - - +
694M SER* 3.3 2.8 + - - -
698M VAL* 4.1 14.8 - - + -
----------------------------------------------------------
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