Contacts of the helix formed by residues 680 - 687 (chain N) in PDB entry 2JA7
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 680 (chain N).
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
36N ALA* 5.0 3.6 - - - -
40N GLU* 3.5 14.3 + - + +
661N LEU* 3.9 2.6 - - - +
664N THR* 6.4 0.4 - - + -
678N GLU* 3.8 13.1 + - - +
679N TYR* 1.3 75.3 - - - +
681N TRP* 1.3 62.4 + - - +
682N SER* 3.1 19.9 + - - -
683N SER* 2.4 29.9 + - - -
684N LEU* 3.1 17.6 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with TRP 681 (chain N).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
33N VAL* 3.6 35.0 - - + -
36N ALA* 3.9 16.9 + - - +
37N PHE* 3.7 42.8 - + + -
40N GLU* 3.8 25.1 - - + +
41N LYS* 4.9 2.7 - - + -
542N MET* 4.7 4.3 - - + -
636N PRO* 3.6 36.1 - - + -
680N THR* 1.3 76.3 - - - +
682N SER* 1.3 59.7 + - - +
683N SER 2.9 1.3 - - - -
684N LEU* 2.5 46.6 + - + +
685N LEU* 3.0 16.5 + - + +
690N VAL* 4.1 22.0 - - + -
692N TYR* 2.9 33.6 + + - -
743N ILE* 4.9 2.2 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with SER 682 (chain N).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
40N GLU* 3.4 20.2 + - - -
680N THR* 3.1 9.8 + - - -
681N TRP* 1.3 81.5 - - - +
683N SER* 1.3 49.9 + - - +
685N LEU* 3.1 14.6 + - - +
686N ASN* 2.7 53.2 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with SER 683 (chain N).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
678N GLU 5.3 2.0 - - - -
679N TYR* 3.2 31.3 - - - -
680N THR* 2.4 47.5 + - - -
681N TRP 2.7 4.2 + - - -
682N SER* 1.3 72.4 - - - +
684N LEU* 1.3 53.2 + - - -
685N LEU 2.7 15.1 + - - -
686N ASN* 3.2 4.4 + - - +
687N GLU* 3.0 33.0 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with LEU 684 (chain N).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
33N VAL* 4.6 17.9 - - + -
36N ALA* 4.4 4.0 - - + -
653N VAL* 4.4 26.9 - - + -
657N HIS* 5.2 4.0 - - + -
661N LEU* 3.5 35.0 - - + -
679N TYR* 5.0 7.4 - - + +
680N THR 3.1 23.3 - - - +
681N TRP* 2.5 35.6 + - + +
683N SER* 1.3 75.7 + - - +
685N LEU* 1.3 54.0 + - - -
687N GLU 4.3 1.1 - - - -
689N LEU* 3.4 23.0 + - + +
690N VAL* 3.2 34.7 + - + +
----------------------------------------------------------
Back to top of page
Residues in contact with LEU 685 (chain N).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
604N ARG* 5.3 3.5 - - + +
605N ARG* 3.6 10.6 - - - +
611N PRO* 3.5 42.8 - - + -
681N TRP* 3.0 12.8 + - + +
682N SER* 3.2 21.1 - - - +
683N SER 2.7 1.6 + - - -
684N LEU* 1.3 78.6 - - - +
686N ASN* 1.3 62.5 + - - +
687N GLU 3.0 10.1 + - - -
688N GLY* 3.1 14.0 + - - -
689N LEU 4.4 0.2 + - - -
690N VAL* 3.3 23.4 - - + +
691N GLU* 4.9 6.3 - - + -
692N TYR* 4.4 28.0 - - + +
----------------------------------------------------------
Back to top of page
Residues in contact with ASN 686 (chain N).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
604N ARG 5.4 0.2 - - - +
605N ARG 3.9 5.8 - - - +
606N LYS* 3.5 27.0 - - - +
607N GLY* 3.8 11.8 - - - -
611N PRO* 4.6 5.7 - - - +
682N SER* 2.7 38.9 + - - +
683N SER* 3.2 4.7 + - - +
685N LEU* 1.3 79.9 - - - +
687N GLU* 1.3 59.3 + - - +
688N GLY 3.4 2.0 - - - -
----------------------------------------------------------
Back to top of page
Residues in contact with GLU 687 (chain N).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
605N ARG 4.0 0.2 - - - -
657N HIS* 3.4 18.4 - - - -
660N LYS* 5.2 5.1 + - - -
679N TYR* 3.3 37.5 + - - -
683N SER* 3.0 17.4 + - - +
685N LEU 3.0 1.6 - - - -
686N ASN* 1.3 80.0 - - - +
688N GLY* 1.3 66.6 + - - +
689N LEU* 3.0 22.6 - - + +
----------------------------------------------------------
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