Contacts of the helix formed by residues 56 - 62 (chain V) 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 LEU 56 (chain V).
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
780N VAL* 3.7 40.2 - - + -
783N THR* 5.3 4.7 - - + -
799N PRO* 4.4 7.4 - - + -
816N GLU 3.3 26.5 - - - +
817N LEU* 4.3 7.0 - - + -
818N PRO* 5.7 0.9 - - + -
1V MET* 2.4 27.4 - - + +
54V VAL* 2.7 27.6 + - + +
55V ASP* 1.3 66.1 - - - +
57V ILE* 1.3 55.9 + - - +
59V LYS* 2.5 49.5 + - + +
60V PHE* 2.8 29.7 + - + -
----------------------------------------------------------
Back to top of page
Residues in contact with ILE 57 (chain V).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
57O VAL* 5.1 1.3 - - + -
58O LEU* 3.6 18.4 - - + -
146O LYS* 3.6 33.2 - - + +
1V MET* 2.5 16.1 - - - +
2V ILE* 3.3 53.4 - - + +
55V ASP* 3.3 22.2 - - - +
56V LEU* 1.3 70.0 - - - +
58V GLU* 1.3 61.1 + - - +
60V PHE* 2.7 19.7 + - + +
61V LEU* 2.7 47.6 + - + +
----------------------------------------------------------
Back to top of page
Residues in contact with GLU 58 (chain V).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
110O THR* 4.5 12.5 + - - +
146O LYS* 2.7 31.9 + - - +
55V ASP* 3.2 31.0 - - + +
56V LEU 2.7 4.0 + - - -
57V ILE* 1.3 80.1 - - - +
59V LYS* 1.3 62.6 + - + +
61V LEU* 3.7 13.3 + - - +
62V ARG* 3.6 16.6 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with LYS 59 (chain V).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
190N TYR* 3.3 40.7 - - - +
197N PHE* 3.6 39.2 - - + -
783N THR* 4.8 13.5 - - + -
816N GLU* 3.7 15.5 - - - +
54V VAL* 5.8 4.7 - - - +
55V ASP 4.9 2.0 - - - +
56V LEU* 2.5 36.7 + - + +
58V GLU* 1.3 76.5 - - + +
60V PHE* 1.3 64.9 + - - +
62V ARG* 3.4 6.8 + - - +
63V TYR* 3.8 4.7 - - - -
----------------------------------------------------------
Back to top of page
Residues in contact with PHE 60 (chain V).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
780N VAL* 4.7 2.2 - - + -
783N THR* 3.3 40.6 - - + -
785N TYR* 3.5 22.9 - + - -
786N ASN* 5.7 2.2 - - + -
57O VAL* 3.3 37.9 - - + +
58O LEU* 6.3 1.1 - - + -
1V MET* 3.1 41.7 - - + -
56V LEU* 2.8 31.5 + - + -
57V ILE* 2.7 29.6 + - + +
59V LYS* 1.3 78.6 - - - +
61V LEU* 1.3 61.1 + - - +
63V TYR* 3.1 26.8 + + - +
----------------------------------------------------------
Back to top of page
Residues in contact with LEU 61 (chain V).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
57O VAL* 4.3 9.2 - - + -
110O THR* 4.8 12.1 - - + +
146O LYS* 3.5 26.9 - - + +
147O LEU* 3.4 34.1 - - - +
148O ARG* 3.3 39.5 - - + +
151O GLN* 4.2 9.1 + - - +
57V ILE* 2.7 44.2 + - + +
58V GLU* 3.9 17.7 - - - +
59V LYS 3.3 0.2 - - - -
60V PHE* 1.3 66.6 - - - +
62V ARG* 1.3 53.5 + - - +
63V TYR* 2.7 18.3 + - - +
64V ASN 4.5 0.5 + - - -
----------------------------------------------------------
Back to top of page
Residues in contact with ARG 62 (chain V).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
186N GLU* 3.2 36.9 + - - +
187N SER* 3.7 31.5 - - - +
190N TYR* 3.1 46.3 + - + +
148O ARG* 4.0 20.2 + - - +
58V GLU 3.6 9.8 + - - +
59V LYS* 3.4 5.1 + - - +
60V PHE 3.2 1.4 - - - -
61V LEU* 1.3 78.3 - - - +
63V TYR* 1.3 61.9 + - - +
----------------------------------------------------------
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