Contacts of the helix formed by residues 92 - 102 (chain V) in PDB entry 1JJ2
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 ASP 92 (chain V).
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
81V ASP* 2.9 25.9 - - + +
84V VAL* 3.5 16.7 - - - +
90V TYR* 3.5 1.9 - - - +
91V ASP* 1.3 87.6 + - - +
93V ILE* 1.3 64.5 + - - +
94V SER* 3.4 23.5 + - - -
95V GLY* 3.0 22.8 + - - -
96V LEU 3.2 9.4 + - - -
----------------------------------------------------------
Back to top of page
Residues in contact with ILE 93 (chain V).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
63V GLU* 3.8 33.4 - - + +
66V LEU* 4.0 15.9 - - + -
67V ALA* 3.4 30.7 - - + -
79V VAL* 3.6 16.8 - - + +
80V ASP* 3.9 9.2 - - - -
81V ASP* 2.8 25.1 + - - +
84V VAL* 3.7 25.0 - - + +
92V ASP* 1.3 70.5 - - - +
94V SER* 1.3 52.9 + - - +
96V LEU* 2.9 7.2 + - + +
97V ALA* 2.7 32.2 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with SER 94 (chain V).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
59V GLN* 3.1 7.6 + - - -
63V GLU* 2.7 39.0 + - - -
81V ASP* 4.6 0.4 + - - -
92V ASP* 3.2 17.4 + - - -
93V ILE* 1.3 77.7 - - - +
95V GLY* 1.3 57.7 + - - +
98V PHE* 2.9 28.6 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with GLY 95 (chain V).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
90V TYR* 3.2 25.4 - - - -
91V ASP 5.4 0.4 - - - -
92V ASP* 3.0 17.9 + - - -
94V SER* 1.3 79.4 - - - +
96V LEU* 1.3 61.3 + - - +
98V PHE* 3.6 6.2 + - - +
99V ALA* 3.2 17.3 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with LEU 96 (chain V).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
66V LEU* 4.5 11.4 - - + -
79V VAL* 5.4 1.3 - - + -
83V TRP* 6.1 0.2 - - + -
84V VAL* 4.2 26.2 - - + -
88V THR* 4.9 4.5 - - - +
90V TYR* 3.7 20.9 - - + +
92V ASP 3.2 8.7 + - - +
93V ILE* 2.9 9.1 + - + +
95V GLY* 1.3 72.5 - - - +
97V ALA* 1.3 68.9 + - - +
99V ALA* 3.1 4.3 + - - +
100V LEU* 2.9 46.1 + - + +
105V THR* 4.2 4.3 - - + -
106V THR 5.6 0.2 - - - +
107V LEU* 5.1 2.2 - - + -
110V GLN* 4.0 26.2 - - + -
112V LEU* 3.9 27.6 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with ALA 97 (chain V).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
59V GLN* 3.2 21.3 - - - +
62V LEU* 3.8 14.8 - - + +
63V GLU* 3.7 16.4 - - + -
66V LEU* 3.9 19.7 - - + +
93V ILE 2.7 20.2 + - - +
94V SER 3.5 0.2 - - - +
96V LEU* 1.3 72.4 - - - +
98V PHE* 1.3 63.8 + - - +
100V LEU* 3.1 5.0 + - - +
101V LEU* 2.9 25.9 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with PHE 98 (chain V).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
59V GLN* 3.2 22.8 - - - +
94V SER 2.9 17.1 + - - +
95V GLY* 3.8 6.5 - - - +
97V ALA* 1.3 75.7 - - - +
99V ALA* 1.3 56.4 + - + +
101V LEU* 3.4 6.3 + - + +
102V SER* 2.6 57.9 + - - -
----------------------------------------------------------
Back to top of page
Residues in contact with ALA 99 (chain V).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
90V TYR* 3.2 46.0 - - + +
95V GLY 3.2 2.9 + - - +
96V LEU 3.1 7.5 + - - +
98V PHE* 1.3 79.4 - - + +
100V LEU* 1.3 63.8 + - - +
102V SER* 3.2 7.3 + - - -
103V GLU 3.1 2.9 + - - -
104V GLU* 2.8 36.3 + - + -
105V THR* 3.7 9.1 + - + -
----------------------------------------------------------
Back to top of page
Residues in contact with LEU 100 (chain V).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
1V MET* 3.6 24.9 - - + +
34V LEU* 3.5 25.1 - - + -
62V LEU* 4.2 4.0 - - + -
66V LEU* 3.8 32.5 - - + -
96V LEU* 2.9 24.6 + - + +
97V ALA 3.4 4.7 - - - +
99V ALA* 1.3 77.2 - - - +
101V LEU* 1.3 54.3 + - - +
103V GLU* 2.7 26.7 + - - -
105V THR* 3.9 13.9 - - + +
106V THR* 3.9 14.1 - - - -
107V LEU* 3.8 34.1 - - + +
----------------------------------------------------------
Back to top of page
Residues in contact with LEU 101 (chain V).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
1V MET* 3.6 29.1 + - + +
56V GLU* 4.6 16.9 - - + +
57V PRO* 3.7 28.7 - - + +
58V SER 4.2 0.9 - - - +
59V GLN* 3.7 46.4 - - + +
62V LEU* 3.7 15.7 - - + -
97V ALA 2.9 13.4 + - - +
98V PHE* 3.7 7.6 - - + +
100V LEU* 1.3 78.4 - - - +
102V SER* 1.3 56.5 + - - +
103V GLU* 3.2 12.5 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with SER 102 (chain V).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
98V PHE* 2.6 46.5 + - - -
99V ALA* 3.2 11.6 + - - -
101V LEU* 1.3 73.9 - - - +
103V GLU* 1.3 71.6 + - - +
104V GLU* 3.1 16.7 + - - +
----------------------------------------------------------
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