Contacts of the helix formed by residues 132 - 139 (chain J) in PDB entry 1VQ9
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 132 (chain J).
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
19J MET* 3.2 37.7 - - + -
41J ALA 3.5 26.7 - - - +
44J ALA* 3.1 19.1 + - + +
45J VAL* 4.8 0.8 - - - +
46J ILE* 5.1 5.5 - - + +
57J TYR* 5.6 0.7 - - + -
75J PRO* 3.6 27.6 - - + +
78J ILE* 3.5 26.0 - - + -
79J PHE* 3.8 12.6 - - + -
130J VAL 4.2 0.6 + - - -
131J THR* 1.3 71.8 - - - +
133J GLY* 1.3 61.9 + - - +
135J ILE* 3.3 19.0 + - + +
136J SER* 3.1 25.2 + - - -
----------------------------------------------------------
Back to top of page
Residues in contact with GLY 133 (chain J).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
42J GLU* 3.0 16.9 + - - -
75J PRO* 4.6 1.3 - - - -
131J THR* 3.0 11.0 - - - +
132J LEU* 1.3 75.6 - - - +
134J GLU* 1.3 63.0 + - - +
136J SER* 3.3 2.3 + - - -
137J GLU* 3.1 23.3 + - - +
145J TRP* 3.3 33.1 - - - -
----------------------------------------------------------
Back to top of page
Residues in contact with GLU 134 (chain J).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
50J GLU* 4.6 11.9 - - - +
129J PHE* 4.8 2.3 - - - +
130J VAL* 3.2 17.3 - - + +
131J THR* 2.5 48.0 + - + +
133J GLY* 1.3 71.6 - - - +
135J ILE* 1.3 67.3 + - - +
137J GLU* 3.1 16.7 + - - +
138J THR* 3.0 26.0 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with ILE 135 (chain J).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
46J ILE* 4.4 20.6 - - + -
50J GLU* 5.9 0.2 - - - -
53J ILE* 3.7 29.6 - - + -
54J VAL* 4.6 12.6 - - + -
57J TYR* 4.3 26.2 - - + -
78J ILE* 5.4 1.8 - - + -
130J VAL* 3.9 16.6 - - + +
131J THR 3.1 11.1 + - - +
132J LEU* 3.5 18.8 - - + +
134J GLU* 1.3 76.8 - - - +
136J SER* 1.3 58.2 + - - +
138J THR* 3.1 8.9 + - - -
139J LEU* 2.8 51.5 + - + +
----------------------------------------------------------
Back to top of page
Residues in contact with SER 136 (chain J).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
73J LYS 2.7 28.0 + - - -
74J ARG 3.4 0.3 - - - -
75J PRO* 2.7 23.7 - - - +
78J ILE* 4.6 2.1 - - - +
132J LEU 3.1 10.5 + - - -
133J GLY 3.6 3.1 - - - -
134J GLU 3.2 0.2 - - - -
135J ILE* 1.3 76.0 - - - +
137J GLU* 1.3 63.9 + - - +
139J LEU* 3.0 10.3 + - - +
140J GLY 3.1 0.2 + - - -
141J ALA* 2.9 27.3 + - - +
145J TRP* 3.5 24.9 - - - -
----------------------------------------------------------
Back to top of page
Residues in contact with GLU 137 (chain J).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
28030 C 4.4 3.1 + - - -
133J GLY 3.1 16.5 + - - +
134J GLU* 3.1 16.6 + - - +
136J SER* 1.3 77.6 - - - +
138J THR* 1.3 63.2 + - - +
140J GLY* 3.0 14.2 + - - -
141J ALA 4.4 9.5 - - - +
143J LYS* 3.6 37.9 + - + +
145J TRP* 4.0 14.0 + - + -
----------------------------------------------------------
Back to top of page
Residues in contact with THR 138 (chain J).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
27730 G 6.2 0.4 - - - +
28030 C 4.1 15.9 + - - +
50J GLU* 4.5 10.6 + - - -
54J VAL* 3.4 34.4 - - + +
58J GLU* 4.3 12.7 - - - +
134J GLU 3.0 14.0 + - - -
135J ILE* 3.4 10.7 - - - -
137J GLU* 1.3 78.4 - - - +
139J LEU* 1.3 57.8 + - - +
140J GLY 3.0 4.9 + - - -
----------------------------------------------------------
Back to top of page
Residues in contact with LEU 139 (chain J).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
28030 C 4.2 11.2 - - - +
54J VAL* 4.9 3.1 - - + -
57J TYR* 4.2 12.1 - - + +
58J GLU* 3.9 42.0 - - + +
61J VAL* 4.2 18.2 - - + +
71J TYR* 5.4 0.2 - - + -
72J PRO 4.5 0.4 - - - +
73J LYS* 3.7 55.7 + - + +
78J ILE* 4.4 9.4 - - + -
135J ILE* 2.8 32.4 + - + +
136J SER* 3.0 9.1 + - - +
138J THR* 1.3 76.2 - - - +
140J GLY* 1.3 59.5 + - - +
141J ALA 3.5 0.2 - - - -
----------------------------------------------------------
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