Contacts of the helix formed by residues 96 - 107 (chain A) in PDB entry 2J9R
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 96 (chain A).
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
70A ALA* 5.6 0.9 - - - +
71A SER* 3.8 10.3 - - - -
72A LYS* 3.4 46.4 + - + +
94A ASP* 2.9 22.7 + - - +
95A GLY* 1.3 76.0 - - - +
97A ILE* 1.3 63.9 + - - +
98A VAL 3.2 2.7 - - - -
99A GLU* 2.9 15.3 + - - +
100A VAL* 2.9 21.1 + - + -
----------------------------------------------------------
Back to top of page
Residues in contact with ILE 97 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
71A SER* 3.4 25.7 + - - +
74A ILE* 4.3 6.7 - - + -
87A ILE* 4.2 16.6 - - + -
90A VAL* 4.6 12.8 - - + +
93A PHE* 3.7 32.5 - - + +
94A ASP 3.2 14.8 + - - +
95A GLY 3.3 0.6 - - - -
96A ASP* 1.3 78.1 - - - +
98A VAL* 1.3 66.7 + - + +
100A VAL* 4.2 2.9 - - + -
101A VAL* 3.0 40.7 + - + +
127A GLN* 3.6 26.5 - - + -
131A LEU* 4.5 10.5 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with VAL 98 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
95A GLY 5.0 4.5 - - - +
96A ASP 3.2 0.8 - - - -
97A ILE* 1.3 78.8 - - - +
99A GLU* 1.3 58.1 + - - +
101A VAL* 3.5 3.6 - - - +
102A GLN* 3.0 31.3 + - + +
127A GLN* 4.0 26.9 - - + +
130A GLN* 3.7 30.5 - - + -
131A LEU* 4.1 13.0 - - + -
134A ILE* 3.9 26.5 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with GLU 99 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
72A LYS* 3.9 25.7 + - - -
95A GLY 5.3 0.2 + - - -
96A ASP* 2.9 13.5 + - - +
98A VAL* 1.3 75.8 - - - +
100A VAL* 1.3 67.8 + - + +
102A GLN* 3.3 7.4 + - + +
103A VAL* 2.9 44.4 + - + +
----------------------------------------------------------
Back to top of page
Residues in contact with VAL 100 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
71A SER* 3.8 38.1 - - - +
72A LYS* 3.9 21.3 - - + +
74A ILE* 4.1 15.9 - - + -
75A PHE* 4.1 20.5 - - + -
96A ASP* 2.9 18.3 + - + +
97A ILE* 3.9 10.3 - - + +
99A GLU* 1.3 78.7 - - + +
101A VAL* 1.3 63.4 + - + +
103A VAL* 3.4 2.4 + - - +
104A LEU* 3.1 44.0 + - + +
----------------------------------------------------------
Back to top of page
Residues in contact with VAL 101 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
10A ILE* 3.9 22.3 - - + +
87A ILE* 3.9 28.3 - - + -
97A ILE* 3.0 25.3 + - + +
98A VAL 3.5 6.7 - - - +
100A VAL* 1.3 73.5 - - + +
102A GLN* 1.3 68.6 + - - +
104A LEU* 3.1 7.7 + - + +
105A ALA* 2.9 26.2 + - - +
111A VAL* 4.1 17.5 - - + +
113A VAL* 4.3 7.4 - - + -
131A LEU* 3.5 27.4 - - + -
134A ILE* 4.0 2.0 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with GLN 102 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
10A ILE* 3.7 12.0 - - - +
98A VAL* 3.0 17.8 + - + +
99A GLU* 3.6 8.1 - - + +
101A VAL* 1.3 76.8 - - - +
103A VAL* 1.3 59.8 + - + +
105A ALA* 3.5 3.8 + - - +
106A ASN* 2.9 47.9 + - - +
134A ILE* 3.7 43.7 + - + +
----------------------------------------------------------
Back to top of page
Residues in contact with VAL 103 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
75A PHE* 4.1 17.3 - - + -
99A GLU* 2.9 39.6 + - + +
100A VAL 3.9 3.4 - - - +
102A GLN* 1.3 74.2 - - + +
104A LEU* 1.3 60.9 + - - +
106A ASN* 3.2 10.9 + - + +
107A ARG* 2.9 61.8 + - + +
----------------------------------------------------------
Back to top of page
Residues in contact with LEU 104 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
74A ILE* 4.1 16.6 - - + -
75A PHE* 3.7 20.2 - - + -
78A ILE* 3.6 24.0 - - + -
85A ILE* 4.0 25.1 - - + -
87A ILE* 5.2 1.6 - - + -
100A VAL* 3.1 37.0 + - + +
101A VAL* 3.1 8.3 + - + +
103A VAL* 1.3 73.2 - - - +
105A ALA* 1.3 64.3 - - - +
107A ARG* 3.0 14.4 + - - +
109A TYR* 3.2 39.4 + - + -
111A VAL* 3.6 16.8 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with ALA 105 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
6A GLN 3.7 1.8 - - - +
8A GLY* 3.3 19.2 + - - +
9A TRP* 4.0 17.5 - - - +
10A ILE* 3.9 23.6 - - + -
101A VAL 2.9 16.1 + - - +
102A GLN* 3.7 7.6 - - - +
104A LEU* 1.3 76.5 - - - +
106A ASN* 1.3 57.5 + - - +
108A GLY 2.8 17.5 + - - -
109A TYR 3.8 11.4 - - - -
111A VAL* 4.0 3.2 - - + +
136A GLU* 5.4 2.0 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with ASN 106 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
3A LEU* 6.1 4.6 - - + +
4A ILE 4.5 1.9 - - - +
5A ASN* 3.2 41.1 + - - +
6A GLN* 2.9 30.6 + - - +
102A GLN* 2.9 39.2 + - - +
103A VAL* 3.2 12.6 + - - +
105A ALA* 1.3 76.9 - - - +
107A ARG* 1.3 59.4 + - + +
108A GLY 3.3 0.2 - - - -
----------------------------------------------------------
Back to top of page
Residues in contact with ARG 107 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
6A GLN* 3.2 23.2 + - - +
75A PHE* 3.9 26.9 - - - +
103A VAL* 2.9 35.2 + - + +
104A LEU* 3.4 12.4 - - - +
105A ALA 3.0 0.6 - - - -
106A ASN* 1.3 78.4 - - + +
108A GLY* 1.3 57.6 + - - +
109A TYR* 3.6 23.0 - - + -
----------------------------------------------------------
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