Contacts of the helix formed by residues 78 - 99 (chain A) in PDB entry 1OVI
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 ASN 78 (chain A).
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
21A MET* 3.4 11.8 + - + +
24A LEU* 5.6 8.1 - - + +
76A ALA 3.9 0.2 + - - -
77A TRP* 1.3 71.4 - - - +
79A THR* 1.3 52.7 + - - +
80A THR* 3.1 16.9 + - - -
81A LEU* 2.7 72.5 + - + +
82A LEU 2.8 13.9 + - - -
----------------------------------------------------------
Back to top of page
Residues in contact with THR 79 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
72A ARG* 5.4 12.3 - - - +
77A TRP* 2.8 14.5 + - - +
78A ASN* 1.3 70.3 + - - +
80A THR* 1.3 56.2 + - - -
82A LEU* 2.9 12.3 + - + +
83A GLU* 2.7 35.7 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with THR 80 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
78A ASN* 3.1 11.4 + - - -
79A THR* 1.3 77.9 + - - +
81A LEU* 1.3 66.4 + - + +
83A GLU* 3.1 15.6 + - - +
84A GLN* 2.9 29.3 + - + +
----------------------------------------------------------
Back to top of page
Residues in contact with LEU 81 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
17A LEU* 3.3 24.1 - - + +
20A ARG* 3.4 48.7 - - - +
21A MET* 3.9 8.5 - - + -
24A LEU* 5.3 3.1 - - + -
78A ASN* 2.7 49.2 + - + +
80A THR* 1.3 81.2 - - + +
82A LEU* 1.3 58.1 + - - +
84A GLN* 3.2 18.8 - - - +
85A LEU 2.9 23.2 + - - -
----------------------------------------------------------
Back to top of page
Residues in contact with LEU 82 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
21A MET* 3.3 32.2 - - + -
68A PHE* 3.6 38.4 - - + -
72A ARG* 3.2 46.2 - - + +
77A TRP* 4.9 8.5 - - + -
78A ASN 2.8 7.3 + - - +
79A THR* 2.9 15.0 + - + +
81A LEU* 1.3 76.0 - - - +
83A GLU* 1.3 65.4 + - - +
85A LEU* 3.0 14.2 + - + +
86A CYS* 2.9 31.2 + - - -
----------------------------------------------------------
Back to top of page
Residues in contact with GLU 83 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
79A THR 2.7 15.5 + - - +
80A THR* 3.5 18.0 - - - +
82A LEU* 1.3 72.9 - - - +
84A GLN* 1.3 57.8 + - - +
86A CYS* 2.8 17.1 + - + +
87A THR* 2.8 32.8 + - + -
----------------------------------------------------------
Back to top of page
Residues in contact with GLN 84 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
17A LEU* 3.2 33.6 - - + +
20A ARG* 5.8 1.0 - - - -
80A THR* 2.9 14.5 + - - +
81A LEU* 3.2 22.3 - - - +
83A GLU* 1.3 75.9 + - - +
85A LEU* 1.3 63.3 + - - +
87A THR* 3.3 13.7 - - + +
88A GLY* 2.9 22.2 + - - -
----------------------------------------------------------
Back to top of page
Residues in contact with LEU 85 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
14A ASN* 3.3 52.2 - - - +
17A LEU* 3.7 14.0 - - + +
18A LEU* 4.1 14.1 - - + -
21A MET* 4.1 9.6 - - + -
68A PHE* 3.7 35.9 - - + -
81A LEU 2.9 15.4 + - - +
82A LEU* 3.1 24.5 - - + +
84A GLN* 1.3 72.7 - - - +
86A CYS* 1.3 58.5 - - - +
88A GLY* 3.3 0.9 + - - -
89A LEU* 2.8 33.9 + - + +
148A MET* 4.7 1.3 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with CYS 86 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
65A PHE* 3.7 36.4 - - + -
68A PHE* 4.3 22.2 - - - -
72A ARG* 6.2 0.4 - - - -
82A LEU* 2.9 27.6 + - - -
83A GLU* 2.8 19.3 + - + +
85A LEU* 1.3 73.1 - - - +
87A THR* 1.3 57.3 + - - +
89A LEU* 3.5 8.5 - - - +
90A GLN* 2.8 30.8 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with THR 87 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
83A GLU* 2.8 17.5 + - + +
84A GLN* 3.3 24.0 - - + +
86A CYS* 1.3 70.3 - - - +
88A GLY* 1.3 63.4 + - - +
90A GLN* 3.8 8.1 + - - +
91A GLN* 2.9 43.9 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with GLY 88 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
10A ASP* 4.8 10.7 - - - +
13A GLU* 6.5 1.6 - - - -
14A ASN* 5.4 3.1 - - - -
84A GLN 2.9 14.1 + - - -
85A LEU* 3.7 2.7 - - - -
87A THR* 1.3 80.3 - - - +
89A LEU* 1.3 61.9 + - - +
91A GLN* 3.4 16.7 - - - +
92A GLN* 3.1 23.7 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with LEU 89 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
14A ASN* 3.3 27.8 - - - +
61A LEU* 3.4 55.2 - - + +
64A SER* 4.1 11.2 - - - +
65A PHE* 3.5 32.1 - - + +
68A PHE* 5.1 7.0 - - + -
85A LEU* 2.8 20.9 + - + +
86A CYS* 3.5 7.0 - - - +
88A GLY* 1.3 76.3 - - - +
90A GLN* 1.3 57.3 + - - +
92A GLN* 2.8 12.2 + - - +
93A LEU* 2.8 33.3 + - + +
148A MET* 5.7 0.2 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with GLN 90 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
65A PHE* 5.9 6.8 - - + -
86A CYS 2.8 22.3 + - - +
87A THR* 3.8 9.1 + - - +
89A LEU* 1.3 70.5 - - - +
91A GLN* 1.3 68.1 + - + +
93A LEU* 2.9 24.3 + - + +
94A GLU* 2.9 40.7 + - + +
----------------------------------------------------------
Back to top of page
Residues in contact with GLN 91 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
6A ARG* 4.7 13.9 + - - -
10A ASP* 6.3 2.2 - - + -
87A THR* 2.9 30.7 + - - +
88A GLY* 3.4 17.0 - - - +
90A GLN* 1.3 77.9 - - - +
92A GLN* 1.3 57.7 + - + +
94A GLU* 3.8 4.7 - - - +
95A ASP* 2.7 35.8 + - + +
----------------------------------------------------------
Back to top of page
Residues in contact with GLN 92 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
7A LEU* 2.8 47.9 + - - +
10A ASP* 2.9 41.9 + - + +
11A ALA* 3.5 14.0 + - - +
14A ASN* 5.2 3.5 + - - +
57A LEU* 5.2 0.5 - - - +
61A LEU* 3.6 29.0 - - + +
88A GLY 3.1 6.8 + - - +
89A LEU* 2.8 17.0 + - - +
91A GLN* 1.3 73.2 - - + +
93A LEU* 1.3 70.0 + - - +
95A ASP* 4.5 2.9 - - + +
96A LEU* 2.9 33.9 + - + +
152A LEU* 5.8 0.9 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with LEU 93 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
58A TYR* 3.7 31.3 - - + +
61A LEU* 3.7 16.4 - - + -
62A GLN* 3.7 40.2 - - + +
65A PHE* 5.1 11.4 - - + -
89A LEU* 2.8 37.5 + - + +
90A GLN* 2.9 25.4 + - + +
92A GLN* 1.3 77.1 - - - +
94A GLU* 1.3 58.9 + - - +
96A LEU* 3.4 2.6 - - - +
97A ASP* 2.9 25.3 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with GLU 94 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
90A GLN* 2.9 32.1 + - + +
91A GLN* 3.9 4.7 - - - +
93A LEU* 1.3 73.7 - - - +
95A ASP* 1.3 56.8 + - - +
97A ASP* 3.0 7.5 + - + -
98A THR* 2.7 46.3 + - + +
----------------------------------------------------------
Back to top of page
Residues in contact with ASP 95 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
1A CYS 2.5 33.2 + - - -
2A TYR 3.0 15.7 + - - +
3A LEU* 4.1 3.8 - - - +
6A ARG* 3.6 32.0 + - - +
91A GLN* 2.7 23.4 + - + +
92A GLN* 4.4 4.0 - - + +
94A GLU* 1.3 73.1 - - - +
96A LEU* 1.4 63.0 + - + +
98A THR* 3.7 9.2 - - - +
99A CYS* 3.1 22.2 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with LEU 96 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
3A LEU* 3.7 28.8 - - + +
7A LEU* 3.8 24.0 - - + -
54A PHE* 3.6 31.3 - - + +
57A LEU* 3.8 11.0 - - + -
58A TYR* 3.6 25.6 - - + +
61A LEU* 3.9 9.2 - - + -
92A GLN* 2.9 37.3 + - + +
93A LEU 3.4 3.1 - - - +
95A ASP* 1.4 80.5 - - + +
97A ASP* 1.3 70.0 + - - +
99A CYS* 3.4 3.1 - - - +
100A ARG* 3.4 16.3 + - - +
101A GLY 4.2 1.0 + - - -
----------------------------------------------------------
Back to top of page
Residues in contact with ASP 97 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
58A TYR* 3.3 35.6 + - + +
93A LEU 2.9 13.2 + - - +
94A GLU* 3.0 10.3 + - + +
96A LEU* 1.3 75.3 - - - +
98A THR* 1.3 54.8 + - - +
99A CYS 2.6 14.7 + - - -
101A GLY* 2.6 35.0 + - - +
102A PRO* 3.8 15.4 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with THR 98 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
1A CYS* 4.9 8.1 - - + +
94A GLU* 2.7 35.2 + - + +
95A ASP* 3.7 15.7 - - + +
97A ASP* 1.3 74.7 + - - +
99A CYS* 1.3 59.6 + - - +
102A PRO* 4.3 15.6 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with CYS 99 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
1A CYS* 2.0 60.1 - - - -
3A LEU* 3.3 29.6 - - + -
95A ASP 3.1 19.1 - - - +
96A LEU 3.4 4.9 - - - +
97A ASP 2.6 5.9 + - - -
98A THR* 1.3 79.3 - - - +
100A ARG* 1.3 65.4 + - - +
----------------------------------------------------------
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