Contacts of the helix formed by residues 51 - 70 (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 ALA 51 (chain A).
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
50A GLU* 1.3 76.6 - - - +
52A GLN* 1.4 56.1 + - - +
53A ALA* 3.2 3.1 - - - -
54A PHE* 2.8 32.3 + - + +
55A CYS* 2.9 14.0 + - + -
100A ARG* 4.0 17.3 - - + +
104A MET* 4.0 31.2 - - + -
107A LYS* 5.0 12.3 - - + +
108A ASP* 6.0 3.8 - - + +
----------------------------------------------------------
Back to top of page
Residues in contact with GLN 52 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
41A GLU* 5.9 1.7 - - - +
42A MET* 5.2 2.6 - - - +
46A ASP* 4.4 23.3 + - - +
50A GLU* 3.5 17.1 - - + +
51A ALA* 1.4 76.9 - - - +
53A ALA* 1.3 65.8 + - - +
55A CYS* 2.9 8.3 + - - -
56A VAL* 2.8 46.1 + - + +
107A LYS* 6.1 0.4 - - - +
111A LEU* 3.8 36.6 - - + +
114A MET* 4.0 15.0 - - - +
116A PRO* 4.7 10.7 - - - +
117A ILE* 4.6 5.6 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with ALA 53 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
50A GLU* 5.2 3.1 - - - +
51A ALA 4.6 1.3 - - - +
52A GLN* 1.3 79.9 - - - +
54A PHE* 1.3 77.0 + - + +
56A VAL* 3.6 6.9 + - - +
57A LEU* 3.2 23.9 + - - +
158A LEU* 6.4 3.1 - - + -
159A GLN* 6.3 3.8 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with PHE 54 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
3A LEU* 3.4 53.4 - - + -
7A LEU* 4.6 10.1 - - + -
50A GLU 5.2 0.9 - - - -
51A ALA* 2.8 14.5 + - + +
53A ALA* 1.3 83.2 - - + +
55A CYS* 1.4 67.9 + - - +
57A LEU* 3.2 7.6 - - - +
58A TYR* 2.9 23.5 + - - +
96A LEU* 3.6 11.9 - - + +
100A ARG* 3.4 54.3 - - + -
159A GLN* 5.9 4.3 - - + -
162A LEU* 4.6 22.0 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with CYS 55 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
51A ALA* 2.9 14.6 + - + +
52A GLN* 2.9 8.6 + - - +
54A PHE* 1.4 75.6 - - - +
56A VAL* 1.3 53.4 + - - +
58A TYR* 2.8 15.0 + - - +
59A GLU* 2.7 43.1 + - - +
108A ASP* 3.0 38.1 - - - +
111A LEU* 3.5 26.5 - - + -
117A ILE* 5.4 4.3 - - - -
----------------------------------------------------------
Back to top of page
Residues in contact with VAL 56 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
42A MET* 3.7 46.0 - - + -
52A GLN* 2.8 44.4 + - + +
53A ALA* 3.7 6.3 - - - +
55A CYS* 1.3 70.5 - - - +
57A LEU* 1.3 70.8 + - + +
59A GLU* 3.4 8.4 + - - +
60A MET* 3.1 26.7 + - + +
117A ILE* 4.8 14.1 - - + -
120A VAL* 5.1 6.6 - - + +
158A LEU* 6.4 1.6 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with LEU 57 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
7A LEU* 4.0 25.8 - - + -
11A ALA* 6.5 1.6 - - + -
53A ALA 3.2 12.3 + - - +
54A PHE* 3.2 13.0 - - - +
56A VAL* 1.3 87.6 - - + +
58A TYR* 1.4 51.8 + - - +
60A MET* 2.9 7.0 + - + +
61A LEU* 2.7 54.5 + - + -
92A GLN* 5.2 0.4 - - - +
96A LEU* 3.8 6.3 - - + -
152A LEU* 6.1 1.8 - - + -
155A SER* 2.3 44.6 - - - +
159A GLN* 3.7 23.6 - - + +
----------------------------------------------------------
Back to top of page
Residues in contact with TYR 58 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
54A PHE 2.9 9.1 + - - +
55A CYS* 2.8 16.3 + - - +
57A LEU* 1.4 74.7 - - - +
59A GLU* 1.3 62.6 + - - +
61A LEU* 3.7 6.1 - - - -
62A GLN* 3.0 51.3 + - - +
93A LEU* 3.7 49.3 - - + +
96A LEU* 3.6 14.4 - - + +
97A ASP* 3.3 35.5 + - + +
108A ASP* 4.8 14.8 - - - -
----------------------------------------------------------
Back to top of page
Residues in contact with GLU 59 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
55A CYS* 2.7 24.7 + - - +
56A VAL* 3.6 8.5 - - - +
58A TYR* 1.3 74.5 - - - +
60A MET* 1.3 66.0 + - - +
62A GLN* 3.2 12.3 - - - +
63A GLN* 2.8 58.3 + - - +
117A ILE* 3.5 17.4 - - + +
120A VAL* 3.9 15.0 - - + -
121A LYS* 3.1 32.2 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with MET 60 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
38A LEU* 5.9 4.0 - - + -
39A PRO* 6.3 1.6 - - + -
42A MET* 4.8 19.3 - - + -
56A VAL* 3.1 13.4 + - + +
57A LEU* 2.9 9.1 + - + +
59A GLU* 1.3 82.6 - - - +
61A LEU* 1.3 55.1 + - + +
63A GLN* 3.1 1.9 + - - +
64A SER* 2.8 36.8 + - - -
120A VAL* 5.0 9.2 - - + -
123A TYR* 5.1 5.8 - - + -
124A PHE* 3.6 33.7 - - + -
151A ALA* 3.4 45.1 - - + +
152A LEU* 5.3 0.7 - - - -
155A SER* 4.5 14.8 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with LEU 61 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
14A ASN* 5.4 0.2 - - - +
57A LEU* 2.7 35.5 + - + +
58A TYR* 3.3 11.7 - - - +
59A GLU 3.2 0.2 + - - -
60A MET* 1.3 77.1 - - + +
62A GLN* 1.3 64.3 + - - +
64A SER* 3.1 17.8 - - - -
65A PHE 3.2 4.3 + - - -
89A LEU* 3.4 31.2 - - + +
92A GLN* 3.6 41.7 - - + +
93A LEU* 3.7 10.1 - - + +
96A LEU* 3.9 27.6 - - + -
152A LEU* 5.3 12.8 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with GLN 62 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
58A TYR* 3.0 54.2 + - - +
59A GLU* 3.2 20.6 - - - +
61A LEU* 1.3 77.3 - - - +
63A GLN* 1.3 60.4 + - + +
65A PHE* 2.8 24.1 + - + +
66A ASN* 2.8 26.5 + - - +
93A LEU* 3.7 26.8 - - + +
----------------------------------------------------------
Back to top of page
Residues in contact with GLN 63 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
59A GLU* 2.8 58.0 + - - +
60A MET 3.7 3.4 - - - +
62A GLN* 1.3 76.6 - - + +
64A SER* 1.3 63.6 + - - +
66A ASN* 2.9 21.1 + - + +
67A LEU* 2.9 25.9 + - + +
120A VAL* 4.0 7.2 - - - +
121A LYS* 4.4 14.1 - - - +
124A PHE* 2.9 52.3 - - + +
128A HIS* 4.6 5.7 + - + -
----------------------------------------------------------
Back to top of page
Residues in contact with SER 64 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
60A MET* 2.8 14.0 + - - -
61A LEU* 3.1 17.0 - - - -
63A GLN* 1.3 75.8 - - - +
65A PHE* 1.3 59.9 + - - -
67A LEU* 3.0 17.5 + - - +
68A PHE* 3.2 21.1 + - - -
89A LEU* 4.1 6.9 - - - +
124A PHE* 4.1 9.7 - - - -
148A MET* 3.0 44.9 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with PHE 65 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
61A LEU 3.2 3.0 + - - -
62A GLN* 2.8 22.9 + - + +
64A SER* 1.3 73.4 - - - +
66A ASN* 1.3 64.1 + - - -
68A PHE* 2.8 21.7 + - + +
69A HIS* 3.0 39.4 + + + -
86A CYS* 3.7 46.9 - - + -
89A LEU* 3.5 16.4 - - + +
90A GLN* 5.9 6.1 - - + -
93A LEU* 5.1 9.4 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with ASN 66 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
62A GLN* 2.8 35.6 + - - +
63A GLN* 2.9 26.3 + - + +
65A PHE* 1.3 76.9 - - - +
67A LEU* 1.3 64.6 + - + +
69A HIS* 3.4 24.6 - - - +
70A THR* 3.6 8.7 + - - -
128A HIS* 5.0 9.9 - - + +
----------------------------------------------------------
Back to top of page
Residues in contact with LEU 67 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
63A GLN 2.9 18.9 + - - +
64A SER* 3.0 14.5 + - - +
66A ASN* 1.3 78.1 - - - +
68A PHE* 1.3 61.7 - - + +
69A HIS 3.1 0.2 - - - -
70A THR* 3.0 21.5 + - - -
124A PHE* 3.8 22.9 - - + -
127A ILE* 3.9 18.2 - - + -
128A HIS* 3.7 32.8 - - + +
131A LEU* 4.9 6.7 - - + -
141A TRP* 3.1 28.7 - - + -
144A VAL* 3.7 27.4 - - + +
148A MET* 5.4 9.6 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with PHE 68 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
18A LEU* 5.3 2.7 - - + -
21A MET* 5.6 1.1 - - + -
22A ASN* 5.4 5.2 - - - -
64A SER* 3.2 25.5 + - - -
65A PHE* 2.8 13.9 + - - +
67A LEU* 1.3 74.0 - - + +
69A HIS* 1.3 56.4 + - - +
70A THR 3.2 0.2 - - - -
72A ARG* 2.8 38.2 + - - -
77A TRP* 4.4 12.6 - + - -
82A LEU* 3.6 32.1 - - + -
85A LEU* 3.7 26.7 - - + -
86A CYS* 4.3 16.6 - - - -
89A LEU* 5.1 3.8 - - + -
141A TRP* 3.8 28.3 - + - -
144A VAL* 6.2 0.7 - - + -
145A ARG* 6.2 4.3 - - - -
148A MET* 3.2 37.2 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with HIS 69 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
65A PHE* 3.0 35.3 + + + +
66A ASN* 3.4 22.9 - - - +
68A PHE* 1.3 79.9 - - - +
70A THR* 1.4 61.3 + - - +
71A GLU* 3.7 2.4 + - - +
72A ARG* 3.7 5.1 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with THR 70 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
66A ASN 3.6 8.0 + - - -
67A LEU* 3.0 18.1 + - - +
68A PHE 3.6 1.0 - - - +
69A HIS* 1.4 79.1 - - - +
71A GLU* 1.3 68.9 + - - +
72A ARG* 2.6 26.8 + - - -
131A LEU* 4.7 9.4 - - + +
136A TYR* 3.5 43.1 - - + +
141A TRP* 3.9 5.3 - - - -
----------------------------------------------------------
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