Contacts of the helix formed by residues 76 - 82 (chain D) in PDB entry 1OVM
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 GLY 76 (chain D).
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
407C TRP* 3.8 12.6 - - - -
75D PHE* 1.3 69.5 - - - +
77D VAL* 1.3 63.2 + - - -
78D GLY 3.2 0.4 - - - -
79D GLU* 2.8 17.3 + - - +
80D LEU* 3.0 30.7 + - - +
116D HIS 3.9 3.4 - - - -
126D PHE* 3.6 27.8 - - - -
----------------------------------------------------------
Back to top of page
Residues in contact with VAL 77 (chain D).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
84C ASN* 3.6 11.9 - - - +
407C TRP* 3.1 49.7 - - + +
409C SER* 3.8 15.3 - - - -
600C TPP 3.4 35.9 - - + +
74D THR* 3.6 17.0 - - + -
75D PHE 2.9 7.3 + - - +
76D GLY* 1.3 71.1 - - - +
78D GLY* 1.3 62.4 + - - +
81D SER* 2.9 27.4 + - - -
116D HIS* 3.4 15.5 - - + +
----------------------------------------------------------
Back to top of page
Residues in contact with GLY 78 (chain D).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
52D GLU* 3.1 41.6 - - - +
73D THR* 3.6 8.6 - - - +
74D THR* 3.0 24.5 + - - -
77D VAL* 1.3 81.7 - - - +
79D GLU* 1.3 64.1 + - - +
81D SER 3.2 5.9 + - - -
82D ALA 3.4 3.3 + - - -
----------------------------------------------------------
Back to top of page
Residues in contact with GLU 79 (chain D).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
73D THR* 3.4 16.7 + - - +
74D THR 3.1 5.1 + - - +
75D PHE* 3.4 19.6 - - - -
76D GLY* 2.8 32.8 + - - +
78D GLY* 1.3 74.8 - - - +
80D LEU* 1.3 67.4 + - + +
82D ALA* 3.1 13.0 + - - +
83D MET* 3.3 16.2 + - + +
98D HIS* 3.8 19.6 - - + -
100D VAL* 3.6 8.6 - - + +
126D PHE* 3.4 26.6 - - + +
130D SER* 5.6 0.2 - - - -
164D TYR* 2.5 33.4 + - + -
----------------------------------------------------------
Back to top of page
Residues in contact with LEU 80 (chain D).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
80C LEU 4.3 2.8 - - - +
81C SER 5.8 0.2 - - - +
83C MET* 4.1 13.9 - - + +
84C ASN* 3.9 18.4 + - + +
87C ALA* 3.5 32.5 - - + -
407C TRP* 4.1 7.2 - - + -
76D GLY 3.0 17.7 + - - +
79D GLU* 1.3 78.1 - - + +
81D SER* 1.3 63.8 + - - +
83D MET* 3.1 40.8 + - + +
126D PHE* 4.0 35.0 - - + -
129D MET* 3.8 28.7 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with SER 81 (chain D).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
53C LEU* 5.0 11.7 - - - +
57C TYR* 4.8 1.4 + - - -
80C LEU 5.6 0.9 - - - +
81C SER* 5.5 6.6 - - - +
84C ASN* 3.0 23.1 + - - +
600C TPP 4.3 5.5 - - - +
51D ASN* 6.3 0.4 - - - -
52D GLU* 3.2 29.9 + - - +
53D LEU* 3.5 29.4 - - - +
77D VAL 2.9 17.4 + - - -
78D GLY 3.2 0.6 + - - -
79D GLU 3.2 0.4 - - - -
80D LEU* 1.3 78.6 - - - +
82D ALA* 1.3 57.9 + - - +
83D MET 3.8 0.5 + - - -
84D ASN* 4.9 1.2 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with ALA 82 (chain D).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
52D GLU* 3.8 22.2 - - + +
53D LEU* 4.4 0.4 - - - +
56D SER* 3.9 4.9 + - - -
71D LEU* 3.9 24.2 - - + -
73D THR* 4.5 0.7 - - + -
78D GLY 3.4 8.0 + - - +
79D GLU 3.1 9.5 + - - +
80D LEU 3.0 0.8 - - - -
81D SER* 1.3 78.1 - - - +
83D MET* 1.3 64.2 + - - +
84D ASN 3.3 2.2 - - - -
85D GLY* 2.9 15.0 + - - -
86D ILE* 3.1 14.0 + - + +
98D HIS* 4.2 8.1 - - + -
----------------------------------------------------------
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