Contacts of the helix formed by residues 444 - 451 (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 GLU 444 (chain D).
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
49D CYS* 3.2 23.9 - - - +
50D ALA* 3.2 18.5 + - - +
54D ASN* 2.8 44.9 - - + +
414D LEU* 5.0 4.5 - - + +
415D ALA* 4.3 20.0 - - + +
418D PHE* 4.1 17.0 - - + -
441D THR 3.0 12.8 + - - +
442D ILE 2.8 4.6 + - - -
443D GLN* 1.3 72.6 - - - +
445D LEU* 1.3 60.4 + - - +
446D GLY 3.0 2.2 - - - -
447D SER* 2.8 42.9 + - - +
448D MET* 3.1 16.4 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with LEU 445 (chain D).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
414D LEU* 4.8 7.6 - - + +
441D THR 4.4 0.4 + - - -
442D ILE* 2.7 25.3 + - + +
444D GLU* 1.3 78.3 - - - +
446D GLY* 1.3 60.7 + - - +
448D MET* 3.3 27.1 + - - -
449D LEU* 3.1 29.2 + - + +
457D ILE* 3.6 15.7 - - + -
489D ILE* 3.4 31.9 - - + -
490D PRO* 4.3 14.8 - - + -
493D LEU* 4.1 3.1 - - + -
523D LEU* 3.6 20.6 - - + -
525D LEU* 4.4 11.4 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with GLY 446 (chain D).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
482C ALA* 3.7 11.9 - - - +
484C TRP* 4.2 6.3 - - - -
443D GLN 3.1 11.7 + - - -
444D GLU 3.0 1.0 - - - -
445D LEU* 1.3 81.5 - - - +
447D SER* 1.3 56.2 + - - +
449D LEU* 3.6 3.4 + - - +
450D ARG* 3.0 26.9 + - - +
493D LEU* 3.9 31.7 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with SER 447 (chain D).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
482C ALA* 5.0 0.7 - - - -
48D GLY 4.3 0.3 + - - -
49D CYS* 4.3 2.1 - - - -
50D ALA* 4.1 8.8 + - - +
418D PHE* 3.5 29.7 - - - -
443D GLN 3.8 3.6 + - - -
444D GLU* 2.8 36.7 + - - -
446D GLY* 1.3 77.2 - - - +
448D MET* 1.3 64.6 + - - +
449D LEU 3.2 0.2 - - - -
450D ARG* 3.8 18.1 + - - +
451D ASP* 3.0 22.2 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with MET 448 (chain D).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
414D LEU* 3.8 26.9 - - + +
417D ALA* 3.8 19.5 - - + -
418D PHE* 3.9 15.0 - - + +
421D GLN* 5.6 0.4 - - + -
431D VAL* 4.7 0.9 - - + -
444D GLU 3.1 10.5 + - - +
445D LEU* 3.5 35.9 - - + +
447D SER* 1.3 76.6 - - - +
449D LEU* 1.3 64.3 + - - +
451D ASP 3.3 1.0 + - - -
452D LYS 3.0 4.9 + - - -
453D GLN* 3.0 54.1 + - + +
455D PRO* 3.9 22.7 - - + -
457D ILE* 3.9 15.0 - - + -
523D LEU* 4.6 5.8 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with LEU 449 (chain D).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
445D LEU* 3.1 21.3 + - + +
446D GLY* 3.6 6.7 - - - +
448D MET* 1.3 80.9 - - - +
450D ARG* 1.3 63.7 + - - +
452D LYS* 2.8 21.3 + - - +
453D GLN 5.4 0.4 - - - +
490D PRO* 3.8 35.2 - - + +
493D LEU* 4.2 8.7 - - + +
494D SER* 4.1 24.9 - - - +
497D PRO* 4.7 6.7 - - + -
498D GLN* 5.1 8.1 + - + +
499D SER* 4.5 8.1 - - - -
523D LEU* 2.7 44.6 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with ARG 450 (chain D).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
480C ASP 5.3 2.8 + - - -
481C ILE* 4.8 6.8 - - - +
482C ALA* 3.9 35.5 - - + +
47D VAL* 4.4 5.3 - - - +
48D GLY* 2.9 36.2 + - - +
49D CYS 5.8 0.6 - - - -
418D PHE* 4.0 10.9 - - - -
446D GLY 3.0 19.1 + - - +
447D SER* 3.4 12.7 + - - +
449D LEU* 1.3 78.0 - - - +
451D ASP* 1.3 89.9 + - - +
452D LYS* 3.4 11.8 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with ASP 451 (chain D).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
47D VAL* 4.2 6.1 - - - +
418D PHE* 3.2 19.9 - - + -
422D THR* 5.0 1.6 + - - -
447D SER 3.0 14.3 + - - +
450D ARG* 1.3 111.4 + - - +
452D LYS* 1.3 71.1 + - - +
453D GLN* 3.3 18.5 + - + +
----------------------------------------------------------
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