Contacts of the helix formed by residues 443 - 451 (chain A) 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 GLN 443 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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50A ALA* 3.2 30.9 - - + +
51A ASN* 3.7 7.1 - - - +
54A ASN* 3.5 10.9 - - - +
440A LEU 3.8 0.7 - - - +
441A THR* 3.1 16.1 - - - -
442A ILE* 1.3 75.9 - - - +
444A GLU* 1.3 59.0 + - - +
445A LEU 3.0 1.3 - - - -
446A GLY* 3.1 15.1 + - - -
447A SER* 3.8 2.6 + - - -
493A LEU* 4.6 4.7 - - - -
439B GLN 3.1 26.8 + - - +
440B LEU 3.2 12.9 + - - -
442B ILE* 4.0 4.8 - - + +
443B GLN* 2.9 43.1 + - - +
484B TRP* 3.7 22.0 - - + -
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Residues in contact with GLU 444 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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49A CYS* 3.2 23.7 - - - +
50A ALA* 3.1 20.9 + - - +
54A ASN* 2.8 46.1 - - + +
414A LEU* 5.2 3.8 - - + +
415A ALA* 4.3 20.0 - - + +
418A PHE* 4.2 18.3 - - + -
441A THR 3.0 12.7 + - - +
442A ILE 2.9 2.0 + - - -
443A GLN* 1.3 75.4 - - - +
445A LEU* 1.3 64.0 + - - +
446A GLY 3.0 2.0 - - - -
447A SER* 2.7 36.8 + - - -
448A MET* 3.2 17.0 + - - +
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Residues in contact with LEU 445 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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414A LEU* 4.9 8.7 - - + +
441A THR 4.4 0.4 + - - -
442A ILE* 2.8 26.4 + - + +
444A GLU* 1.3 79.2 - - - +
446A GLY* 1.3 60.7 + - - +
448A MET* 3.2 16.5 + - - +
449A LEU* 3.1 32.0 + - + +
457A ILE* 3.7 30.1 - - + -
489A ILE* 3.6 28.5 - - + -
490A PRO* 4.3 14.6 - - + -
493A LEU* 4.2 3.6 - - + -
523A LEU* 4.2 17.0 - - + -
525A LEU* 4.4 12.1 - - + -
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Residues in contact with GLY 446 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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443A GLN 3.1 11.2 + - - -
444A GLU 3.0 0.6 - - - -
445A LEU* 1.3 81.2 - - - +
447A SER* 1.3 55.7 + - - +
449A LEU* 3.5 4.3 + - - +
450A ARG* 2.9 27.4 + - - +
493A LEU* 3.9 31.7 - - - +
482B ALA* 3.8 11.3 - - - +
484B TRP* 4.1 6.7 - - - -
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Residues in contact with SER 447 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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48A GLY 4.3 2.3 + - - -
49A CYS* 4.3 4.5 - - - -
50A ALA* 4.1 8.0 + - - +
418A PHE* 3.6 21.2 - - - -
443A GLN 3.8 2.7 + - - -
444A GLU* 2.7 39.2 + - - -
446A GLY* 1.3 75.8 - - - +
448A MET* 1.3 65.5 + - - +
450A ARG* 3.7 14.4 + - - +
451A ASP* 2.9 29.5 + - - +
482B ALA* 5.1 1.1 - - - -
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Residues in contact with MET 448 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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414A LEU* 3.6 33.2 - - + +
417A ALA* 3.7 12.3 - - + -
418A PHE* 3.7 24.0 - - + +
431A VAL* 4.9 0.7 - - + -
444A GLU 3.2 10.7 + - - +
445A LEU* 3.2 33.2 + - - +
447A SER* 1.3 76.4 - - - +
449A LEU* 1.3 63.1 + - - +
451A ASP 3.3 0.9 + - - -
452A LYS 3.0 16.8 + - - -
453A GLN* 3.0 37.9 + - + +
455A PRO* 4.1 17.7 - - + -
457A ILE* 3.9 12.3 - - + -
523A LEU* 4.1 12.8 - - + -
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Residues in contact with LEU 449 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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445A LEU* 3.1 28.2 + - + +
446A GLY* 3.6 7.6 - - - +
448A MET* 1.3 75.9 - - - +
450A ARG* 1.3 66.9 + - - +
452A LYS* 2.9 21.3 + - - +
453A GLN 5.2 0.9 - - - +
490A PRO* 3.9 32.1 - - + +
493A LEU* 4.3 11.2 - - + +
494A SER* 4.1 22.0 - - - +
497A PRO* 4.8 5.4 - - + -
498A GLN* 4.9 9.9 + - + +
499A SER* 4.6 10.5 - - - +
523A LEU* 3.6 37.0 - - + -
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Residues in contact with ARG 450 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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47A VAL* 4.3 6.3 - - - +
48A GLY* 2.9 37.0 + - - +
49A CYS 5.8 0.4 - - - -
418A PHE* 4.1 10.3 - - - -
446A GLY 2.9 18.0 + - - +
447A SER* 3.7 11.5 + - - +
449A LEU* 1.3 77.4 - - - +
451A ASP* 1.3 90.7 + - - +
452A LYS* 3.3 11.4 + - - +
480B ASP 5.2 3.4 + - - -
481B ILE* 4.7 7.7 - - - +
482B ALA* 3.9 35.3 - - + +
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Residues in contact with ASP 451 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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47A VAL* 4.3 5.0 - - - +
418A PHE* 3.3 19.2 - - + -
422A THR* 5.1 1.0 + - - -
447A SER 2.9 14.2 + - - +
448A MET 4.1 1.3 - - - +
450A ARG* 1.3 111.0 + - - +
452A LYS* 1.3 69.1 + - - +
453A GLN* 3.3 16.5 + - + +
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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
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Atomic class I II III IV V VI VII VIII
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I (Hydrophilic) + + + - + + + +
II (Acceptor) + - + - + + + -
III (Donor) + + - - + + - +
IV (Hydrophobic) - - - + + + + +
V (Aromatic) + + + + + + + +
VI (Neutral) + + + + + + + +
VII (Neutral-donor) + + - + + + - +
VIII (Neutral-acceptor) + - + + + + + -
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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