Contacts of the helix formed by residues 443 - 451 (chain C) 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 C).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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50C ALA* 3.3 26.8 - - + +
51C ASN* 3.7 10.8 - - - +
54C ASN* 3.6 6.5 - - - +
440C LEU 3.8 0.3 - - - +
441C THR* 3.1 14.6 - - - -
442C ILE* 1.3 75.8 - - - +
444C GLU* 1.3 60.5 + - - +
445C LEU 3.0 1.1 - - - -
446C GLY* 3.0 16.1 + - - -
447C SER* 3.8 2.4 + - - -
493C LEU* 4.6 4.0 - - - -
439D GLN 3.1 24.3 + - - +
440D LEU 3.0 20.4 + - - -
441D THR 4.0 0.2 - - - +
442D ILE* 4.0 4.9 - - + +
443D GLN* 2.8 43.8 + - - +
484D TRP* 3.7 22.1 - - + -
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Residues in contact with GLU 444 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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49C CYS* 3.2 23.7 - - - +
50C ALA* 3.2 18.9 + - - +
54C ASN* 2.8 43.9 - - + +
414C LEU* 5.1 3.4 - - + +
415C ALA* 4.3 20.2 - - + +
418C PHE* 4.0 19.8 - - + -
441C THR 3.1 13.2 + - - +
442C ILE 2.8 1.8 + - - -
443C GLN* 1.3 74.9 - - - +
445C LEU* 1.3 63.8 + - - +
446C GLY 3.0 2.2 - - - -
447C SER* 2.9 37.0 + - - +
448C MET* 3.1 17.4 + - - +
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Residues in contact with LEU 445 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
414C LEU* 4.9 8.5 - - + +
441C THR 4.4 0.4 + - - -
442C ILE* 2.8 26.4 + - + +
444C GLU* 1.3 78.5 - - - +
446C GLY* 1.3 61.5 + - - +
448C MET* 3.3 14.1 + - - +
449C LEU* 3.1 29.8 + - + +
457C ILE* 3.6 31.0 - - + -
489C ILE* 3.4 33.4 - - + -
490C PRO* 4.4 13.9 - - + -
493C LEU* 4.1 3.4 - - + -
523C LEU* 4.3 15.3 - - + -
525C LEU* 4.5 9.9 - - + -
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Residues in contact with GLY 446 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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443C GLN 3.0 10.6 + - - -
444C GLU 3.0 0.8 - - - -
445C LEU* 1.3 80.6 - - - +
447C SER* 1.3 56.1 + - - +
449C LEU* 3.5 3.0 + - - +
450C ARG* 2.9 28.1 + - - +
493C LEU* 3.9 31.6 - - - +
482D ALA* 3.6 10.9 - - - +
484D TRP* 4.1 6.7 - - - -
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Residues in contact with SER 447 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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48C GLY 4.2 2.4 + - - -
49C CYS 4.6 0.2 - - - -
50C ALA* 4.1 8.7 + - - +
418C PHE* 3.6 22.3 - - - -
443C GLN 3.8 2.5 + - - -
444C GLU* 2.9 37.5 + - - -
446C GLY* 1.3 76.5 - - - +
448C MET* 1.3 65.3 - - - +
450C ARG* 3.6 19.8 + - - +
451C ASP* 2.9 27.7 + - - +
482D ALA* 4.9 2.8 - - - +
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Residues in contact with MET 448 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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414C LEU* 3.7 32.1 - - + +
417C ALA* 3.8 12.6 - - + -
418C PHE* 3.7 24.2 - - + +
421C GLN* 5.6 0.2 - - + -
431C VAL* 4.8 0.7 - - + -
444C GLU 3.1 12.2 + - - +
445C LEU* 3.5 30.7 - - - +
447C SER* 1.3 76.8 - - - +
449C LEU* 1.3 63.3 + - - +
451C ASP 3.4 0.9 + - - -
452C LYS 3.0 3.8 + - - -
453C GLN* 2.9 51.9 + - + +
455C PRO* 4.0 20.0 - - + -
457C ILE* 3.9 11.2 - - + -
523C LEU* 4.2 11.7 - - + -
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Residues in contact with LEU 449 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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445C LEU* 3.1 27.8 + - + +
446C GLY* 3.6 7.2 - - - +
448C MET* 1.3 76.7 - - - +
450C ARG* 1.3 67.6 + - - +
452C LYS* 2.7 21.5 + - - +
453C GLN 5.4 0.7 - - - +
490C PRO* 3.9 32.8 - - + +
493C LEU* 4.2 11.0 - - + +
494C SER* 4.1 22.0 - - - +
497C PRO* 4.8 5.8 - - + -
498C GLN* 5.0 8.5 - - + +
499C SER* 4.7 9.9 - - - -
523C LEU* 3.6 37.0 - - + -
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Residues in contact with ARG 450 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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47C VAL* 4.3 5.7 - - - +
48C GLY* 2.9 36.5 + - - +
49C CYS* 5.4 0.4 - - - +
418C PHE* 4.0 10.7 - - - -
446C GLY 2.9 17.9 + - - +
447C SER* 3.3 11.9 + - - +
449C LEU* 1.3 76.6 - - - +
451C ASP* 1.3 90.0 + - - +
452C LYS* 3.3 12.0 + - - +
480D ASP 5.1 3.2 + - - -
481D ILE* 4.6 7.2 - - - +
482D ALA* 3.7 37.2 - - + +
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Residues in contact with ASP 451 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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47C VAL* 4.3 5.2 - - - +
418C PHE* 3.3 19.5 - - + -
422C THR* 5.2 1.4 + - - -
447C SER 2.9 12.4 + - - +
448C MET 4.2 1.3 - - - +
450C ARG* 1.3 114.3 + - - +
452C LYS* 1.3 69.6 + - - +
453C GLN* 3.3 17.1 + - + +
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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