Contacts of the helix formed by residues 443 - 451 (chain B) 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 B).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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439A GLN 3.1 26.8 + - - +
440A LEU 3.1 13.9 + - - -
442A ILE* 4.0 5.3 - - + +
443A GLN* 2.9 42.8 + - - +
484A TRP* 3.7 22.7 - - + -
50B ALA* 3.3 29.9 - - + +
51B ASN* 3.5 11.9 - - - +
54B ASN* 3.5 7.6 - - - +
440B LEU 3.8 0.5 - - - +
441B THR* 3.0 16.6 - - - -
442B ILE* 1.3 76.7 - - - +
444B GLU* 1.3 57.0 + - - +
445B LEU 3.0 0.7 - - - -
446B GLY* 3.0 20.2 + - - -
447B SER 3.8 2.1 + - - -
493B LEU* 4.5 4.3 - - - -
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Residues in contact with GLU 444 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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49B CYS* 3.2 23.9 - - - +
50B ALA* 3.2 18.1 + - - +
54B ASN* 2.8 45.6 - - + +
414B LEU* 5.1 3.1 - - + +
415B ALA* 4.3 19.5 - - + +
418B PHE* 4.0 19.4 - - + -
441B THR 3.0 12.3 + - - +
442B ILE 2.8 1.8 + - - -
443B GLN* 1.3 74.3 - - - +
445B LEU* 1.3 64.6 + - - +
446B GLY 3.0 2.0 - - - -
447B SER* 2.7 37.5 + - - -
448B MET* 3.1 16.9 + - - +
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Residues in contact with LEU 445 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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414B LEU* 4.8 9.4 - - + +
441B THR 4.4 0.2 + - - -
442B ILE* 2.7 26.7 + - + +
444B GLU* 1.3 78.4 - - - +
446B GLY* 1.3 59.8 + - - +
448B MET* 3.3 15.9 + - - -
449B LEU* 3.1 28.6 + - + +
457B ILE* 3.7 30.3 - - + -
489B ILE* 3.5 32.5 - - + -
490B PRO* 4.4 13.5 - - + -
493B LEU* 4.1 3.4 - - + -
523B LEU* 4.2 14.4 - - + -
525B LEU* 4.5 9.9 - - + -
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Residues in contact with GLY 446 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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482A ALA* 3.8 11.3 - - - +
484A TRP* 4.2 6.5 - - - -
443B GLN 3.0 10.8 + - - -
444B GLU 3.0 1.0 - - - -
445B LEU* 1.3 80.4 - - - +
447B SER* 1.3 56.6 + - - +
449B LEU* 3.5 4.2 + - - +
450B ARG* 2.9 27.7 + - - +
493B LEU* 3.9 31.0 - - - +
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Residues in contact with SER 447 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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482A ALA* 5.1 1.1 - - - -
49B CYS* 4.2 2.3 - - - -
50B ALA* 4.1 8.5 + - - +
418B PHE* 3.5 23.2 - - - -
443B GLN 3.8 2.6 + - - -
444B GLU* 2.7 39.3 + - - -
446B GLY* 1.3 76.2 - - - +
448B MET* 1.3 65.3 + - - +
450B ARG* 3.7 18.4 + - - +
451B ASP* 2.9 28.9 + - - +
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Residues in contact with MET 448 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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414B LEU* 3.7 32.3 - - + +
417B ALA* 3.8 11.7 - - + -
418B PHE* 3.8 23.3 - - + +
431B VAL* 4.8 1.1 - - + -
444B GLU 3.1 10.4 + - - +
445B LEU* 3.5 33.0 - - - +
446B GLY 3.3 0.2 - - - -
447B SER* 1.3 77.9 - - - +
449B LEU* 1.3 64.3 + - - +
451B ASP 3.4 0.9 + - - -
452B LYS 3.0 4.7 + - - -
453B GLN* 3.0 51.1 + - + +
455B PRO* 3.9 21.3 - - + -
457B ILE* 4.1 11.2 - - + -
523B LEU* 4.1 11.9 - - + -
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Residues in contact with LEU 449 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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445B LEU* 3.1 25.4 + - + +
446B GLY* 3.6 7.9 - - - +
447B SER 3.2 0.2 - - - -
448B MET* 1.3 77.2 - - - +
450B ARG* 1.3 66.7 + - - +
452B LYS* 2.8 20.9 + - - +
453B GLN 5.4 0.7 - - - +
490B PRO* 3.9 34.5 - - + +
493B LEU* 4.3 7.4 - - + +
494B SER* 4.1 24.9 - - - +
497B PRO* 4.7 6.3 - - + -
498B GLN* 4.9 10.0 - - + +
499B SER* 4.7 9.6 - - - -
523B LEU* 3.7 36.3 - - + -
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Residues in contact with ARG 450 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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480A ASP 5.2 2.6 + - - -
481A ILE* 4.7 7.4 - - - +
482A ALA* 3.9 36.2 - - + +
47B VAL* 4.3 5.7 - - - +
48B GLY* 2.9 36.3 + - - +
49B CYS 5.9 0.6 - - - -
418B PHE* 4.0 10.1 - - - -
446B GLY 2.9 18.0 + - - +
447B SER* 3.3 10.6 + - - +
449B LEU* 1.3 77.0 - - - +
451B ASP* 1.3 89.7 + - - +
452B LYS* 3.4 11.3 + - - +
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Residues in contact with ASP 451 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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47B VAL* 4.1 6.7 - - - +
418B PHE* 3.2 29.6 - - + -
422B THR* 5.2 0.7 + - - -
447B SER 2.9 14.2 + - - +
448B MET 4.1 2.0 - - - +
450B ARG* 1.3 100.6 + - - +
452B LYS* 1.3 70.8 + - - +
453B GLN* 3.3 16.2 + - + +
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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