Contacts of the helix formed by residues 506 - 518 (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 GLU 506 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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358A GLY* 3.0 26.2 - - - +
359A SER* 3.4 9.2 + - - -
360A LEU* 3.7 3.8 - - - -
504A VAL* 3.7 5.5 - - - +
505A SER* 1.3 102.0 + - - +
507A ALA* 1.3 65.3 + - - +
508A GLU* 3.4 22.1 - - - +
509A GLN* 3.1 31.6 + - + +
510A LEU* 3.1 17.7 + - - +
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Residues in contact with ALA 507 (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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356A PRO* 5.6 4.5 - - + -
357A ASP* 4.2 17.9 - - + +
358A GLY 2.7 16.2 + - - +
360A LEU* 3.8 19.7 - - + +
364A ASN* 4.5 15.0 - - + -
368A THR* 4.8 9.5 + - - +
506A GLU* 1.3 72.5 - - - +
508A GLU* 1.3 66.1 + - - +
510A LEU* 3.4 4.1 + - - +
511A ALA* 3.2 23.7 + - - +
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Residues in contact with GLU 508 (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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356A PRO* 6.5 0.4 - - + -
357A ASP 2.9 26.2 - - - +
358A GLY* 2.9 19.7 - - - +
506A GLU* 3.4 20.6 - - + +
507A ALA* 1.3 79.3 - - - +
509A GLN* 1.3 58.0 + - + +
511A ALA* 3.5 5.0 + - - +
512A ASP* 3.0 28.9 + - - +
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Residues in contact with GLN 509 (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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503A ARG 4.4 4.3 + - - +
504A VAL* 3.7 16.6 - - + -
505A SER* 2.9 34.1 + - - -
506A GLU* 3.1 29.4 + - + +
508A GLU* 1.3 77.4 - - + +
510A LEU* 1.3 59.2 + - - +
512A ASP* 3.6 6.5 - - - +
513A VAL* 2.9 34.2 + - + +
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Residues in contact with LEU 510 (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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360A LEU* 4.4 9.0 - - + -
365A PHE* 3.6 33.9 - - + +
368A THR* 3.7 28.0 - - + +
369A LEU* 5.1 1.1 - - + +
458A LEU* 4.8 10.3 - - + -
504A VAL* 4.0 19.3 - - + +
506A GLU 3.1 12.7 + - - +
507A ALA* 3.7 10.1 - - - +
508A GLU 3.3 0.2 - - - -
509A GLN* 1.3 78.1 - - - +
511A ALA* 1.3 57.8 + - - +
513A VAL* 3.8 0.8 - - + -
514A LEU* 2.8 54.9 + - + +
526A ILE* 5.1 9.9 - - + -
528A VAL* 5.2 2.5 - - + -
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Residues in contact with ALA 511 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
368A THR* 4.2 16.7 - - + +
507A ALA 3.2 14.6 + - - +
508A GLU* 3.7 5.6 - - - +
510A LEU* 1.3 79.5 - - - +
512A ASP* 1.3 55.7 + - - +
514A LEU* 3.3 3.6 + - - +
515A GLU* 2.7 46.3 + - - +
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Residues in contact with ASP 512 (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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508A GLU 3.0 17.9 + - - +
509A GLN* 3.6 8.9 - - - +
510A LEU 3.2 0.2 - - - -
511A ALA* 1.3 75.4 - - - +
513A VAL* 1.3 66.1 + - - +
515A GLU* 2.9 20.2 + - - +
516A LYS* 3.1 36.0 + - - +
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Residues in contact with VAL 513 (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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502A TRP* 3.4 54.5 - - + +
504A VAL* 4.6 7.6 - - + -
509A GLN 2.9 21.6 + - - +
510A LEU 3.9 2.9 - - - +
512A ASP* 1.3 73.5 - - - +
514A LEU* 1.3 64.7 + - - +
516A LYS* 2.9 22.9 + - + +
517A VAL* 3.0 12.2 + - + +
526A ILE* 3.2 42.0 - - + -
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Residues in contact with LEU 514 (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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368A THR* 4.0 18.4 - - + +
369A LEU* 4.4 9.9 - - + -
372A PHE* 3.2 62.7 - - + -
456A ILE* 4.7 2.7 - - + -
458A LEU* 4.7 9.9 - - + -
510A LEU* 2.8 46.5 + - + +
511A ALA* 3.6 6.1 - - - +
512A ASP 3.2 0.2 - - - -
513A VAL* 1.3 72.7 - - - +
515A GLU* 1.3 61.2 + - - +
517A VAL* 3.6 4.9 - - + +
518A ALA* 3.1 21.5 + - - +
526A ILE* 4.1 19.1 - - + -
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Residues in contact with GLU 515 (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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372A PHE* 4.6 6.1 - - - -
511A ALA* 2.7 33.4 - - - +
512A ASP* 2.9 11.4 + - - +
514A LEU* 1.3 83.6 - - - +
516A LYS* 1.3 66.6 + - + +
517A VAL 3.5 0.3 + - - -
518A ALA* 3.5 18.0 + - - +
519A HIS* 5.3 0.7 + - - -
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Residues in contact with LYS 516 (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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500A GLU* 5.3 5.2 - - - +
502A TRP* 4.1 28.3 - - + +
512A ASP* 3.1 38.4 + - - +
513A VAL* 2.9 13.8 + - - +
515A GLU* 1.3 80.3 - - + +
517A VAL* 1.3 64.9 + - + +
518A ALA 3.7 0.2 + - - -
519A HIS 4.9 1.2 + - - -
521A GLU* 4.5 11.4 - - - +
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Residues in contact with VAL 517 (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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372A PHE* 4.5 8.5 - - + -
456A ILE* 4.4 22.5 - - + +
500A GLU* 4.3 6.1 - - - +
502A TRP* 3.4 38.8 - - + -
513A VAL* 3.0 19.3 + - + +
514A LEU* 3.6 12.8 - - - +
516A LYS* 1.3 74.0 - - - +
518A ALA* 1.3 56.6 + - - +
519A HIS 3.1 2.7 - - - -
520A HIS* 2.7 33.0 + - - +
521A GLU* 5.8 0.9 - - - +
524A SER* 3.6 27.8 - - - +
526A ILE* 4.5 2.2 - - + -
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Residues in contact with ALA 518 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
372A PHE* 4.0 4.5 - - + -
428A ARG* 3.0 43.7 + - - +
514A LEU 3.1 14.6 + - - +
515A GLU* 3.5 16.8 - - - +
516A LYS 3.4 1.4 - - - -
517A VAL* 1.3 75.2 - - - +
519A HIS* 1.3 76.3 + - + +
520A HIS* 3.5 0.9 + - - -
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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