Contacts of the helix formed by residues 536 - 551 (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 PRO 536 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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362A GLN* 3.1 31.9 - - + +
366A TRP* 4.2 2.9 - - + +
385A THR* 3.7 33.2 - - + +
388A PHE 3.8 21.3 - - - +
389A GLY* 4.1 7.6 - - - +
535A ILE* 1.3 99.7 - - - +
537A PRO* 1.3 79.2 - - + +
539A LEU* 3.2 20.7 + - + -
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Residues in contact with PRO 537 (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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362A GLN* 6.1 0.4 - - + -
363A GLU* 6.0 2.7 - - - +
366A TRP* 6.3 1.1 - - + -
392A ASP* 4.8 13.2 - - - +
535A ILE 3.8 1.3 - - - +
536A PRO* 1.3 89.8 - - + +
538A LEU* 1.3 64.2 + - - +
540A GLY* 3.1 12.1 + - - -
541A ALA* 3.9 3.5 + - - +
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Residues in contact with LEU 538 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
262A SER* 3.7 15.3 - - - +
265A ALA* 3.6 34.8 - - + +
388A PHE* 3.7 29.6 - - + +
391A ILE* 3.5 45.1 - - + -
392A ASP* 4.9 5.1 + - - +
536A PRO 3.5 0.6 - - - -
537A PRO* 1.3 79.2 - - - +
539A LEU* 1.3 62.8 + - - +
541A ALA* 3.0 19.2 + - - +
542A LEU* 3.2 27.4 + - + +
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Residues in contact with LEU 539 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
385A THR* 3.9 12.3 - - + -
388A PHE* 3.3 41.2 - - + +
467A VAL* 3.2 33.7 - - + -
535A ILE* 3.3 28.9 - - + -
536A PRO* 3.2 27.6 + - + +
538A LEU* 1.3 78.7 - - - +
540A GLY* 1.3 56.9 + - - +
542A LEU* 3.9 9.2 - - + -
543A THR* 2.8 42.3 + - - +
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Residues in contact with GLY 540 (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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535A ILE* 3.8 12.7 - - - +
536A PRO 3.4 3.6 + - - -
537A PRO 3.1 10.9 + - - -
538A LEU 3.1 0.2 + - - -
539A LEU* 1.3 76.9 - - - +
541A ALA* 1.3 62.5 + - - +
543A THR* 3.1 12.3 - - - +
544A LYS* 3.0 24.1 + - - +
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Residues in contact with ALA 541 (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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265A ALA* 3.9 25.8 - - + -
293A ALA* 4.8 5.2 - - + -
537A PRO 3.9 3.7 + - - +
538A LEU* 3.0 12.1 + - - +
540A GLY* 1.3 75.0 - - - +
542A LEU* 1.3 63.8 + - - +
544A LYS* 3.1 17.0 + - - +
545A ALA* 3.1 13.8 + - - +
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Residues in contact with LEU 542 (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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262A SER* 5.7 1.1 - - - +
289A ASP 4.6 0.9 - - - +
290A THR* 3.4 24.2 - - + +
293A ALA* 3.0 43.5 - - + +
388A PHE* 3.4 45.8 - - + -
538A LEU* 3.2 29.3 + - + +
539A LEU* 3.9 9.2 - - + +
541A ALA* 1.3 76.2 - - - +
543A THR* 1.3 62.2 + - - +
545A ALA* 3.3 7.7 + - - +
546A LEU* 3.1 31.1 + - + +
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Residues in contact with THR 543 (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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467A VAL* 3.8 1.7 + - - +
470A ALA* 3.2 42.2 - - + +
471A ILE* 3.4 24.6 - - - +
539A LEU* 2.8 24.2 + - - +
540A GLY* 3.1 16.8 - - - +
542A LEU* 1.3 74.9 - - - +
544A LYS* 1.3 71.9 + - + +
546A LEU* 3.4 4.6 + - - +
547A GLU* 3.3 22.0 + - - +
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Residues in contact with LYS 544 (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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540A GLY 3.0 12.8 + - - +
541A ALA* 3.1 6.5 + - - +
543A THR* 1.3 84.2 - - + +
545A ALA* 1.3 60.9 + - - +
547A GLU* 3.8 4.0 + - - +
548A ALA* 3.2 22.3 + - - +
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Residues in contact with ALA 545 (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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293A ALA 4.3 20.2 - - - +
294A GLY* 4.3 13.2 - - - +
541A ALA 3.1 11.3 + - - +
542A LEU 3.6 9.0 - - - +
543A THR 3.2 0.2 - - - -
544A LYS* 1.3 76.9 - - - +
546A LEU* 1.3 66.0 + - + +
548A ALA* 3.2 10.0 + - - +
549A CYS* 3.2 27.6 + - - -
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Residues in contact with LEU 546 (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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289A ASP* 4.2 13.9 - - + +
290A THR* 5.7 8.1 - - + -
471A ILE* 3.5 32.8 - - + -
542A LEU* 3.1 21.5 + - + +
543A THR* 3.4 5.1 + - - +
545A ALA* 1.3 78.8 - - + +
547A GLU* 1.3 61.3 + - - +
549A CYS* 3.1 22.5 + - + +
550A ASN* 3.2 16.9 + - - -
29B ASP* 3.7 22.8 - - + +
115B HIS* 4.0 23.8 - - + +
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Residues in contact with GLU 547 (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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471A ILE* 2.7 30.8 - - + +
472A HIS* 3.0 30.5 - - - +
543A THR 3.3 11.8 + - - +
544A LYS* 4.3 4.5 - - - +
546A LEU* 1.3 76.7 - - - +
548A ALA* 1.3 64.8 + - - +
550A ASN* 3.0 23.1 + - - +
551A ASN* 2.9 35.6 + - - +
33B GLN* 3.1 20.7 - - - +
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Residues in contact with ALA 548 (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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544A LYS 3.2 16.0 + - - +
545A ALA* 3.2 15.7 - - - +
546A LEU 3.2 1.0 - - - -
547A GLU* 1.3 77.2 - - - +
549A CYS* 1.3 61.6 + - - +
551A ASN* 3.4 23.4 + - - +
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Residues in contact with CYS 549 (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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294A GLY* 6.3 3.1 - - - -
545A ALA 3.2 19.0 + - - -
546A LEU* 3.1 18.1 + - + +
547A GLU 3.1 0.6 - - - -
548A ALA* 1.3 76.4 - - - +
550A ASN* 1.3 60.1 + - - +
551A ASN 3.1 10.5 + - - +
30B TYR* 6.4 1.6 - - + -
104B GLY* 5.8 3.3 + - - -
114B LEU* 6.6 0.4 - - - -
169B ALA* 5.9 0.9 - - - +
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Residues in contact with ASN 550 (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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471A ILE* 4.0 7.5 - - - +
472A HIS* 5.5 0.2 - - - +
546A LEU 3.2 17.5 + - - -
547A GLU* 3.0 24.1 + - - +
549A CYS* 1.3 78.4 - - - +
551A ASN* 1.3 60.0 + - - +
29B ASP* 3.4 33.8 + - - +
30B TYR* 4.6 7.3 - - - -
32B LEU* 5.5 1.6 - - - +
33B GLN* 3.5 25.5 - - + +
169B ALA* 4.3 23.6 - - + +
170B ASP* 5.7 1.6 + - - -
173B LYS* 2.8 26.2 + - - +
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Residues in contact with ASN 551 (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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547A GLU* 2.9 39.5 + - - +
548A ALA* 3.4 16.4 + - - +
549A CYS 3.1 6.1 - - - +
550A ASN* 1.3 81.3 - - - +
33B GLN* 3.2 8.2 + - - +
170B ASP* 6.1 1.2 - - - +
173B LYS* 2.8 29.8 + - - +
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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