Contacts of the helix formed by residues 536 - 551 (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 PRO 536 (chain B).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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362B GLN* 3.2 31.2 - - + +
366B TRP* 4.4 2.5 - - + +
385B THR* 3.6 35.4 - - + +
388B PHE 3.6 20.9 - - - +
389B GLY* 4.1 6.7 - - - +
392B ASP* 5.8 0.4 - - - +
535B ILE* 1.3 97.3 - - - +
537B PRO* 1.3 80.3 - - + +
539B LEU* 3.1 22.4 + - + -
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Residues in contact with PRO 537 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
362B GLN* 6.1 0.4 - - + -
363B GLU* 6.1 2.2 - - - +
392B ASP* 4.8 13.2 - - - +
535B ILE 3.8 1.5 - - - +
536B PRO* 1.3 88.5 - - + +
538B LEU* 1.3 65.4 + - - +
540B GLY* 3.1 11.6 + - - -
541B ALA* 3.9 3.6 + - - +
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Residues in contact with LEU 538 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
262B SER* 3.6 17.5 - - - +
265B ALA* 3.5 36.8 - - + +
290B THR 6.0 1.1 - - - +
293B ALA* 5.5 2.5 - - + -
388B PHE* 3.8 31.4 + - + +
391B ILE* 3.5 45.5 - - + -
392B ASP* 5.0 5.3 + - - +
536B PRO* 3.4 0.6 - - - +
537B PRO* 1.3 79.1 - - - +
539B LEU* 1.3 65.2 + - - +
541B ALA* 2.9 18.9 + - + +
542B LEU* 3.2 15.4 + - + +
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Residues in contact with LEU 539 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
385B THR* 3.8 12.1 - - + -
388B PHE* 3.3 39.2 + - + +
467B VAL* 3.2 33.0 - - + -
535B ILE* 3.3 27.8 - - + -
536B PRO* 3.1 27.8 + - + +
538B LEU* 1.3 80.2 - - - +
540B GLY* 1.3 57.6 + - - +
542B LEU* 4.5 10.3 - - + -
543B THR* 2.8 41.9 + - - +
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Residues in contact with GLY 540 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
535B ILE* 3.8 12.3 - - - +
536B PRO 3.4 3.8 + - - -
537B PRO 3.1 9.2 + - - -
538B LEU 3.1 1.2 + - - -
539B LEU* 1.3 77.5 - - - +
541B ALA* 1.3 62.8 + - - +
543B THR* 3.1 12.5 - - - +
544B LYS* 3.0 24.3 + - - +
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Residues in contact with ALA 541 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
265B ALA* 3.8 27.4 - - + -
293B ALA* 4.8 5.2 - - + -
537B PRO 3.9 3.7 + - - +
538B LEU* 2.9 12.1 + - - +
540B GLY* 1.3 74.4 - - - +
542B LEU* 1.3 63.8 + - - +
544B LYS* 3.1 17.7 + - - +
545B ALA* 3.1 12.5 + - - +
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Residues in contact with LEU 542 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
289B ASP 3.8 2.7 - - - +
290B THR* 3.3 44.9 - - + +
293B ALA* 3.8 20.1 - - + +
294B GLY 4.6 1.6 - - - +
388B PHE* 3.4 46.0 - - + -
538B LEU* 3.2 14.6 + - + +
539B LEU* 3.9 11.4 - - + +
541B ALA* 1.3 78.3 - - - +
543B THR* 1.3 61.7 + - - +
545B ALA* 3.4 7.0 + - + +
546B LEU* 3.1 43.2 + - + +
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Residues in contact with THR 543 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
467B VAL* 3.8 1.4 + - - +
470B ALA* 3.2 43.6 - - + +
471B ILE* 3.4 24.6 - - - +
539B LEU* 2.8 25.0 + - - +
540B GLY* 3.1 15.7 - - - +
542B LEU* 1.3 76.1 - - - +
544B LYS* 1.3 71.7 + - + +
546B LEU* 3.3 13.3 + - - +
547B GLU* 3.3 15.1 + - - +
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Residues in contact with LYS 544 (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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540B GLY 3.0 12.2 + - - +
541B ALA* 3.1 6.2 + - - +
543B THR* 1.3 85.9 - - + +
545B ALA* 1.3 61.4 + - - +
547B GLU* 3.8 4.2 + - - +
548B ALA* 3.2 21.7 + - - +
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Residues in contact with ALA 545 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
293B ALA 4.2 20.9 - - - +
294B GLY* 4.3 13.0 - - - -
541B ALA 3.1 10.8 + - - +
542B LEU* 3.7 9.6 - - + +
544B LYS* 1.3 75.9 - - - +
546B LEU* 1.3 67.2 + - + +
548B ALA* 3.2 8.8 + - - +
549B CYS* 3.2 27.1 + - - -
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Residues in contact with LEU 546 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
29A ASP* 3.8 17.1 - - + +
115A HIS* 3.7 31.2 - - + +
289B ASP* 4.3 8.5 - - + +
290B THR* 5.6 4.9 - - + -
471B ILE* 3.3 34.1 - - + -
542B LEU* 3.1 39.8 + - + +
543B THR* 3.3 5.6 + - - +
545B ALA* 1.3 78.4 - - + +
547B GLU* 1.3 61.4 + - - +
549B CYS* 3.1 26.4 + - + +
550B ASN* 3.3 13.3 + - - -
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Residues in contact with GLU 547 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
33A GLN* 3.1 23.0 - - - +
470B ALA 5.7 0.2 - - - +
471B ILE* 2.6 31.4 - - + +
472B HIS* 2.9 32.8 - - - +
543B THR 3.3 11.6 + - - +
544B LYS* 4.3 4.7 - - - +
546B LEU* 1.3 76.2 - - - +
548B ALA* 1.3 64.6 + - - +
549B CYS 3.1 0.7 - - - -
550B ASN* 3.1 22.3 + - - +
551B ASN* 2.9 34.1 + - - +
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Residues in contact with ALA 548 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
544B LYS* 3.2 16.2 + - + +
545B ALA* 3.2 14.8 + - - +
546B LEU 3.2 0.6 - - - -
547B GLU* 1.3 76.9 - - - +
549B CYS* 1.3 62.3 + - - +
551B ASN* 3.3 23.6 + - - +
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Residues in contact with CYS 549 (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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30A TYR* 6.4 2.2 - - + -
104A GLY* 5.8 2.9 + - - -
114A LEU* 6.5 1.1 - - - -
169A ALA* 5.8 0.7 - - - +
294B GLY* 6.3 2.7 - - - -
545B ALA* 3.2 18.3 + - - -
546B LEU* 3.1 19.2 + - + +
547B GLU 3.1 0.4 - - - -
548B ALA* 1.3 75.3 - - - +
550B ASN* 1.3 58.9 + - - +
551B ASN 3.1 11.4 + - - +
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Residues in contact with ASN 550 (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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29A ASP* 3.5 33.3 + - - +
30A TYR* 4.5 6.8 - - - -
32A LEU* 5.4 1.4 - - - +
33A GLN* 3.4 26.2 - - + +
169A ALA* 4.2 24.4 - - + +
170A ASP* 5.7 1.6 + - - -
173A LYS* 2.8 26.0 + - - +
471B ILE* 4.1 6.7 - - - +
472B HIS* 5.5 0.4 - - - +
546B LEU 3.3 17.1 + - - -
547B GLU* 3.1 23.1 + - - +
549B CYS* 1.3 78.2 - - - +
551B ASN* 1.3 59.6 + - - +
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Residues in contact with ASN 551 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
33A GLN* 3.1 8.8 + - - +
170A ASP* 6.1 0.9 - - - +
173A LYS* 2.7 31.1 + - - +
547B GLU* 2.9 38.0 + - - +
548B ALA* 3.3 17.2 + - - +
549B CYS 3.1 6.9 - - - +
550B ASN* 1.3 81.1 - - - +
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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
------------------------------------------------------------
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