Contacts of the helix formed by residues 536 - 551 (chain D) 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 D).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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362D GLN* 3.2 32.1 - - + +
366D TRP* 4.3 2.5 - - + +
385D THR* 3.6 34.1 - - + +
388D PHE 3.8 20.9 - - - +
389D GLY* 4.1 6.5 - - - -
392D ASP* 5.8 0.4 - - - +
535D ILE* 1.3 97.8 - - - +
537D PRO* 1.3 80.4 - - + +
539D LEU* 3.1 22.1 + - + -
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Residues in contact with PRO 537 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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362D GLN* 6.0 0.9 - - + -
363D GLU* 6.1 2.7 - - - +
366D TRP* 6.4 0.9 - - + -
392D ASP* 4.8 13.7 - - - +
535D ILE 3.8 1.5 - - - +
536D PRO* 1.3 88.0 - - + +
538D LEU* 1.3 65.7 + - - +
540D GLY* 3.0 12.0 + - - -
541D ALA* 3.8 2.9 + - - +
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Residues in contact with LEU 538 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
262D SER* 3.8 15.9 - - - +
265D ALA* 3.6 35.4 - - + +
290D THR 6.0 1.1 - - - +
293D ALA* 5.4 2.5 - - + -
388D PHE* 3.7 33.7 - - + +
391D ILE* 3.4 45.8 - - + -
392D ASP* 5.0 5.3 + - - +
536D PRO 3.5 0.4 - - - -
537D PRO* 1.3 79.6 - - - +
539D LEU* 1.3 66.6 + - - +
541D ALA* 2.8 25.2 + - + +
542D LEU* 3.3 11.9 + - + +
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Residues in contact with LEU 539 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
385D THR* 3.8 12.3 - - + -
388D PHE* 3.3 39.3 - - + +
467D VAL* 3.1 33.7 - - + -
535D ILE* 3.3 27.8 - - + -
536D PRO* 3.1 26.3 + - + +
538D LEU* 1.3 79.5 - - - +
540D GLY* 1.3 56.8 + - - +
542D LEU* 3.4 11.2 + - + -
543D THR* 2.8 43.2 + - - +
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Residues in contact with GLY 540 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
535D ILE* 3.8 12.9 - - - +
536D PRO 3.3 3.6 + - - -
537D PRO 3.0 11.0 + - - -
538D LEU 3.0 0.4 + - - -
539D LEU* 1.3 76.9 - - - +
541D ALA* 1.3 62.6 + - - +
543D THR* 3.1 12.3 - - - +
544D LYS* 3.0 24.3 + - - +
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Residues in contact with ALA 541 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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265D ALA* 3.9 27.1 - - + -
293D ALA* 4.8 4.9 - - + -
537D PRO 3.8 4.0 + - - +
538D LEU* 2.8 13.1 + - - +
540D GLY* 1.3 74.8 - - - +
542D LEU* 1.3 63.0 + - - +
544D LYS* 3.1 16.8 + - - +
545D ALA* 3.1 13.8 + - - +
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Residues in contact with LEU 542 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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289D ASP 3.9 7.0 - - - +
290D THR* 3.3 45.3 - - + +
293D ALA* 3.9 15.0 - - + +
294D GLY 4.7 0.9 - - - +
388D PHE* 3.3 45.5 - - + -
538D LEU* 3.3 14.0 + - + +
539D LEU* 3.9 13.0 - - + +
541D ALA* 1.3 78.9 - - - +
543D THR* 1.3 61.4 + - - +
545D ALA* 3.3 8.0 + - + +
546D LEU* 3.1 42.9 + - + +
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Residues in contact with THR 543 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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467D VAL* 3.7 1.9 + - - +
470D ALA* 3.1 45.4 - - + +
471D ILE* 3.5 23.5 - - - +
539D LEU* 2.8 24.7 + - - +
540D GLY* 3.1 14.6 - - - +
542D LEU* 1.3 77.8 - - - +
544D LYS* 1.3 67.8 + - + +
546D LEU* 3.5 4.6 + - - +
547D GLU* 3.4 21.8 + - - +
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Residues in contact with LYS 544 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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540D GLY 3.0 13.1 + - - +
541D ALA* 3.1 6.7 + - - +
543D THR* 1.3 84.3 - - + +
545D ALA* 1.3 61.4 + - - +
547D GLU* 3.9 4.5 + - - +
548D ALA* 3.3 21.3 + - - +
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Residues in contact with ALA 545 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
293D ALA 4.1 21.1 - - - +
294D GLY* 4.3 12.3 - - - +
541D ALA 3.1 10.5 + - - +
542D LEU* 3.6 10.1 - - + +
543D THR 3.2 0.2 - - - -
544D LYS* 1.3 76.4 - - - +
546D LEU* 1.3 65.8 + - + +
548D ALA* 3.2 9.2 + - - +
549D CYS* 3.2 26.8 + - - -
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Residues in contact with LEU 546 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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29C ASP* 3.6 28.8 - - + +
115C HIS* 3.7 20.2 - - + +
289D ASP* 4.3 7.9 - - + +
290D THR* 5.5 4.3 - - + -
471D ILE* 3.4 33.7 - - + -
542D LEU* 3.1 38.5 + - + +
543D THR* 3.8 5.6 - - - +
544D LYS 3.4 0.2 - - - -
545D ALA* 1.3 77.6 - - + +
547D GLU* 1.3 60.9 + - - +
549D CYS* 3.1 24.2 + - + +
550D ASN* 3.2 14.3 + - - -
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Residues in contact with GLU 547 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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33C GLN* 3.0 23.4 - - - +
471D ILE* 2.6 30.5 - - + +
472D HIS* 2.9 32.7 - - - +
543D THR 3.4 12.5 + - - +
544D LYS* 4.4 4.3 - - - +
546D LEU* 1.3 73.2 - - - +
548D ALA* 1.3 63.6 + - - +
549D CYS 3.1 2.0 - - - -
550D ASN* 3.1 24.7 + - - +
551D ASN* 2.9 34.1 + - - +
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Residues in contact with ALA 548 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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544D LYS 3.3 16.0 + - - +
545D ALA* 3.2 14.8 + - - +
546D LEU 3.2 0.2 - - - -
547D GLU* 1.3 76.9 - - - +
549D CYS* 1.3 61.1 + - - +
551D ASN* 3.4 23.1 + - - +
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Residues in contact with CYS 549 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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30C TYR* 6.4 2.9 - - + -
169C ALA* 5.7 1.2 - - - +
294D GLY* 6.4 2.2 - - - -
545D ALA* 3.2 18.8 + - - -
546D LEU* 3.1 15.6 + - + +
547D GLU 3.1 0.2 - - - -
548D ALA* 1.3 75.4 - - - +
550D ASN* 1.3 61.3 + - - +
551D ASN 3.1 10.7 + - - +
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Residues in contact with ASN 550 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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29C ASP* 3.5 32.2 + - - +
30C TYR* 4.5 6.2 - - - -
32C LEU* 5.5 1.6 - - - +
33C GLN* 3.3 27.1 - - + +
169C ALA* 4.2 26.1 - - + +
170C ASP* 5.5 1.7 + - - +
173C LYS* 2.8 31.5 + - - +
471D ILE* 4.0 6.9 - - - +
472D HIS* 5.5 0.2 - - - +
546D LEU 3.2 17.6 + - - -
547D GLU* 3.1 23.4 + - - +
549D CYS* 1.3 77.6 - - - +
551D ASN* 1.3 55.0 + - - +
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Residues in contact with ASN 551 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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33C GLN* 3.2 8.9 + - - +
170C ASP* 5.9 3.1 - - - +
173C LYS* 2.6 30.4 + - - +
547D GLU* 2.9 38.8 + - - +
548D ALA* 3.4 16.3 + - - +
549D CYS 3.1 5.8 - - - +
550D ASN* 1.3 81.0 - - - +
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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