Contacts of the helix formed by residues 432 - 446 (chain A) in PDB entry 2OK5
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 ASP 432 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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25A ARG* 3.5 26.1 + - - -
405A VAL* 3.5 10.2 - - - +
430A VAL* 3.3 9.6 + - - +
431A LYS* 1.3 85.6 - - + +
433A MET* 1.3 59.5 + - - +
434A GLU* 3.7 15.8 - - - +
435A ASN* 3.4 30.9 - - - +
436A LEU* 2.9 24.6 + - - +
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Residues in contact with MET 433 (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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255A SER* 5.7 1.8 - - - +
256A ILE* 3.9 41.1 - - + +
263A GLY* 3.9 28.9 - - - -
264A ALA* 4.0 2.7 - - - +
267A CYS* 4.5 3.6 - - - -
362A MET* 4.8 1.6 - - + -
405A VAL* 3.5 15.3 - - + +
432A ASP* 1.3 72.5 + - - +
434A GLU* 1.3 59.2 + - - +
436A LEU* 3.3 27.5 + - + -
437A GLU* 2.9 42.2 + - - +
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Residues in contact with GLU 434 (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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432A ASP* 3.2 16.0 - - + +
433A MET* 1.3 78.9 - - - +
435A ASN* 1.3 63.2 + - - +
437A GLU* 3.6 12.7 + - - +
438A ASP* 3.2 35.6 + - - +
682A LYS* 5.1 5.2 - - - +
683A ARG* 3.7 38.5 + - - +
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Residues in contact with ASN 435 (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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202A PRO* 3.4 17.4 - - + +
430A VAL* 4.1 4.9 - - + -
431A LYS* 4.2 7.9 - - - +
432A ASP* 3.1 33.4 + - + +
434A GLU* 1.3 82.4 - - - +
436A LEU* 1.3 65.6 + - - +
438A ASP* 3.1 22.7 + - - +
439A VAL* 3.2 12.5 + - - +
1354A GOL 2.7 56.4 + - - +
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Residues in contact with LEU 436 (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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267A CYS* 3.7 8.1 - - - -
362A MET* 3.6 37.0 - - + -
403A PHE* 3.8 34.3 - - + -
405A VAL* 3.5 22.4 - - + -
430A VAL* 3.8 17.8 - - + +
432A ASP 2.9 13.3 + - - +
433A MET* 3.6 18.4 - - + +
435A ASN* 1.3 76.8 - - - +
437A GLU* 1.3 60.9 + - - +
439A VAL* 3.2 14.3 + - + +
440A PHE* 3.2 31.7 - - + -
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Residues in contact with GLU 437 (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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263A GLY* 3.4 36.2 - - - +
266A LYS* 3.9 30.8 + - + +
267A CYS* 3.7 12.0 - - - +
270A ASN* 5.1 1.2 + - - -
433A MET* 2.9 27.1 + - - +
434A GLU* 3.6 12.2 + - - +
436A LEU* 1.3 76.0 - - - +
438A ASP* 1.3 57.4 - - - +
440A PHE* 3.3 5.8 + - - +
441A TYR* 3.1 36.6 + - + -
683A ARG* 3.2 31.2 + - - +
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Residues in contact with ASP 438 (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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202A PRO* 3.7 12.7 - - + +
203A GLN* 5.6 0.2 + - - -
434A GLU* 3.2 17.1 + - - +
435A ASN* 3.1 21.2 + - - +
437A GLU* 1.3 74.3 - - - +
439A VAL* 1.3 62.9 + - - +
441A TYR* 3.8 8.3 - - - +
442A GLN* 3.0 26.2 + - - +
683A ARG* 3.0 57.6 + - - -
684A SER* 3.5 17.6 + - - +
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Residues in contact with VAL 439 (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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202A PRO* 3.6 27.1 - - + -
205A VAL* 3.7 32.8 - - + -
206A ALA* 3.5 16.4 - - - +
209A PHE* 5.7 0.7 - - + -
403A PHE* 4.5 2.2 - - + -
430A VAL* 4.2 10.8 - - + -
435A ASN 3.2 15.0 + - - +
436A LEU* 3.2 15.4 + - + +
438A ASP* 1.3 76.5 - - - +
440A PHE* 1.3 77.6 + - + +
442A GLN 3.6 0.2 + - - -
443A MET* 3.2 33.1 + - - +
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Residues in contact with PHE 440 (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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209A PHE* 4.7 5.4 - + - -
267A CYS* 3.8 28.7 - - + +
268A LEU* 5.8 2.0 - - + -
270A ASN* 3.8 20.8 - - + +
271A LEU* 3.9 43.1 - - + +
360A ILE* 5.9 1.1 - - + -
362A MET* 5.3 5.8 - - - -
403A PHE* 4.0 26.9 - + - -
436A LEU* 3.2 42.4 - - + -
437A GLU 3.3 5.1 + - - +
438A ASP 3.2 0.2 - - - -
439A VAL* 1.3 79.3 - - + +
441A TYR* 1.3 60.5 + - - +
443A MET* 3.8 27.4 - - + +
444A ILE* 3.2 32.6 + - - +
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Residues in contact with TYR 441 (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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266A LYS* 3.8 26.2 - - + +
270A ASN* 3.4 25.4 - - - -
437A GLU* 3.1 32.5 + - + +
438A ASP* 3.9 9.9 - - - +
439A VAL 3.4 0.2 - - - -
440A PHE* 1.3 76.3 - - - +
442A GLN* 1.3 59.0 + - - +
444A ILE* 3.4 7.8 + - + +
445A ASP* 3.0 35.7 + - - +
583A ARG* 3.6 60.5 + - + +
683A ARG* 3.5 31.1 + - - +
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Residues in contact with GLN 442 (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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202A PRO 4.8 1.1 - - - +
203A GLN* 3.6 26.8 + - - +
206A ALA* 3.6 20.2 - - + -
438A ASP 3.0 18.9 + - - +
439A VAL* 3.6 5.6 - - - +
441A TYR* 1.3 73.9 - - - +
443A MET* 1.3 63.5 + - - +
445A ASP* 3.1 17.7 + - - +
446A GLU 3.1 10.2 + - - -
455A MET* 3.8 16.9 - - - +
456A VAL 2.9 27.0 + - - +
457A TRP* 3.6 24.9 - - + +
458A GLU 4.3 1.0 - - - +
583A ARG* 4.8 0.6 - - - +
684A SER* 3.8 27.3 - - - +
685A ARG* 5.5 0.2 - - - -
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Residues in contact with MET 443 (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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206A ALA* 3.8 16.2 - - + -
209A PHE* 3.8 32.3 - - + -
210A LEU* 3.8 25.8 - - + -
213A LEU* 5.8 0.7 - - + -
270A ASN 5.7 0.2 - - - +
271A LEU* 4.1 14.1 - - + -
274A LYS* 2.8 58.3 + - + +
439A VAL* 3.2 26.3 + - - +
440A PHE* 3.8 26.7 - - + +
441A TYR 3.4 0.4 - - - -
442A GLN* 1.3 75.2 - - - +
444A ILE* 1.3 60.9 + - - +
446A GLU* 3.3 6.3 - - - +
457A TRP* 4.3 7.0 - - - -
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Residues in contact with ILE 444 (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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270A ASN* 3.5 39.5 - - - +
273A GLU* 3.7 30.7 - - + +
274A LYS* 3.9 21.1 - - + +
440A PHE 3.2 18.0 + - - +
441A TYR* 3.6 8.5 - - + +
442A GLN 3.2 0.2 - - - -
443A MET* 1.3 80.0 - - - +
445A ASP* 1.3 66.6 + - - +
446A GLU 3.4 0.7 + - - -
447A SER* 3.9 7.6 + - - -
448A GLN* 3.0 23.5 - - - +
583A ARG* 5.6 2.5 - - - +
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Residues in contact with ASP 445 (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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441A TYR 3.0 16.8 + - - +
442A GLN* 3.1 8.8 + - - +
444A ILE* 1.3 82.0 - - - +
446A GLU* 1.3 64.6 + - - +
447A SER 3.4 0.4 - - - -
448A GLN* 3.4 23.1 + - - +
452A LEU* 3.7 20.2 - - + +
455A MET* 3.8 19.5 - - - +
568A ARG* 5.5 0.3 + - - -
583A ARG* 2.6 41.2 + - - -
685A ARG* 3.1 21.3 + - - -
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Residues in contact with GLU 446 (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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210A LEU* 3.3 13.3 - - - +
234A ARG* 2.9 37.2 + - - +
274A LYS* 3.0 19.4 + - - -
278A TYR* 4.1 2.4 + - - -
442A GLN 3.1 4.9 + - - -
443A MET 3.3 12.6 - - - +
444A ILE 3.2 1.0 - - - -
445A ASP* 1.3 79.1 - - - +
447A SER* 1.3 62.1 + - - +
448A GLN 3.5 5.4 + - - +
450A LEU* 6.2 0.2 - - - +
455A MET* 4.9 6.6 - - - +
457A TRP* 3.5 39.6 + - + -
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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