Contacts of the helix formed by residues 471 - 488 (chain B) in PDB entry 3ZVU
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 471 (chain B).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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188B PRO 5.5 0.2 - - - +
189B LEU* 3.9 17.5 - - + +
190B TRP 3.0 29.0 + - - +
454B TRP* 5.8 1.0 - - - -
455B HIS* 4.7 1.9 + - - -
466B ARG* 2.7 31.7 + - - -
469B GLY 3.5 3.0 + - - -
470B ILE* 1.3 69.2 - - - +
472B PRO* 1.4 74.3 - - - +
473B ALA* 3.6 12.1 + - - +
474B CYS* 3.0 40.1 + - - +
475B GLN* 3.0 10.9 + - - +
500B ASP* 4.6 5.9 - - - +
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Residues in contact with PRO 472 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
454B TRP* 3.7 36.8 - - + +
466B ARG* 5.7 0.2 - - - +
470B ILE* 3.3 24.2 - - + +
471B ASP* 1.4 88.1 - - - +
473B ALA* 1.3 56.2 + - - +
475B GLN* 3.3 3.1 + - + +
476B ALA* 2.8 28.4 + - - +
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Residues in contact with ALA 473 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
451B ILE* 3.9 19.3 - - + +
454B TRP* 3.8 34.9 - - + -
455B HIS* 3.7 24.0 - - + +
471B ASP* 3.2 11.9 + - - +
472B PRO* 1.3 75.7 - - - +
474B CYS* 1.3 66.3 + - - +
476B ALA* 3.1 4.2 + - - +
477B ALA* 3.0 22.3 + - - +
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Residues in contact with CYS 474 (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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189B LEU 3.8 7.9 - - - -
190B TRP 3.4 6.3 - - - -
191B GLY* 3.3 23.3 - - - +
451B ILE* 4.2 12.6 - - - -
471B ASP* 3.0 20.1 + - - +
473B ALA* 1.3 77.1 - - - +
475B GLN* 1.3 57.9 + - - +
477B ALA* 3.1 5.0 + - - +
478B ALA* 2.9 28.1 + - - +
498B VAL* 3.5 14.8 - - + +
499B ILE 4.4 0.7 - - - -
500B ASP* 3.5 37.9 - - - -
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Residues in contact with GLN 475 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
191B GLY* 3.3 6.9 - - - -
192B THR* 2.8 46.1 + - - +
193B VAL* 4.8 0.2 - - - +
470B ILE* 3.6 32.9 - - + +
471B ASP 3.0 12.2 + - - +
472B PRO* 3.4 9.2 - - + +
474B CYS* 1.3 78.6 - - - +
476B ALA* 1.3 60.8 + - - +
478B ALA* 3.3 2.0 + - - +
479B ASP* 3.0 57.5 + - - +
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Residues in contact with ALA 476 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
450B ARG* 4.6 10.2 - - + +
454B TRP* 4.3 18.6 - - + -
472B PRO 2.8 14.6 + - - +
473B ALA* 3.1 12.1 + - - +
475B GLN* 1.3 74.8 - - - +
477B ALA* 1.3 58.8 + - - +
479B ASP* 3.9 7.2 - - - +
480B TYR* 3.0 31.4 + - - +
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Residues in contact with ALA 477 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
447B ALA* 3.7 32.1 - - + +
450B ARG* 3.7 17.8 - - + +
451B ILE* 4.0 7.4 - - + -
473B ALA 3.0 12.4 + - - +
474B CYS 3.1 8.5 + - - +
476B ALA* 1.3 78.8 - - - +
478B ALA* 1.3 60.4 + - - +
480B TYR* 3.4 2.3 + - - +
481B LEU* 3.1 30.8 + - - +
498B VAL* 4.2 8.1 - - + -
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Residues in contact with ALA 478 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
191B GLY 4.1 15.5 - - - +
192B THR* 4.2 11.4 - - - +
193B VAL* 3.5 25.5 - - + +
474B CYS 2.9 14.9 + - - +
475B GLN 3.9 3.4 - - - +
477B ALA* 1.3 74.1 - - - +
479B ASP* 1.3 65.6 + - - +
481B LEU* 3.3 5.0 + - - +
482B SER 3.2 17.7 + - - -
496B ILE* 4.2 7.8 - - + +
498B VAL* 3.9 18.8 - - + +
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Residues in contact with ASP 479 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
193B VAL* 4.0 13.5 - - - +
475B GLN* 3.0 46.7 + - - +
476B ALA* 3.9 6.1 - - - +
478B ALA* 1.3 75.6 - - - +
480B TYR* 1.3 63.9 + - - +
482B SER* 3.1 19.1 + - - -
483B MET* 3.2 12.0 + - - +
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Residues in contact with TYR 480 (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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446B ILE* 3.7 23.3 - - + -
450B ARG* 3.5 58.3 + - - -
476B ALA 3.0 18.8 + - - +
477B ALA 3.9 3.1 - - - +
478B ALA 3.2 0.4 - - - -
479B ASP* 1.3 76.3 - - - +
481B LEU* 1.3 58.0 + - - +
483B MET* 3.3 17.9 - - + +
484B LEU* 2.9 59.2 + - + +
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Residues in contact with LEU 481 (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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428B ILE* 5.2 0.7 - - + -
434B LEU* 4.0 6.2 - - + +
438B MET* 3.9 25.1 - - + -
443B VAL* 4.1 28.3 - - + +
446B ILE* 3.7 25.4 - - + -
447B ALA* 4.3 16.8 - - + -
477B ALA 3.1 21.4 + - - +
478B ALA 3.3 4.7 + - - +
480B TYR* 1.3 76.9 - - - +
482B SER* 1.3 58.0 + - - +
484B LEU* 3.3 5.8 + - + +
485B ALA* 2.9 27.4 + - - +
496B ILE* 3.9 21.1 - - + -
498B VAL* 4.2 20.6 - - + -
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Residues in contact with SER 482 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
193B VAL* 3.8 32.8 - - - +
195B ILE* 4.7 11.2 - - - +
478B ALA 3.2 8.0 + - - -
479B ASP* 3.1 11.3 + - - -
480B TYR 3.3 0.2 - - - -
481B LEU* 1.3 74.1 - - - +
483B MET* 1.3 62.4 + - - +
485B ALA* 3.3 8.1 + - - +
486B LEU* 2.9 36.2 + - - +
494B ILE* 4.3 13.9 - - - +
496B ILE* 4.2 4.2 - - - +
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Residues in contact with MET 483 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
479B ASP 3.2 10.5 + - - +
480B TYR* 3.3 25.1 - - + +
482B SER* 1.3 82.9 + - - +
484B LEU* 1.3 65.6 + - - +
486B LEU* 3.4 11.1 + - - +
487B GLN* 2.9 57.0 + - + +
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Residues in contact with LEU 484 (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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438B MET* 4.0 16.8 - - + -
446B ILE* 3.9 26.5 - - + -
480B TYR* 2.9 53.6 + - + +
481B LEU* 3.5 8.3 - - + +
482B SER 3.3 0.4 - - - -
483B MET* 1.3 77.6 - - - +
485B ALA* 1.3 55.5 + - - +
487B GLN* 3.1 27.8 + - + +
488B LYS* 2.8 54.9 + - - +
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Residues in contact with ALA 485 (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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433B GLY 4.0 13.2 - - - +
434B LEU* 4.2 12.1 - - + -
437B VAL* 3.7 15.8 - - + +
438B MET* 4.4 3.5 - - - -
481B LEU 2.9 19.0 + - - +
482B SER* 3.3 8.5 + - - +
484B LEU* 1.3 70.8 - - - +
486B LEU* 1.3 62.4 - - - +
488B LYS* 3.2 9.5 + - - +
489B GLY 3.3 0.2 + - - -
490B SER* 3.1 22.7 + - - -
494B ILE* 3.8 19.3 - - + -
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Residues in contact with LEU 486 (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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195B ILE* 3.9 22.7 - - + -
197B GLY* 4.7 12.3 - - - -
198B ASN* 5.2 7.4 - - - +
482B SER* 2.9 21.1 + - - +
483B MET* 3.5 11.7 - - - +
485B ALA* 1.3 75.4 - - - +
487B GLN* 1.3 57.4 + - - +
489B GLY* 2.9 21.5 + - - -
490B SER 4.0 14.7 + - - +
494B ILE* 3.8 19.1 - - + -
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Residues in contact with GLN 487 (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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483B MET* 2.9 47.7 + - + +
484B LEU* 3.3 30.4 - - - +
486B LEU* 1.3 75.4 - - - +
488B LYS* 1.3 60.7 + - + +
489B GLY* 3.1 3.5 + - - -
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Residues in contact with LYS 488 (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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437B VAL* 3.7 37.3 - - + +
438B MET* 3.8 31.9 - - + -
442B GLU* 4.1 14.2 + - - -
484B LEU* 2.8 35.8 + - - +
485B ALA 3.2 4.7 + - - +
487B GLN* 1.3 77.1 - - + +
489B GLY* 1.3 59.8 + - - +
490B SER 3.6 1.3 - - - -
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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