Contacts of the helix formed by residues 469 - 480 (chain B) in PDB entry 5ZE3
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 GLY 469 (chain B).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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467B ASN 3.2 4.4 + - - -
468B TRP* 1.3 74.7 - - - +
470B ILE* 1.3 64.5 + - - -
471B VAL 3.4 2.9 + - - -
472B GLU* 3.0 19.6 + - - +
473B ALA 3.3 13.0 + - - -
488B ALA* 3.1 17.7 - - - +
490B GLN* 5.5 0.7 - - - -
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Residues in contact with ILE 470 (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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469B GLY* 1.3 71.2 - - - -
471B VAL* 1.3 63.6 + - - +
473B ALA* 3.5 3.5 - - - +
474B MET* 2.9 32.4 + - + +
485B ALA* 3.7 4.3 - - + +
486B SER 4.0 15.9 - - - +
487B ASN* 3.9 9.6 - - - +
488B ALA* 3.6 22.6 - - + +
718B PHE* 3.7 19.1 + - + +
719B GLU 3.8 17.0 - - - +
721B ALA* 3.6 30.7 - - + +
725B TYR* 3.4 28.7 - - + +
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Residues in contact with VAL 471 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
469B GLY 3.4 0.6 - - - -
470B ILE* 1.3 75.9 - - - +
472B GLU* 1.3 70.8 + - - +
474B MET* 2.9 20.2 + - + +
475B VAL* 3.1 13.5 + - - +
510B LYS* 5.8 3.1 - - - +
511B CYS* 3.9 11.0 - - - +
512B SER 3.6 9.6 - - - +
513B GLY* 3.5 33.2 - - - +
718B PHE* 4.3 37.5 - - + -
725B TYR* 4.5 11.9 - - + -
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Residues in contact with GLU 472 (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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467B ASN 4.0 4.8 - - - +
468B TRP* 3.8 33.7 - - + -
469B GLY* 3.0 33.6 + - - +
471B VAL* 1.3 76.3 + - - +
473B ALA* 1.3 62.0 + - - +
475B VAL* 3.1 5.0 + - - +
476B VAL* 3.0 25.3 + - - +
509B VAL* 3.8 19.1 - - + +
510B LYS* 3.2 15.8 + - - +
511B CYS* 2.8 47.8 + - - +
518B LEU* 4.3 0.5 - - - +
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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
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468B TRP* 4.2 1.3 - - - +
469B GLY 3.3 11.6 + - - +
470B ILE* 3.5 9.0 - - - +
471B VAL 3.2 0.6 - - - -
472B GLU* 1.3 79.0 - - - +
474B MET* 1.3 57.8 + - - +
476B VAL* 3.8 1.0 - - - +
477B CYS* 2.9 34.1 + - - +
485B ALA* 3.5 14.4 - - + -
487B ASN 3.6 17.7 - - - +
488B ALA* 3.9 7.0 - - + -
541B VAL* 3.7 23.8 - - + -
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Residues in contact with MET 474 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
470B ILE* 2.9 19.5 + - + +
471B VAL* 2.9 17.5 + - + +
473B ALA* 1.3 74.1 - - - +
475B VAL* 1.3 66.2 + - + +
477B CYS* 3.2 1.2 + - - +
478B ARG* 3.0 40.1 + - - +
483B GLY 4.6 1.3 - - - +
484B PHE* 3.9 20.0 - - + -
485B ALA* 3.3 43.7 - - + +
513B GLY* 5.2 3.1 - - - +
721B ALA* 4.2 4.3 - - + -
722B GLU 3.3 34.5 - - - +
725B TYR* 4.8 10.1 - - + +
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Residues in contact with VAL 475 (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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471B VAL 3.1 9.4 + - - +
472B GLU 3.1 7.4 + - - +
474B MET* 1.3 76.0 - - - +
476B VAL* 1.3 58.0 + - - +
478B ARG* 4.0 4.5 - - - +
479B GLN* 2.9 31.2 + - - +
511B CYS* 3.6 16.2 - - + -
513B GLY* 4.0 11.9 - - - +
515B GLU* 3.3 46.0 - - - +
516B LEU 5.1 0.2 - - - +
517B SER 3.5 8.1 - - - +
518B LEU* 3.4 36.6 - - + +
521B CYS* 3.7 4.7 - - - -
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Residues in contact with VAL 476 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
435B LEU* 3.9 20.0 - - + -
437B LEU* 4.2 8.3 - - + -
448B VAL* 3.7 24.7 - - + -
468B TRP* 3.6 17.9 - - + -
472B GLU 3.0 16.1 + - - +
473B ALA 3.8 4.3 - - - +
475B VAL* 1.3 77.1 - - - +
477B CYS* 1.3 62.5 + - - +
479B GLN* 3.3 8.5 + - - +
480B LEU* 3.1 25.7 + - + +
518B LEU* 3.5 28.9 - - + -
541B VAL* 4.2 10.5 - - + -
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Residues in contact with CYS 477 (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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473B ALA 2.9 24.3 + - - +
474B MET 3.2 1.8 + - - +
476B VAL* 1.3 77.3 - - - +
478B ARG* 1.3 60.1 + - - +
480B LEU* 3.7 2.4 + - - -
481B GLY 3.5 2.4 + - - -
482B LEU* 2.8 29.7 + - - +
483B GLY 3.7 7.6 - - - +
485B ALA* 3.6 20.2 - - - +
541B VAL* 3.8 10.8 - - - -
542B ALA 3.5 13.0 - - - -
543B CYS* 2.0 49.4 - - + -
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Residues in contact with ARG 478 (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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332B ALA 4.3 16.4 + - - +
333B TYR* 4.8 9.6 - - + +
334B ILE* 3.8 34.1 - - - +
474B MET* 3.0 28.7 + - - +
475B VAL* 4.1 4.0 - - - +
477B CYS* 1.3 74.4 - - - +
479B GLN* 1.3 69.7 + - - +
480B LEU 3.1 1.3 - - - -
481B GLY* 3.0 14.0 + - - +
482B LEU 4.3 2.2 - - - +
483B GLY 3.7 13.9 - - - +
513B GLY 2.5 30.7 + - - -
514B THR* 3.2 16.2 + - - +
515B GLU 3.0 24.5 + - - +
516B LEU* 4.9 4.7 - - - +
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Residues in contact with GLN 479 (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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434A LYS* 5.3 1.8 + - - +
429B MET* 5.3 6.8 - - - +
432B GLN* 2.7 43.1 + - + +
434B LYS* 5.5 0.8 - - - +
435B LEU* 3.9 31.2 - - + +
475B VAL 2.9 20.4 + - - +
476B VAL* 3.3 6.8 + - - +
478B ARG* 1.3 79.1 - - - +
480B LEU* 1.3 58.0 + - - +
481B GLY 3.5 0.5 + - - -
516B LEU 3.9 17.9 - - - +
517B SER* 3.7 17.6 - - - -
518B LEU* 2.8 32.3 + - - +
519B ALA 5.8 0.2 - - - +
802B SO4 3.9 10.3 + - - -
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Residues in contact with LEU 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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432B GLN* 4.0 18.4 - - + -
435B LEU* 3.6 40.2 - - + +
436B ARG* 4.6 2.2 - - - -
437B LEU* 3.5 46.2 - - + +
476B VAL* 3.1 17.7 + - + +
477B CYS* 3.7 2.4 + - - +
478B ARG 3.1 0.2 - - - -
479B GLN* 1.3 74.6 - - - +
481B GLY* 1.3 63.0 - - - +
482B LEU* 3.4 26.5 - - + +
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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