Contacts of the helix formed by residues 469 - 481 (chain A) 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 A).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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467A ASN 3.7 1.2 + - - -
468A TRP* 1.3 74.8 + - - +
470A ILE* 1.3 66.1 + - - -
471A VAL 3.3 3.1 - - - -
472A GLU* 2.5 19.3 + - - +
473A ALA 3.1 16.5 + - - -
488A ALA* 3.2 15.7 - - - +
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Residues in contact with ILE 470 (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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469A GLY* 1.3 72.3 - - - -
471A VAL* 1.3 56.7 + - + +
473A ALA* 3.0 4.4 + - - +
474A MET* 2.7 47.9 + - + +
485A ALA* 4.4 4.0 - - + -
486A SER 4.1 7.2 - - - +
487A ASN* 3.7 16.8 - - - +
488A ALA* 3.6 25.5 - - + +
718A PHE* 3.4 25.3 + - - +
719A GLU* 4.4 12.1 - - - +
721A ALA* 4.0 14.6 - - + +
725A TYR* 3.2 25.8 - - + +
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Residues in contact with VAL 471 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
469A GLY 3.3 0.6 - - - -
470A ILE* 1.3 76.1 - - - +
472A GLU* 1.3 71.9 + - - +
474A MET* 3.3 11.0 + - + +
475A VAL* 3.1 20.6 + - - +
511A CYS* 3.5 16.2 - - - +
512A SER 3.3 26.2 - - - +
513A GLY* 3.5 13.2 - - - +
718A PHE* 4.4 33.7 - - + -
725A TYR* 4.8 11.0 - - + -
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Residues in contact with GLU 472 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
467A ASN 3.9 5.3 - - - +
468A TRP* 3.6 28.4 - - + -
469A GLY* 2.5 39.3 + - - +
471A VAL* 1.3 79.0 + - - +
473A ALA* 1.3 56.1 + - - +
475A VAL* 2.8 23.6 + - - +
476A VAL* 3.0 14.0 + - - +
509A VAL* 3.9 26.5 - - + +
510A LYS* 3.6 10.0 - - - +
511A CYS* 3.2 45.2 + - - +
518A LEU* 4.7 0.2 - - - +
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Residues in contact with ALA 473 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
468A TRP* 4.2 2.1 - - - +
469A GLY 3.1 13.9 + - - +
470A ILE* 3.0 10.4 + - - +
472A GLU* 1.3 75.8 - - - +
474A MET* 1.3 56.7 + - - +
476A VAL* 3.0 3.7 + - - +
477A CYS* 2.9 32.4 + - - -
485A ALA* 3.6 16.2 - - + -
487A ASN 3.8 4.5 - - - +
488A ALA* 3.7 18.4 - - + -
541A VAL* 3.8 24.7 - - + -
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Residues in contact with MET 474 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
470A ILE* 2.7 33.4 + - + +
471A VAL* 3.3 13.0 - - + +
473A ALA* 1.3 71.1 - - - +
475A VAL* 1.3 64.8 + - + +
477A CYS* 4.0 0.3 - - - +
478A ARG* 2.9 38.4 + - - +
483A GLY 4.8 1.2 - - - +
484A PHE* 4.1 18.8 - - + -
485A ALA* 3.3 43.2 - - + +
513A GLY* 5.2 3.8 - - - +
722A GLU 3.0 39.3 - - - +
725A TYR* 4.2 7.4 - - + +
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Residues in contact with VAL 475 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
471A VAL 3.1 12.9 + - - +
472A GLU 2.8 15.0 + - - +
474A MET* 1.3 73.4 - - - +
476A VAL* 1.3 61.1 + - - +
478A ARG* 3.7 5.5 - - - +
479A GLN* 2.9 21.7 + - - +
511A CYS* 3.7 16.2 - - + -
513A GLY 3.8 15.9 - - - +
515A GLU* 3.6 45.3 - - + +
516A LEU 4.5 0.2 - - - -
517A SER 3.7 9.2 - - - +
518A LEU* 3.7 27.6 - - + +
521A CYS* 4.3 0.7 - - - -
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Residues in contact with VAL 476 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
435A LEU* 3.9 11.9 - - + -
437A LEU* 4.0 14.1 - - + -
448A VAL* 4.6 10.5 - - + -
468A TRP* 3.8 33.0 - - + -
472A GLU 3.0 9.7 + - - +
473A ALA 3.0 5.8 + - - +
475A VAL* 1.3 75.5 - - - +
477A CYS* 1.3 64.4 + - - +
479A GLN* 3.1 8.3 + - - +
480A LEU* 2.9 42.6 + - + +
518A LEU* 3.9 17.0 - - + -
541A VAL* 4.2 13.0 - - + -
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Residues in contact with CYS 477 (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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473A ALA 2.9 20.1 + - - +
474A MET 4.0 1.3 - - - +
476A VAL* 1.3 76.5 - - - +
478A ARG* 1.3 64.2 + - - +
480A LEU* 3.3 4.1 + - - -
481A GLY 2.9 18.9 + - - -
482A LEU 3.0 10.4 + - - -
483A GLY 3.6 10.0 + - - +
484A PHE 3.5 20.4 - - - +
485A ALA* 3.7 9.0 - - - +
541A VAL* 4.1 9.6 - - - -
542A ALA 4.1 0.9 - - - -
543A CYS* 2.0 53.4 - - + -
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Residues in contact with ARG 478 (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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332A ALA 4.1 20.6 + - - +
333A TYR* 5.3 9.4 - - + +
334A ILE* 4.2 30.5 - - + +
474A MET* 2.9 33.5 + - - +
475A VAL* 3.7 6.0 - - - +
477A CYS* 1.3 76.1 - - - +
479A GLN* 1.3 65.6 + - - +
481A GLY* 2.9 15.6 + - - -
483A GLY 3.7 9.9 + - - +
513A GLY 2.3 33.5 + - - -
514A THR* 3.2 12.3 + - - +
515A GLU 3.0 27.0 + - - +
516A LEU* 4.5 8.3 - - + +
453B GLU* 5.7 0.2 - - - -
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Residues in contact with GLN 479 (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 GLN* 3.2 41.5 - - + +
434A LYS* 5.6 2.4 - - - +
435A LEU* 3.6 35.9 - - + +
475A VAL 2.9 20.4 + - - +
476A VAL* 3.6 4.0 - - - +
478A ARG* 1.3 75.6 - - - +
480A LEU* 1.3 59.4 + - - +
481A GLY 3.5 0.3 + - - -
516A LEU 3.9 18.6 + - - +
517A SER* 3.5 18.2 - - - -
518A LEU* 2.8 28.3 + - - +
434B LYS* 4.4 3.9 + - - +
802B SO4 4.5 5.9 + - - -
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Residues in contact with LEU 480 (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 GLN* 4.2 19.3 - - + -
435A LEU* 3.9 34.1 - - + +
436A ARG* 4.5 3.4 - - - -
437A LEU* 3.5 45.3 - - + +
476A VAL* 2.9 26.2 + - + +
477A CYS* 4.0 4.5 - - - +
479A GLN* 1.3 75.1 - - - +
481A GLY* 1.3 62.5 + - - +
482A LEU* 3.4 19.7 + - + +
543A CYS* 6.0 0.2 - - - -
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Residues in contact with GLY 481 (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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333A TYR* 3.4 24.8 + - - -
477A CYS 2.9 0.4 + - - -
478A ARG 2.9 16.3 + - - -
479A GLN 3.3 1.4 + - - -
480A LEU* 1.3 78.9 - - - +
482A LEU* 1.3 65.2 + - - +
483A GLY 3.4 2.5 - - - -
545A GLU* 4.4 1.9 - - - +
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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