Contacts of the helix formed by residues 447 - 461 (chain A) in PDB entry 2ZNS
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 447 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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428A PRO 3.2 13.2 - - - -
429A TYR 3.3 4.5 - - - -
431A MET* 4.2 1.3 - - - -
446A GLU* 1.3 80.5 - - - +
448A TYR* 1.3 67.3 + - - -
449A CYS 3.2 2.5 - - - -
450A LEU* 3.1 2.6 + - - +
451A ASP* 3.0 20.2 + - - -
783A TRP* 3.4 28.4 - - - -
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Residues in contact with TYR 448 (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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428A PRO 2.9 15.7 + - - +
429A TYR* 3.9 11.4 - + + -
447A GLY* 1.3 72.0 - - - +
449A CYS* 1.4 70.7 + - - +
451A ASP* 3.4 3.2 + - - +
452A LEU* 3.0 31.8 + - + +
518A PHE* 3.6 42.9 + + - +
519A MET* 3.5 26.6 - - + +
776A LEU* 4.0 18.8 + - - +
779A MET* 3.5 44.3 - - + +
780A LYS* 3.6 9.4 - - - -
783A TRP* 3.4 18.4 - - + -
784A TRP* 3.8 19.1 - + + -
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Residues in contact with CYS 449 (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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429A TYR* 2.7 35.3 + - - +
430A VAL* 3.9 6.7 - - + -
448A TYR* 1.4 87.3 - - - +
450A LEU* 1.3 59.3 + - - +
452A LEU* 3.5 5.9 - - - +
453A LEU* 2.9 28.6 + - - +
499A VAL* 3.7 22.6 - - + +
500A ALA* 3.7 34.8 - - - -
501A PRO* 3.9 0.7 - - - -
518A PHE* 4.5 9.6 - - - -
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Residues in contact with LEU 450 (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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423A THR* 5.9 0.7 - - + -
429A TYR 4.0 4.0 - - - +
430A VAL* 4.0 19.7 - - + -
442A ASN* 5.0 4.5 - - + +
445A PHE* 3.7 37.7 - - + +
446A GLU* 3.7 22.4 - - - +
447A GLY 3.1 10.9 + - - +
449A CYS* 1.3 77.6 - - + +
451A ASP* 1.3 67.4 + - - +
453A LEU* 3.5 12.8 + - + +
454A LYS* 3.0 40.8 + - - +
464A TYR* 4.6 4.0 + - + +
466A VAL* 4.0 28.7 - - + -
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Residues in contact with ASP 451 (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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447A GLY 3.0 10.6 + - - +
448A TYR 3.7 7.0 - - - +
450A LEU* 1.3 75.0 - - - +
452A LEU* 1.3 65.8 + - - +
454A LYS* 3.1 19.4 + - - +
455A GLU* 3.0 28.5 + - + +
779A MET* 4.0 18.4 - - + +
782A LYS* 2.9 28.2 + - - +
783A TRP* 2.7 33.0 + - - +
789A CYS* 5.3 1.2 - - - -
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Residues in contact with LEU 452 (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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448A TYR* 3.0 24.1 + - + +
449A CYS* 3.5 6.1 - - - +
451A ASP* 1.3 78.3 - - - +
453A LEU* 1.3 56.3 + - - +
455A GLU* 3.2 2.6 + - - +
456A LEU* 2.8 51.7 + - + +
499A VAL* 4.0 16.8 - - + -
518A PHE* 3.8 45.8 - - + -
751A VAL* 4.6 0.9 - - + -
767A ILE* 4.9 2.2 - - + -
770A LEU* 3.8 24.7 - - + -
776A LEU* 4.2 17.3 - - + -
779A MET* 3.9 11.1 - - + -
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Residues in contact with LEU 453 (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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421A VAL* 3.8 33.0 - - + -
449A CYS 2.9 17.2 + - - +
450A LEU* 3.6 14.4 - - + +
451A ASP 3.3 0.2 - - - -
452A LEU* 1.3 75.5 - - - +
454A LYS* 1.3 56.5 + - - +
456A LEU* 3.3 5.2 + - + +
457A SER* 2.9 31.7 + - - -
462A PHE* 4.2 21.5 - - + -
464A TYR* 3.5 34.3 - - + -
466A VAL* 3.8 15.7 - - + -
497A LEU* 4.7 1.1 - - + -
499A VAL* 4.1 21.5 - - + +
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Residues in contact with LYS 454 (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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433A ARG* 4.5 15.0 - - - +
445A PHE 5.2 0.4 + - - -
450A LEU* 3.0 40.8 + - - +
451A ASP* 3.4 18.4 + - - +
453A LEU* 1.3 75.6 - - - +
455A GLU* 1.3 61.0 + - + +
457A SER* 3.1 6.1 + - - -
458A ASN* 2.8 39.3 + - - +
464A TYR* 3.5 20.5 + - - +
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Residues in contact with GLU 455 (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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451A ASP* 3.0 21.0 + - - +
452A LEU 3.8 3.8 - - - +
454A LYS* 1.3 76.9 - - + +
456A LEU* 1.3 65.1 + - - +
458A ASN* 3.1 16.5 + - - +
459A ILE* 2.9 30.4 + - - +
770A LEU* 3.7 24.1 - - + +
775A LYS* 3.3 37.6 + - - +
779A MET* 4.3 15.5 - - - +
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Residues in contact with LEU 456 (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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452A LEU* 2.8 34.4 + - + +
453A LEU* 3.7 9.6 - - + +
455A GLU* 1.3 75.3 - - - +
457A SER* 1.3 58.1 + - - +
459A ILE* 3.3 0.9 + - - -
460A LEU* 2.8 38.3 + - + +
462A PHE* 4.0 13.9 - - + -
497A LEU* 5.8 1.1 - - + -
499A VAL* 4.9 8.3 - - + -
751A VAL* 4.1 26.9 - - + -
763A ILE* 4.1 16.4 - - + +
766A ALA* 3.6 28.3 - - + -
767A ILE* 3.9 20.2 - - + -
770A LEU* 4.0 12.8 - - + -
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Residues in contact with SER 457 (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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453A LEU 2.9 14.2 + - - -
454A LYS* 3.1 12.6 + - - -
456A LEU* 1.3 74.1 - - - +
458A ASN* 1.3 64.3 + - - +
461A GLY* 2.9 28.2 + - - -
462A PHE* 3.4 46.6 + - - +
464A TYR* 3.3 19.3 - - - -
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Residues in contact with ASN 458 (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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454A LYS* 2.8 27.4 + - - +
455A GLU* 3.4 21.2 - - - +
457A SER* 1.3 85.3 + - - +
459A ILE* 1.3 63.7 + - + +
461A GLY* 4.1 4.3 + - - -
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Residues in contact with ILE 459 (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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455A GLU* 2.9 17.9 + - - +
456A LEU 3.9 2.7 - - - +
458A ASN* 1.3 79.2 - - + +
460A LEU* 1.3 69.7 + - + +
461A GLY 3.7 0.2 + - - -
765A ILE* 6.1 2.7 - - + -
766A ALA* 3.7 39.0 - - + +
769A GLN* 3.6 37.5 - - - +
770A LEU* 3.6 32.3 - - + -
773A GLU* 5.3 0.2 - - - +
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Residues in contact with LEU 460 (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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456A LEU* 2.8 22.6 + - + +
459A ILE* 1.3 85.6 - - + +
461A GLY* 1.3 63.4 + - - +
462A PHE* 3.6 20.3 - - + +
759A TYR* 6.3 0.2 - - + -
762A LYS* 3.4 56.3 - - + +
763A ILE* 3.8 23.6 - - + -
765A ILE* 5.9 3.1 - - + -
766A ALA* 3.9 10.8 - - + +
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Residues in contact with GLY 461 (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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416A ASN* 4.3 14.0 + - - +
457A SER 2.9 15.7 + - - -
458A ASN 4.6 4.3 - - - -
459A ILE 3.4 1.8 - - - -
460A LEU* 1.3 79.7 - - - +
462A PHE* 1.3 57.0 + - - +
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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
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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