Contacts of the helix formed by residues 463 - 471 (chain E) in PDB entry 4ZZ7
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 TYR 463 (chain E).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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107E ASN* 3.4 25.1 - - + +
157E TRP* 3.3 67.1 + + - +
161E MET* 5.7 1.8 - - + -
244E GLN* 4.9 1.8 + - - -
442E VAL* 3.8 5.4 - - - +
443E PRO 2.8 22.6 + - - -
444E VAL 3.5 13.9 - - - -
445E ALA* 4.0 4.0 - - - -
447E HIS 3.1 30.1 - - - -
448E SER* 2.6 23.7 + - - -
449E PHE* 3.3 36.6 - - + +
462E ALA* 1.3 80.9 - - - +
464E GLY* 1.3 64.6 + - - +
467E ALA* 3.1 26.4 + - - +
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Residues in contact with GLY 464 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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110E TYR* 3.5 24.2 - - - -
161E MET* 4.2 3.3 - - - +
445E ALA 3.5 6.1 + - - -
447E HIS 3.4 11.2 - - - -
463E TYR* 1.3 84.7 - - - +
465E PRO* 1.3 75.3 - - - +
467E ALA* 3.1 12.1 + - - +
468E VAL* 3.5 8.0 + - - +
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Residues in contact with PRO 465 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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110E TYR* 3.5 20.1 - - - +
446E TYR 3.6 12.8 - - - +
447E HIS* 3.8 7.4 - - - -
448E SER* 3.4 10.1 - - - +
464E GLY* 1.3 83.2 - - - +
466E ASP* 1.3 62.6 + - - +
468E VAL* 3.2 24.9 - - + +
469E ARG* 3.4 9.5 + - - +
121F GLU* 4.0 12.8 - - - +
474F ARG* 4.2 16.2 - - - +
116G GLU* 5.7 0.4 - - - +
119G LYS* 3.7 18.4 - - - +
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Residues in contact with ASP 466 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
448E SER* 3.0 11.8 + - - +
460E LEU* 3.7 9.6 - - - +
461E HIS* 2.9 44.8 + - - +
465E PRO* 1.3 76.1 - - - +
467E ALA* 1.3 59.0 + - - +
469E ARG* 2.9 11.3 + - - +
470E PHE* 2.8 27.6 + - - +
469F ARG* 2.8 27.0 + - - -
474F ARG* 2.8 40.4 + - - -
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Residues in contact with ALA 467 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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157E TRP 4.9 0.2 - - - +
161E MET* 3.7 17.7 - - + -
244E GLN* 5.2 1.8 - - - +
461E HIS 3.9 3.7 + - - -
463E TYR* 3.1 37.1 + - - +
464E GLY 3.1 5.1 + - - +
466E ASP* 1.3 76.5 - - - +
468E VAL* 1.3 53.1 + - - +
470E PHE* 3.1 8.0 + - - -
471E TYR* 2.7 55.5 + - + -
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Residues in contact with VAL 468 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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110E TYR* 4.9 0.2 - - - +
117E LEU* 3.5 40.8 - - + +
118E LEU* 4.4 9.4 - - + -
136E PHE* 5.8 4.3 - - + -
161E MET* 3.6 23.5 - - + +
165E CYS* 4.1 18.6 - - - -
464E GLY 3.6 10.3 - - - +
465E PRO* 3.2 18.4 - - + +
466E ASP 3.1 0.2 - - - -
467E ALA* 1.3 77.8 - - - +
469E ARG* 1.3 57.6 + - + +
471E TYR 3.7 0.3 + - - -
472E THR* 2.4 37.0 + - - +
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Residues in contact with ARG 469 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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136E PHE* 3.7 39.9 - - - -
242E ARG* 3.2 3.8 + - - -
460E LEU* 3.8 23.4 - - + +
465E PRO 3.4 10.1 + - - +
466E ASP* 2.9 10.3 + - - +
468E VAL* 1.3 80.7 - - + +
470E PHE* 1.3 59.5 + - - +
472E THR* 2.6 36.5 + - - +
473E LYS* 5.2 0.4 - - - +
474E ARG* 3.6 16.4 - - - +
459F ASP 4.6 7.5 + - - +
460F LEU* 4.2 11.9 - - - +
466F ASP* 2.7 42.4 + - - -
469F ARG* 6.2 4.0 - - + +
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Residues in contact with PHE 470 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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139E MET* 4.1 3.1 - - - +
219E ALA* 4.0 12.5 - - + +
220E VAL 3.8 7.2 - - - -
221E SER* 3.2 18.6 - - - -
242E ARG* 2.8 41.5 + - + +
243E CYS* 3.6 33.9 - - - -
244E GLN* 3.2 45.1 - - + +
460E LEU* 3.5 13.4 - - + +
466E ASP 2.8 11.9 + - - +
467E ALA* 3.6 7.0 - - - +
469E ARG* 1.3 78.4 - - - +
471E TYR* 1.3 79.2 + + - +
472E THR 3.2 0.7 + - - -
459F ASP* 3.6 20.2 - - - -
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Residues in contact with TYR 471 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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139E MET* 3.7 9.0 + - - +
142E VAL* 3.7 31.0 - - + -
157E TRP 4.7 1.3 + - - -
158E MET* 3.4 43.2 - - - +
161E MET* 4.0 2.0 - - + -
162E ALA* 3.5 31.2 - - + -
165E CYS* 3.9 7.4 - - + +
167E ASN* 2.7 38.7 + - - +
169E PHE* 4.5 0.9 - + - -
219E ALA* 5.2 0.7 - - + -
221E SER* 3.0 28.9 + - - -
244E GLN* 4.3 3.7 + - - -
467E ALA* 2.7 45.0 + - + +
468E VAL 4.0 0.2 - - - -
470E PHE* 1.3 85.3 - + - +
472E THR* 1.3 64.6 + - - +
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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