Contacts of the helix formed by residues 463 - 471 (chain F) 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 F).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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107F ASN* 3.3 21.5 - - + +
157F TRP* 3.4 67.1 + + - +
161F MET* 5.8 1.3 - - + -
244F GLN* 5.2 1.4 + - - -
442F VAL* 3.7 13.3 - - - +
443F PRO 2.5 22.8 + - - -
444F VAL 3.3 12.1 - - - -
445F ALA* 3.7 9.2 - - - -
447F HIS 3.1 29.6 - - - -
448F SER* 2.5 24.9 + - - -
449F PHE* 3.3 29.1 - - + +
462F ALA* 1.3 88.0 - - - +
464F GLY* 1.3 64.4 + - - +
467F ALA* 3.3 26.7 + - - +
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Residues in contact with GLY 464 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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110F TYR* 3.6 16.8 - - - -
161F MET* 4.4 2.7 - - - +
445F ALA 3.4 19.7 + - - -
447F HIS 3.4 3.8 - - - -
448F SER* 3.4 1.6 - - - -
463F TYR* 1.3 84.4 - - - +
465F PRO* 1.3 73.0 - - - +
467F ALA* 3.2 12.9 + - - +
468F VAL* 3.5 9.0 + - - +
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Residues in contact with PRO 465 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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121E GLU* 4.0 11.7 - - - +
474E ARG* 3.9 18.2 - - - +
110F TYR* 3.5 12.8 - - - +
446F TYR 3.4 17.7 - - - +
447F HIS* 3.9 3.8 - - - -
448F SER* 3.2 9.4 - - - +
464F GLY* 1.3 83.6 - - - +
466F ASP* 1.3 61.5 + - - +
468F VAL* 3.4 20.7 + - + +
469F ARG* 3.6 11.1 + - - +
116H GLU* 5.7 0.7 - - - +
119H LYS* 3.5 24.2 - - - +
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Residues in contact with ASP 466 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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469E ARG* 2.7 30.7 + - - -
474E ARG* 2.7 37.4 + - - -
448F SER* 3.2 8.4 + - - +
460F LEU* 4.1 8.3 - - + +
461F HIS* 3.1 45.1 + - - +
465F PRO* 1.3 71.1 - - - +
467F ALA* 1.3 55.4 + - - +
468F VAL 3.1 1.6 - - - -
469F ARG* 2.8 13.7 + - - +
470F PHE* 2.7 34.4 + - - +
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Residues in contact with ALA 467 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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161F MET* 4.0 15.7 - - + -
244F GLN* 5.5 2.5 - - - +
461F HIS 3.9 3.9 + - - -
463F TYR* 3.3 36.2 + - - +
464F GLY 3.2 6.2 + - - +
466F ASP* 1.3 77.6 - - - +
468F VAL* 1.3 56.5 + - - +
470F PHE* 3.7 8.1 - - - -
471F TYR* 2.9 49.5 + - + -
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Residues in contact with VAL 468 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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110F TYR* 5.0 0.2 - - - +
117F LEU* 3.5 43.7 - - + +
118F LEU* 4.3 16.8 - - + -
136F PHE* 5.8 3.8 - - + -
161F MET* 3.5 29.2 - - + -
165F CYS* 4.2 8.0 - - - -
464F GLY 3.8 11.2 - - - +
465F PRO* 3.4 13.5 - - + +
466F ASP 3.1 0.8 - - - -
467F ALA* 1.3 76.7 - - - +
469F ARG* 1.3 60.3 + - + +
471F TYR 3.5 0.9 + - - -
472F THR* 2.7 37.1 + - - +
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Residues in contact with ARG 469 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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459E ASP 4.4 6.9 + - - +
460E LEU* 4.0 12.5 - - + +
461E HIS* 5.9 0.2 - - - -
466E ASP* 2.8 42.4 + - - -
469E ARG* 6.2 4.2 - - + +
136F PHE* 3.8 40.4 - - - -
242F ARG* 3.2 4.0 + - - -
460F LEU* 3.8 20.1 - - + +
465F PRO 3.8 12.3 - - - +
466F ASP* 2.8 9.5 + - - +
468F VAL* 1.3 81.6 - - + +
470F PHE* 1.3 59.3 + - - +
472F THR* 2.6 34.0 + - - +
473F LYS* 5.2 0.2 - - - +
474F ARG* 3.8 14.3 - - - +
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Residues in contact with PHE 470 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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459E ASP* 3.7 18.6 - - - -
139F MET* 4.2 2.1 - - - +
219F ALA* 4.2 12.4 - - + +
220F VAL 3.9 9.6 - - - -
221F SER* 3.3 19.7 - - - -
242F ARG* 2.8 34.3 + - - +
243F CYS* 3.5 35.4 - - - -
244F GLN* 3.5 41.3 - - + +
460F LEU* 3.5 17.6 - - + +
466F ASP 2.7 18.0 + - - +
467F ALA* 3.9 8.3 - - - +
469F ARG* 1.3 74.7 - - - +
471F TYR* 1.3 76.1 + + - +
472F THR 3.2 0.2 - - - -
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Residues in contact with TYR 471 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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138F PRO* 4.2 0.3 - - - +
139F MET* 3.6 10.7 + - - +
142F VAL* 3.6 32.1 - - + -
157F TRP 4.7 0.6 + - - -
158F MET* 3.3 45.3 - - + +
161F MET* 4.0 5.8 - - + -
162F ALA* 3.5 23.8 - - + -
165F CYS* 4.3 7.4 - - + -
167F ASN* 2.9 40.3 + - - +
219F ALA* 5.2 0.9 - - + -
221F SER* 2.8 28.7 + - - -
244F GLN* 3.9 4.1 + - - -
467F ALA* 2.9 41.7 + - + +
468F VAL 3.5 1.1 + - - +
470F PHE* 1.3 88.4 - + - +
472F THR* 1.3 63.8 + - - +
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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