Contacts of the helix formed by residues 463 - 471 (chain B) 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 B).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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107B ASN* 3.4 25.1 - - + +
157B TRP* 3.3 66.1 + + - +
161B MET* 5.7 1.6 - - + -
244B GLN* 5.3 1.0 + - - -
442B VAL* 3.7 5.4 - - - +
443B PRO* 2.6 23.6 + - - +
444B VAL 3.3 24.7 - - - -
445B ALA* 4.0 4.3 - - - -
447B HIS 3.3 21.8 - - - -
448B SER* 2.7 22.2 + - - -
449B PHE* 3.2 38.4 - - + +
462B ALA* 1.3 83.9 - - - +
464B GLY* 1.3 62.1 + - - +
467B ALA* 3.3 26.8 + - - +
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Residues in contact with GLY 464 (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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107B ASN* 5.0 0.2 - - - +
110B TYR* 3.6 19.6 - - - -
161B MET* 4.1 3.9 - - - +
445B ALA 3.2 14.6 + - - -
447B HIS 2.9 20.9 - - - -
463B TYR* 1.3 82.5 - - - +
465B PRO* 1.4 67.4 - - - +
467B ALA* 3.6 8.5 + - - +
468B VAL* 3.9 5.5 - - - +
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Residues in contact with PRO 465 (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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121A GLU* 3.9 13.2 - - - +
474A ARG* 4.1 13.9 - - - +
110B TYR* 3.4 17.9 - - - +
446B TYR 3.5 13.9 - - - +
447B HIS* 3.6 6.7 - - - -
448B SER* 3.3 11.7 - - - +
464B GLY* 1.4 79.3 - - - +
466B ASP* 1.3 65.1 + - - +
468B VAL* 3.0 24.8 + - + +
469B ARG* 3.7 7.0 + - - +
116D GLU* 5.4 0.9 - - - +
119D LYS* 3.6 18.4 - - - +
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Residues in contact with ASP 466 (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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469A ARG* 2.4 36.3 + - - -
474A ARG* 2.8 30.6 + - - +
448B SER* 3.1 10.5 + - - +
459B ASP 4.6 0.2 - - - +
460B LEU* 3.8 12.2 - - + +
461B HIS* 3.0 45.7 + - - +
465B PRO* 1.3 74.5 - - - +
467B ALA* 1.3 57.0 + - - +
469B ARG* 3.0 10.8 + - - +
470B PHE* 2.9 26.3 + - - +
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Residues in contact with ALA 467 (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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157B TRP 5.0 0.2 - - - +
161B MET* 3.8 16.2 - - + -
244B GLN* 5.5 2.2 - - - +
461B HIS 4.0 2.8 + - - +
463B TYR* 3.3 38.9 + - - +
464B GLY 3.7 3.4 - - - +
465B PRO 3.1 0.8 - - - -
466B ASP* 1.3 76.7 - - - +
468B VAL* 1.3 63.7 + - - +
470B PHE* 3.7 9.0 - - - -
471B TYR* 3.0 41.4 + - + +
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Residues in contact with VAL 468 (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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117B LEU* 3.6 44.0 - - + +
118B LEU* 3.9 22.4 - - + -
136B PHE* 5.7 3.8 - - + -
161B MET* 3.9 16.8 - - - -
165B CYS* 4.0 10.8 - - - -
464B GLY 3.9 10.8 - - - +
465B PRO* 3.0 16.5 + - + +
467B ALA* 1.3 77.0 - - - +
469B ARG* 1.3 59.6 - - + +
471B TYR 3.8 0.2 - - - -
472B THR* 2.7 37.9 + - - +
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Residues in contact with ARG 469 (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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459A ASP 4.4 8.6 + - - +
460A LEU* 4.1 10.8 - - - +
461A HIS* 6.1 0.2 - - - -
466A ASP* 2.7 43.9 + - - -
136B PHE* 3.6 45.1 - - - -
242B ARG* 3.1 5.4 + - - -
460B LEU* 3.7 20.6 - - + +
465B PRO 3.7 9.2 + - - +
466B ASP* 3.0 10.8 + - - +
468B VAL* 1.3 81.8 - - + +
470B PHE* 1.3 58.5 + - - +
471B TYR 3.4 0.2 - - - -
472B THR* 2.8 28.7 + - - +
473B LYS* 5.2 0.2 - - - +
474B ARG* 3.6 15.2 - - - +
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Residues in contact with PHE 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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459A ASP* 3.5 22.7 - - - -
139B MET* 4.2 2.4 - - - +
219B ALA* 4.0 14.8 - - + +
220B VAL 3.6 11.0 - - - -
221B SER* 3.3 18.8 - - - -
242B ARG* 2.7 41.5 + - + +
243B CYS* 3.6 28.0 - - - -
244B GLN* 3.5 46.7 - - + +
460B LEU* 3.5 12.3 - - + +
466B ASP 2.9 13.9 + - - +
467B ALA* 4.0 6.7 - - - +
468B VAL 3.4 0.2 - - - -
469B ARG* 1.3 79.1 - - - +
471B TYR* 1.3 71.5 + + - +
472B THR 3.3 0.7 - - - -
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Residues in contact with TYR 471 (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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139B MET* 3.5 12.3 + - - +
142B VAL* 3.8 29.8 - - + -
157B TRP 4.5 1.5 + - - -
158B MET* 3.1 49.6 - - - +
161B MET* 4.0 7.2 - - + -
162B ALA* 3.5 25.4 - - + -
165B CYS* 4.2 6.7 - - + -
167B ASN* 2.8 33.8 + - - +
169B PHE* 4.4 0.7 - + - -
219B ALA* 5.3 1.1 - - + -
221B SER* 3.1 27.2 + - - -
244B GLN* 4.0 5.5 + - - -
467B ALA* 3.0 36.8 + - + +
470B PHE* 1.3 88.7 - + - +
472B THR* 1.3 64.4 + - - +
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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