Contacts of the helix formed by residues 463 - 471 (chain C) 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 C).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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107C ASN* 3.4 25.4 - - - +
157C TRP* 3.4 66.0 + + - +
161C MET* 5.7 0.9 - - - -
244C GLN* 5.4 0.8 + - - -
442C VAL* 3.7 6.2 - - - +
443C PRO 2.6 30.0 + - - -
444C VAL 3.7 4.9 - - - -
445C ALA* 3.8 8.5 - - - -
447C HIS 3.3 28.9 - - - -
448C SER* 2.5 24.7 + - - -
449C PHE* 3.2 39.3 - - + +
462C ALA* 1.3 86.0 - - - +
464C GLY* 1.3 61.7 + - - +
467C ALA* 3.4 25.9 + - - +
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Residues in contact with GLY 464 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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110C TYR* 3.6 19.4 - - - -
161C MET* 4.0 3.2 - - - +
445C ALA 3.4 14.0 + - - -
447C HIS 3.1 14.8 + - - -
463C TYR* 1.3 83.2 - - - +
465C PRO* 1.3 74.5 - - - +
467C ALA* 3.3 11.1 + - - +
468C VAL* 3.7 6.2 + - - +
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Residues in contact with PRO 465 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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116A GLU* 4.8 0.9 - - - +
119A LYS* 3.7 22.4 - - - +
110C TYR* 3.7 11.6 - - - +
446C TYR 3.8 13.7 - - - +
447C HIS* 3.8 7.2 - - - -
448C SER* 3.4 10.3 - - - +
464C GLY* 1.3 82.5 - - - +
466C ASP* 1.3 61.2 + - - +
468C VAL* 3.3 22.6 + - + +
469C ARG* 3.5 11.3 + - - +
121D GLU* 3.8 13.5 - - - +
474D ARG* 4.0 15.5 - - - +
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Residues in contact with ASP 466 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
448C SER* 3.1 10.5 + - - +
460C LEU* 4.0 8.7 - - + +
461C HIS* 3.1 41.4 + - - +
465C PRO* 1.3 76.9 - - - +
467C ALA* 1.3 62.2 + - - +
469C ARG* 3.1 10.1 + - - +
470C PHE* 2.8 29.6 + - - +
469D ARG* 2.5 35.7 + - - -
474D ARG* 2.9 31.6 + - - +
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Residues in contact with ALA 467 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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157C TRP 5.0 0.2 - - - +
161C MET* 3.8 16.8 - - + -
244C GLN* 5.5 2.0 - - - +
461C HIS 3.9 3.7 + - - +
463C TYR* 3.4 38.0 + - - +
464C GLY 3.3 3.9 + - - +
465C PRO 3.3 0.6 - - - -
466C ASP* 1.3 80.7 - - - +
468C VAL* 1.3 52.5 + - - +
470C PHE* 4.3 6.3 - - - -
471C TYR* 2.8 55.0 + - + +
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Residues in contact with VAL 468 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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117C LEU* 3.6 41.5 - - + +
118C LEU* 4.4 9.4 - - + -
136C PHE* 5.6 4.9 - - + -
161C MET* 3.5 30.7 - - + -
165C CYS* 4.1 15.7 - - - -
464C GLY 3.9 6.5 - - - +
465C PRO* 3.3 13.9 + - + +
466C ASP 3.2 0.4 - - - -
467C ALA* 1.3 76.4 - - - +
469C ARG* 1.3 60.5 + - + +
472C THR* 2.5 38.6 + - - +
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Residues in contact with ARG 469 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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136C PHE* 3.9 35.7 - - - -
242C ARG* 3.2 4.9 + - - -
460C LEU* 3.7 22.3 - - + +
465C PRO 3.9 11.7 - - - +
466C ASP* 3.1 11.4 + - - +
468C VAL* 1.3 81.9 - - + +
470C PHE* 1.3 60.5 + - - +
472C THR* 2.9 27.6 + - - +
473C LYS* 5.4 0.2 - - - +
474C ARG* 3.5 16.0 - - - +
459D ASP 4.4 8.0 + - - +
460D LEU* 4.0 11.6 - - + +
466D ASP* 2.8 43.0 + - - -
469D ARG* 6.1 6.1 - - + +
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Residues in contact with PHE 470 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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139C MET* 4.3 2.6 - - - +
219C ALA* 4.2 14.4 - - + +
220C VAL 3.7 9.4 - - - -
221C SER* 3.2 21.1 - - - -
242C ARG* 2.8 38.2 + - - +
243C CYS* 3.7 28.7 - - - -
244C GLN* 3.5 44.0 - - + +
460C LEU* 3.5 13.4 - - + +
466C ASP 2.8 16.2 + - - +
467C ALA* 3.9 4.5 - - - +
469C ARG* 1.3 79.9 - - - +
471C TYR* 1.3 74.4 + + - +
472C THR 3.3 0.9 - - - -
459D ASP* 3.6 19.7 - - - -
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Residues in contact with TYR 471 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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138C PRO* 4.4 0.5 - - - +
139C MET* 3.6 8.2 + - - +
142C VAL* 3.6 33.2 - - + -
157C TRP 4.8 0.8 + - - -
158C MET* 3.4 44.0 - - + +
161C MET* 4.0 5.2 - - + -
162C ALA* 3.6 23.8 - - + -
165C CYS* 4.1 7.8 - - + +
167C ASN* 2.8 39.7 + - - +
169C PHE* 4.6 0.2 - - - -
219C ALA* 5.2 0.7 - - + -
221C SER* 2.8 29.9 + - - -
244C GLN* 3.7 5.1 + - - -
467C ALA* 2.8 44.5 + - + +
470C PHE* 1.3 86.9 - + - +
472C THR* 1.3 64.8 + - - +
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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