Contacts of the helix formed by residues 463 - 471 (chain K) 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 K).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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103K ARG* 5.7 0.2 + - - -
107K ASN* 3.4 21.5 - - + +
157K TRP* 3.3 67.7 + + - +
161K MET* 5.7 1.6 - - + -
244K GLN* 5.2 1.4 + - - -
442K VAL* 3.9 5.4 - - - +
443K PRO 2.8 21.5 + - - -
444K VAL 3.4 12.6 - - - -
445K ALA* 3.7 8.5 - - - -
447K HIS 3.3 29.4 - - - -
448K SER* 2.4 25.5 + - - -
449K PHE* 3.2 37.0 - - + +
461K HIS 3.7 2.0 + - - +
462K ALA* 1.3 82.3 - - - +
464K GLY* 1.3 63.6 + - - +
467K ALA* 3.3 25.5 + - - +
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Residues in contact with GLY 464 (chain K).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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110K TYR* 3.5 16.9 - - - -
161K MET* 4.3 3.2 - - - +
445K ALA 3.3 12.8 + - - -
447K HIS 3.2 11.7 - - - -
463K TYR* 1.3 81.0 - - - +
465K PRO* 1.3 76.9 - - - +
467K ALA* 3.2 11.6 + - - +
468K VAL* 3.6 12.1 + - - +
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Residues in contact with PRO 465 (chain K).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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116I GLU* 4.8 0.4 - - - +
119I LYS* 3.6 14.1 - - - +
121J GLU* 3.8 12.8 - - - +
474J ARG* 3.9 17.5 - - - +
110K TYR* 3.7 10.8 - - - +
117K LEU* 6.1 0.2 - - + -
446K TYR 3.4 24.7 - - - +
447K HIS* 3.7 7.4 - - - -
448K SER* 3.3 10.1 - - - +
464K GLY* 1.3 84.0 - - - +
466K ASP* 1.3 60.7 + - - +
468K VAL* 3.2 23.5 + - + +
469K ARG* 3.6 10.4 + - - +
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Residues in contact with ASP 466 (chain K).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
469J ARG* 2.9 26.4 + - - -
474J ARG* 2.6 42.5 + - - +
448K SER* 3.2 7.3 + - - +
460K LEU* 4.0 11.0 - - + +
461K HIS* 3.0 48.0 + - - +
464K GLY 3.2 0.8 - - - -
465K PRO* 1.3 75.4 - - - +
467K ALA* 1.3 59.9 + - - +
469K ARG* 3.0 7.5 + - - +
470K PHE* 2.8 28.8 + - - +
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Residues in contact with ALA 467 (chain K).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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157K TRP 4.8 0.4 - - - +
161K MET* 3.7 17.7 - - + -
244K GLN* 5.6 2.0 - - - +
461K HIS 3.9 3.5 + - - +
463K TYR* 3.3 36.0 + - - +
464K GLY 3.2 4.6 + - - +
466K ASP* 1.3 78.8 - - - +
468K VAL* 1.3 56.3 + - - +
470K PHE* 4.2 7.6 - - - -
471K TYR* 2.8 51.2 + - + +
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Residues in contact with VAL 468 (chain K).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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117K LEU* 3.7 40.4 - - + +
118K LEU* 4.0 22.2 - - + -
136K PHE* 5.7 3.6 - - + -
161K MET* 3.6 24.9 - - + -
165K CYS* 4.0 9.9 - - - -
464K GLY 3.7 8.5 - - - +
465K PRO* 3.3 16.4 - - + +
466K ASP 3.1 0.2 - - - -
467K ALA* 1.3 77.3 - - - +
469K ARG* 1.3 61.5 + - + +
471K TYR 3.5 0.5 + - - -
472K THR* 2.7 39.7 + - + +
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Residues in contact with ARG 469 (chain K).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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459J ASP 4.4 7.8 + - - +
460J LEU* 4.1 13.6 - - + +
461J HIS* 6.0 0.2 - - - -
466J ASP* 2.7 40.6 + - - -
469J ARG* 6.3 2.1 - - - +
136K PHE* 3.8 42.6 - - - -
242K ARG* 3.1 5.7 + - - +
460K LEU* 3.9 21.6 - - + +
465K PRO 3.6 11.4 + - - +
466K ASP* 3.0 9.5 + - - +
468K VAL* 1.3 80.4 - - + +
470K PHE* 1.3 59.0 + - - +
472K THR* 2.9 28.3 + - - +
474K ARG* 3.9 14.3 - - - +
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Residues in contact with PHE 470 (chain K).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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459J ASP* 3.7 18.4 - - - -
139K MET* 4.2 2.1 - - - +
219K ALA* 4.2 12.0 - - + +
220K VAL 3.8 11.9 - - - -
221K SER* 3.4 18.6 - - - -
242K ARG* 2.7 36.9 + - - +
243K CYS* 3.7 33.0 - - - -
244K GLN* 3.7 41.1 - - + +
460K LEU* 3.7 11.0 - - + +
466K ASP 2.8 15.5 + - - +
467K ALA* 3.9 7.4 - - - +
469K ARG* 1.3 79.3 - - - +
471K TYR* 1.3 78.2 + + - +
472K THR 3.3 0.8 + - - -
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Residues in contact with TYR 471 (chain K).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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138K PRO* 4.3 0.2 - - - +
139K MET* 3.6 14.4 + - - +
142K VAL* 3.7 33.2 - - + -
157K TRP 4.6 0.8 + - - -
158K MET* 3.3 45.2 - - - +
161K MET* 4.0 4.7 - - + -
162K ALA* 3.4 24.5 - - + -
165K CYS* 4.3 6.3 - - + -
167K ASN* 2.7 35.1 + - - +
169K PHE* 4.5 0.6 - + - -
219K ALA* 5.2 0.7 - - + -
221K SER* 2.8 29.0 + - - -
244K GLN* 4.0 3.8 + - - -
463K TYR 6.0 0.2 - - - -
467K ALA* 2.8 40.6 + - + +
468K VAL 4.3 1.3 - - - +
470K PHE* 1.3 91.4 - + - +
472K THR* 1.3 62.2 + - - +
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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