Contacts of the helix formed by residues 463 - 471 (chain I) 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 I).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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103I ARG* 5.7 0.3 + - - -
107I ASN* 3.3 23.6 - - + +
157I TRP* 3.4 65.8 + + - +
161I MET* 6.1 0.9 - - + -
244I GLN* 5.3 1.6 + - - -
442I VAL* 3.9 5.2 - - - +
443I PRO 2.5 23.5 + - - -
444I VAL 3.6 14.1 - - - -
445I ALA* 3.7 9.9 - - - -
447I HIS 3.5 27.4 - - - -
448I SER* 2.7 19.6 + - - -
449I PHE* 3.3 38.3 - - + +
462I ALA* 1.3 92.3 - - - +
464I GLY* 1.3 60.8 + - - +
467I ALA* 3.3 25.1 + - - +
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Residues in contact with GLY 464 (chain I).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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110I TYR* 3.5 16.3 - - - -
161I MET* 4.1 3.0 - - - +
445I ALA 3.4 12.6 + - - -
447I HIS 3.1 11.9 - - - -
463I TYR* 1.3 80.0 - - - +
465I PRO* 1.3 76.2 - - - +
467I ALA* 3.0 15.4 + - - +
468I VAL* 3.4 8.1 + - - +
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Residues in contact with PRO 465 (chain I).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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110I TYR* 3.3 19.9 - - - +
117I LEU* 5.8 0.4 - - + -
446I TYR 3.8 4.7 - - - +
447I HIS* 3.7 13.5 - - - -
448I SER* 3.3 11.9 - - - +
464I GLY* 1.3 82.6 - - - +
466I ASP* 1.3 59.6 + - - +
468I VAL* 3.3 23.9 - - + +
469I ARG* 3.4 11.1 + - - +
116K GLU* 5.5 1.3 - - - +
119K LYS* 3.5 20.4 - - - +
121L GLU* 4.0 10.8 - - - +
474L ARG* 4.2 14.6 - - - +
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Residues in contact with ASP 466 (chain I).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
448I SER* 3.2 8.8 + - - +
460I LEU* 3.8 10.3 - - + +
461I HIS* 2.8 46.2 + - - +
464I GLY 3.1 1.0 + - - -
465I PRO* 1.3 74.4 - - - +
467I ALA* 1.3 60.9 + - - +
469I ARG* 3.0 7.6 + - - +
470I PHE* 2.9 28.6 + - - +
469L ARG* 2.7 33.2 + - - -
474L ARG* 2.9 30.7 + - - +
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Residues in contact with ALA 467 (chain I).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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157I TRP 5.0 0.2 - - - +
161I MET* 3.9 17.9 - - + -
244I GLN* 5.5 2.0 - - - +
461I HIS 3.9 2.6 + - - -
463I TYR* 3.3 38.3 + - - +
464I GLY 3.0 4.1 + - - +
466I ASP* 1.3 76.6 - - - +
468I VAL* 1.3 58.3 + - - +
470I PHE* 4.4 5.6 - - - +
471I TYR* 2.9 51.1 + - + +
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Residues in contact with VAL 468 (chain I).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
117I LEU* 3.6 45.5 - - + +
118I LEU* 4.4 16.8 - - + -
136I PHE* 5.6 4.5 - - + -
161I MET* 3.6 24.5 - - + -
165I CYS* 4.2 9.1 - - - -
464I GLY 3.4 7.8 + - - +
465I PRO* 3.3 17.0 - - + +
466I ASP 3.2 0.6 - - - -
467I ALA* 1.3 78.8 - - - +
469I ARG* 1.3 58.7 + - + +
471I TYR 3.8 0.2 - - - -
472I THR* 2.7 41.1 + - - +
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Residues in contact with ARG 469 (chain I).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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136I PHE* 3.7 42.0 - - - -
242I ARG* 3.2 5.0 + - - -
460I LEU* 3.7 22.8 - - + +
465I PRO 3.4 10.7 + - - +
466I ASP* 3.0 10.5 + - - +
468I VAL* 1.3 81.0 - - + +
470I PHE* 1.3 57.5 + - - +
472I THR* 2.8 29.2 + - - +
474I ARG* 3.5 17.4 - - - +
459L ASP 4.5 7.9 + - - +
460L LEU* 4.1 11.7 - - + +
461L HIS* 6.0 0.2 - - - -
466L ASP* 2.7 41.6 + - - -
469L ARG* 6.4 0.7 - - - +
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Residues in contact with PHE 470 (chain I).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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139I MET* 4.2 3.3 - - - +
219I ALA* 4.0 14.2 - - + +
220I VAL 3.6 6.5 - - - -
221I SER* 3.6 17.0 - - - -
242I ARG* 3.0 37.4 + - + +
243I CYS* 3.4 33.4 - - - -
244I GLN* 3.4 43.7 - - + +
460I LEU* 3.7 11.2 - - + +
466I ASP 2.9 15.5 + - - +
467I ALA* 4.2 4.7 - - - +
469I ARG* 1.3 76.9 - - - +
471I TYR* 1.3 75.4 + + - +
472I THR 3.3 1.6 - - - -
459L ASP* 3.4 24.2 - - - -
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Residues in contact with TYR 471 (chain I).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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138I PRO* 4.4 0.9 - - - +
139I MET* 3.5 12.3 + - - +
142I VAL* 3.8 28.3 - - + -
157I TRP 4.7 0.6 + - - -
158I MET* 3.3 46.5 - - + +
161I MET* 3.9 7.0 - - + -
162I ALA* 3.5 28.0 - - + -
165I CYS* 4.0 7.7 - - + +
167I ASN* 2.9 34.6 + - - +
169I PHE* 4.7 0.2 - - - -
219I ALA* 5.3 0.7 - - + -
221I SER* 2.7 29.9 + - - -
244I GLN* 3.7 5.9 + - - -
467I ALA* 2.9 39.4 + - + +
470I PHE* 1.3 88.3 - + - +
472I THR* 1.3 63.6 + - - +
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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