Contacts of the helix formed by residues 495 - 504 (chain N) in PDB entry 1ZYR
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 ARG 495 (chain N).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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114N THR* 3.5 37.8 + - + +
115N LEU* 4.3 3.0 + - - -
116N LEU* 4.1 6.1 - - - +
117N ASP* 3.3 47.5 + - - +
473N LEU* 3.2 33.3 - - - +
477N LEU* 3.6 29.8 - - + +
491N LYS* 3.5 31.3 + - - +
492N ALA 4.5 1.1 - - - -
493N ARG 3.0 0.4 - - - -
494N LYS* 1.3 79.1 - - - +
496N LEU* 1.3 58.2 + - - +
497N GLU 3.0 5.9 + - - -
498N VAL* 3.7 9.5 - - - +
499N VAL* 3.5 17.4 - - + +
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Residues in contact with LEU 496 (chain N).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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474N GLU* 3.5 40.6 - - + +
477N LEU* 3.4 26.1 - - + +
478N LEU* 4.6 10.5 - - + +
481N MET* 5.1 4.0 - - - -
492N ALA 3.7 7.4 + - - +
493N ARG* 3.1 13.1 + - + +
495N ARG* 1.3 75.8 - - - +
497N GLU* 1.3 68.4 + - - +
498N VAL 3.6 0.2 - - - -
499N VAL* 3.3 6.8 + - + +
500N ARG* 3.1 47.8 + - + +
1388N ARG* 4.3 26.7 - - + +
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Residues in contact with GLU 497 (chain N).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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493N ARG* 3.6 8.2 + - + +
494N LYS* 3.4 33.1 - - - +
495N ARG 3.0 0.2 - - - -
496N LEU* 1.3 81.0 - - - +
498N VAL* 1.3 65.6 + - + +
499N VAL 2.9 6.6 + - - -
500N ARG* 3.0 13.7 + - - +
501N ALA* 3.3 12.0 + - - +
1390N LEU 5.3 4.5 - - - +
1391N GLU* 5.5 7.6 - - - +
1449N GLU* 5.2 5.7 - - - +
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Residues in contact with VAL 498 (chain N).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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111N LYS* 4.2 35.0 - - + +
114N THR* 4.2 17.9 - - + -
115N LEU* 3.1 37.7 - - + -
494N LYS 4.9 2.5 - - - +
495N ARG 3.7 13.0 - - - +
497N GLU* 1.3 77.7 - - + +
499N VAL* 1.3 60.9 + - + +
500N ARG 3.5 0.2 - - - -
501N ALA* 4.2 6.8 - - - +
502N PHE* 3.2 32.7 + - + -
1452N ILE* 5.2 9.7 - - + +
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Residues in contact with VAL 499 (chain N).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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115N LEU* 4.0 19.3 - - + -
470N LEU* 3.7 41.5 - - + +
473N LEU* 5.4 9.2 - - + -
474N GLU* 4.5 14.4 - - + +
477N LEU* 4.5 8.7 - - + -
495N ARG* 3.5 21.8 - - + +
496N LEU* 3.7 13.5 - - + +
497N GLU 2.9 1.0 + - - -
498N VAL* 1.3 76.9 - - + +
500N ARG* 1.3 66.8 + - - +
502N PHE* 3.9 3.0 - - - +
503N LEU* 3.0 24.3 + - + +
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Residues in contact with ARG 500 (chain N).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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474N GLU* 2.8 34.1 + - - +
478N LEU* 4.1 18.2 - - - +
496N LEU* 3.1 44.8 - - + +
497N GLU* 3.0 7.8 + - - +
499N VAL* 1.3 77.5 - - - +
501N ALA* 1.3 51.5 + - - +
503N LEU* 3.2 5.0 + - - +
504N ASP* 2.4 54.6 + - - +
1386N ASP* 2.8 35.1 + - - +
1387N SER* 5.4 6.5 - - - +
1388N ARG* 4.2 12.3 - - - +
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Residues in contact with ALA 501 (chain N).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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497N GLU 3.3 10.8 + - - +
498N VAL* 4.2 7.4 - - - +
500N ARG* 1.3 76.0 - - - +
502N PHE* 1.3 71.1 + - - +
504N ASP* 3.1 13.7 + - - +
506N GLY* 3.0 20.7 + - - -
1452N ILE* 4.1 8.1 - - + +
1453N ALA* 3.9 26.3 - - + +
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Residues in contact with PHE 502 (chain N).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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12N LEU* 4.5 6.1 - - + -
111N LYS* 5.9 0.9 - - + -
115N LEU* 3.3 37.9 - - + -
470N LEU* 3.8 16.2 - - + -
498N VAL* 3.2 25.6 + - + +
499N VAL* 3.9 1.8 - - - +
500N ARG 3.4 0.2 - - - -
501N ALA* 1.3 82.1 - - - +
503N LEU* 1.3 64.6 + - - +
504N ASP 3.0 1.7 - - - +
506N GLY* 3.0 20.1 - - - +
507N ASN* 3.3 25.3 - - + +
508N ARG 4.1 2.5 - - - -
509N PRO* 3.6 34.3 - - + -
512N MET* 3.8 9.0 - - + -
1452N ILE* 3.1 53.1 + - + -
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Residues in contact with LEU 503 (chain N).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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470N LEU* 3.4 33.4 - - + +
471N GLU* 3.1 36.8 - - - +
474N GLU* 3.7 26.9 - - - +
499N VAL* 3.0 14.2 + - + +
500N ARG* 3.4 4.7 - - - +
502N PHE* 1.3 80.3 - - - +
504N ASP* 1.3 65.2 + - - +
508N ARG* 5.6 5.8 - - - +
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Residues in contact with ASP 504 (chain N).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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500N ARG* 2.4 48.2 + - - +
501N ALA* 3.4 12.2 + - - +
502N PHE 3.0 3.2 + - - +
503N LEU* 1.3 80.9 - - - +
505N SER* 1.3 73.4 + - - +
506N GLY 2.7 8.8 + - - +
1386N ASP* 4.9 8.6 - - - +
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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