Contacts of the helix formed by residues 14 - 21 (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 SER 14 (chain N).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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12N LEU 3.3 5.4 + - - -
13N ALA* 1.3 71.0 - - - +
15N PRO* 1.3 62.2 - - - +
16N GLU* 4.3 7.0 - - - -
17N LYS* 2.4 47.7 + - - +
18N ILE* 2.7 9.3 + - - -
511N TRP* 2.4 50.4 + - - -
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Residues in contact with PRO 15 (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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13N ALA 3.4 5.7 - - - +
14N SER* 1.3 80.5 - - - +
16N GLU* 1.3 60.7 + - + +
18N ILE* 2.6 35.5 + - + +
19N ARG* 2.8 40.2 + - - +
511N TRP* 3.8 23.8 - - + -
513N ILE 4.8 10.1 - - - +
514N LEU* 5.8 1.3 - - + -
515N GLU* 3.9 32.5 - - + +
516N ALA* 4.4 3.8 - - + +
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Residues in contact with GLU 16 (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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14N SER* 2.9 5.8 + - - -
15N PRO* 1.3 79.6 - - + +
17N LYS* 1.3 61.3 + - - +
19N ARG* 3.3 22.6 + - - +
20N SER* 3.4 12.3 + - - -
511N TRP* 3.9 25.0 - - - -
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Residues in contact with LYS 17 (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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1098M ASP* 3.9 36.5 + - + +
11N ALA* 4.3 10.9 - - - +
12N LEU 3.5 24.0 + - - +
13N ALA* 4.8 4.0 - - - -
14N SER* 2.4 39.6 + - - +
16N GLU* 1.3 67.5 - - - +
18N ILE* 1.3 62.8 + - - +
19N ARG 3.0 2.0 - - - -
20N SER* 2.9 30.9 + - - +
21N TRP* 3.4 23.4 + - + +
507N ASN* 5.5 0.4 + - - -
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Residues in contact with ILE 18 (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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1096M ALA* 5.1 0.2 - - - -
13N ALA* 3.3 31.4 - - + +
14N SER 2.7 17.1 + - - +
15N PRO* 2.6 25.8 + - + +
17N LYS* 1.3 73.3 - - - +
19N ARG* 1.3 55.5 + - - -
20N SER 3.6 0.3 + - - -
21N TRP* 3.8 15.4 + - + +
22N SER* 3.7 19.6 + - - -
91N GLY 5.3 0.2 - - - +
92N HIS* 4.5 6.7 - - + +
514N LEU* 4.6 6.1 - - + -
516N ALA* 3.0 36.3 - - + +
517N VAL 4.3 0.7 - - - -
518N PRO* 3.2 40.8 - - + +
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Residues in contact with ARG 19 (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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1118M LYS* 4.2 6.9 + - - -
15N PRO* 2.8 39.2 + - - +
16N GLU* 3.6 18.2 - - - +
17N LYS 3.0 0.4 - - - -
18N ILE* 1.3 77.8 - - - +
20N SER* 1.3 58.6 + - - +
21N TRP 3.3 1.3 - - - -
22N SER* 4.0 18.4 - - - +
92N HIS* 4.1 20.4 - - + +
94N GLU* 2.7 31.6 + - - -
515N GLU* 4.6 13.1 + - - +
516N ALA* 3.9 13.1 - - + +
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Residues in contact with SER 20 (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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1118M LYS* 3.9 30.1 - - - +
16N GLU 3.4 9.5 + - - -
17N LYS* 2.9 26.8 + - - +
19N ARG* 1.3 79.3 - - - +
21N TRP* 1.3 67.1 + - - +
22N SER 3.5 0.9 - - - -
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Residues in contact with TRP 21 (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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1090M LYS* 5.2 3.1 - - - +
1093M GLN* 3.3 67.1 + - + +
1095M LEU 4.2 1.3 - - - -
1096M ALA 3.6 11.4 - - - -
1097M LEU 3.1 24.0 - - - -
1098M ASP* 3.3 23.4 + - + -
1118M LYS* 5.9 0.4 - - - -
13N ALA* 5.3 0.7 - - + -
17N LYS* 3.4 25.6 + - + +
18N ILE* 4.0 20.6 - - + +
19N ARG 3.3 0.2 - - - -
20N SER* 1.3 90.4 + - - +
22N SER* 1.3 60.5 + - - +
23N TYR* 3.8 14.2 - - - -
90N MET* 3.3 28.4 + - + +
518N PRO* 5.0 6.1 - - + -
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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