Contacts of the strand formed by residues 18 - 25 (chain A) in PDB entry 1Z0I
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 18 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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17A ALA* 1.3 73.7 - - - +
19A SER* 1.3 56.5 + - - +
20A PHE* 3.5 37.9 - + + -
66A LYS* 4.2 21.3 - - + -
67A ARG 3.0 19.8 + - - +
68A VAL* 3.5 4.4 - - + -
69A ASN* 2.7 35.6 + - - +
181A ILE* 3.7 46.4 + - + +
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Residues in contact with SER 19 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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17A ALA 3.7 4.5 + - - -
18A TYR* 1.3 72.1 + - - +
20A PHE* 1.3 69.5 + - - +
69A ASN* 3.6 24.7 + - - +
93A ASN* 3.8 6.1 + - - -
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Residues in contact with PHE 20 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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18A TYR* 3.5 42.0 - + + -
19A SER* 1.3 77.5 - - - +
21A LYS* 1.3 60.1 - - - +
68A VAL* 3.9 21.1 - - + -
69A ASN 3.0 9.5 + - - +
70A LEU* 3.9 9.2 - - + +
71A ALA* 3.1 28.5 + - - +
93A ASN* 3.2 23.1 - - + +
177A CYS* 4.1 6.3 - - - -
180A MET* 3.8 58.8 - - + -
181A ILE* 3.7 15.3 - - + -
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Residues in contact with LYS 21 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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20A PHE* 1.3 71.7 - - - +
22A VAL* 1.3 67.6 + - - +
23A VAL* 4.2 2.0 - - - -
71A ALA* 3.7 5.8 - - + -
73A TRP* 3.4 49.0 - - + +
87A ILE 3.6 10.9 + - - -
88A TYR 2.8 26.8 + - - -
90A ARG 2.7 28.6 + - - +
91A ASP* 3.5 19.3 - - + +
92A SER* 3.6 13.2 - - - +
93A ASN* 2.8 37.4 + - - +
94A GLY 3.2 7.1 + - - +
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Residues in contact with VAL 22 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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21A LYS* 1.3 81.1 - - - +
23A VAL* 1.3 68.0 + - - +
24A LEU* 4.7 4.5 - - + -
70A LEU* 3.9 25.8 - - + -
71A ALA 3.0 11.3 + - - +
72A ILE* 4.5 6.0 - - + +
73A TRP* 2.8 30.9 + - - +
94A GLY* 3.5 9.0 - - - +
96A ILE* 3.8 35.4 - - + -
173A PHE* 4.9 4.9 - - + -
176A LEU* 4.0 11.2 - - + -
180A MET* 3.9 22.2 - - + -
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Residues in contact with VAL 23 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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21A LYS* 4.2 2.0 - - - -
22A VAL* 1.3 76.9 - - - +
24A LEU* 1.3 58.4 + - - +
25A LEU* 4.4 14.0 - - + +
73A TRP* 4.0 13.2 - - + -
88A TYR* 3.5 47.3 - - + +
89A TYR* 4.7 9.4 - - + -
92A SER* 3.5 20.4 + - - +
94A GLY 3.4 12.3 + - - +
95A ALA* 3.5 12.6 - - + +
96A ILE* 2.8 31.7 + - - +
117A LEU* 5.5 0.2 - - + -
121A LEU* 5.3 2.2 - - + -
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Residues in contact with LEU 24 (chain A).
Click here for Legend to table.
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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22A VAL* 4.7 1.6 - - + -
23A VAL* 1.3 76.2 - - - +
25A LEU* 1.3 66.8 + - - +
32A LYS* 2.9 56.6 - - + +
35A LEU* 4.6 12.1 - - + -
36A VAL* 4.6 8.3 - - + -
72A ILE* 3.8 28.3 - - + -
73A TRP 3.2 15.6 + - - +
74A ASP* 4.4 7.2 - - - +
75A THR* 4.9 4.3 + - - +
88A TYR* 2.9 18.5 + - - +
96A ILE* 3.4 34.1 - - + +
98A VAL* 5.1 0.7 - - + -
173A PHE* 5.0 3.6 - - + -
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Residues in contact with LEU 25 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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23A VAL* 4.4 14.8 - - + +
24A LEU* 1.3 85.4 - - - +
26A GLY* 1.3 57.6 + - - +
32A LYS* 3.3 14.6 - - - +
75A THR* 6.1 1.1 - - + -
88A TYR* 3.8 21.1 - - + -
89A TYR* 4.1 27.4 - - + +
95A ALA* 4.5 4.7 - - + -
96A ILE 2.8 9.0 + - - +
97A LEU* 3.6 16.2 - - + -
98A VAL 2.9 24.4 + - - -
113A TRP* 4.0 25.1 - - + +
117A LEU* 4.0 32.8 - - + -
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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