Contacts of the strand formed by residues 17 - 23 (chain A) in PDB entry 2Z21
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 VAL 17 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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13A ILE* 3.5 5.6 - - - -
14A GLN* 2.9 44.6 + - - +
15A GLY 3.4 0.6 - - - -
16A SER* 1.3 79.1 - - - +
18A LEU* 1.3 59.9 + - - +
19A THR* 3.9 4.3 - - + -
33A SER* 3.9 23.3 - - - -
34A ILE 3.4 5.4 - - - +
35A ASP* 4.1 15.0 - - + +
34B ILE* 6.3 1.1 - - + -
38B SER* 3.6 15.9 - - - +
39B VAL* 3.4 24.2 - - + -
100B TYR* 3.8 29.4 - - + -
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Residues in contact with LEU 18 (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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4A PHE* 3.9 37.9 - - + -
11A SER* 4.4 6.5 - - - -
12A ALA 3.4 17.0 - - - +
13A ILE* 3.9 19.7 - - + +
16A SER 3.8 2.2 + - - -
17A VAL* 1.3 71.2 - - - +
19A THR* 1.3 67.2 + - - +
33A SER* 3.0 4.2 - - - -
34A ILE* 2.9 46.3 + - + +
36A LEU* 4.2 7.4 - - + -
63A LEU* 4.6 4.0 - - + -
87A LEU* 4.3 13.2 - - + -
91A ILE* 3.9 24.7 - - + -
98A LEU* 3.8 10.8 - - + +
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Residues in contact with THR 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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10A ASN 5.0 1.0 + - - -
11A SER* 3.2 2.1 - - - -
12A ALA* 2.9 34.9 + - - +
14A GLN* 3.3 25.6 + - - +
17A VAL* 3.9 6.5 + - + -
18A LEU* 1.3 78.6 - - - +
20A SER* 1.3 65.4 + - - +
32A SER 3.2 7.2 - - - +
33A SER* 3.7 19.5 - - - -
98A LEU* 4.3 0.4 - - - -
100B TYR* 4.2 5.8 - - + -
102B LEU* 3.3 38.4 - - + +
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Residues in contact with SER 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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4A PHE* 4.4 3.8 - - - -
8A CYS* 3.0 24.0 - - - +
9A TYR 3.3 4.8 + - - -
10A ASN 4.6 2.0 - - - -
11A SER* 2.6 27.1 + - - +
18A LEU* 5.1 0.2 - - - -
19A THR* 1.3 77.4 - - - +
21A THR* 1.3 68.8 + - - +
22A CYS* 3.9 5.9 + - - -
30A ASN 3.8 1.0 - - - +
31A THR* 3.5 2.0 - - - -
32A SER* 2.9 32.1 + - - +
98A LEU* 3.9 17.6 - - - +
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Residues in contact with THR 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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8A CYS* 3.2 1.0 - - - -
9A TYR* 2.9 79.3 + - + +
10A ASN* 4.3 6.6 + - - +
20A SER* 1.3 71.1 - - - +
22A CYS* 1.3 61.7 + - - +
29A TYR* 3.6 27.1 - - + -
30A ASN 3.4 4.0 - - - +
31A THR* 3.1 24.6 - - + +
103B GLU* 3.8 12.5 + - - -
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Residues in contact with CYS 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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7A ALA 3.5 4.0 - - - +
8A CYS* 2.0 45.1 - - - -
9A TYR* 5.2 1.1 - - - -
20A SER* 4.1 8.7 - - - -
21A THR* 1.3 75.2 - - - +
23A ILE* 1.3 65.2 + - - +
29A TYR* 3.2 4.8 - - - -
30A ASN 2.8 30.9 + - - +
93A ALA* 3.8 12.1 - - + -
96A GLY* 3.8 26.0 - - - -
98A LEU* 3.9 17.3 - - - -
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Residues in contact with ILE 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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7A ALA* 3.0 35.3 + - + +
9A TYR* 5.2 4.8 - - + -
22A CYS* 1.3 73.2 - - - +
24A ARG* 1.3 70.3 + - - +
25A THR 4.3 0.3 + - - -
27A GLY* 5.5 3.4 - - - +
28A GLY 3.8 10.3 - - - +
29A TYR* 4.4 2.0 - - - +
95A ASP* 4.0 2.1 + - - -
96A GLY* 3.3 18.7 + - - -
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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