Contacts of the strand formed by residues 16 - 23 (chain A) in PDB entry 2WV4
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 THR 16 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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12A VAL* 2.6 29.2 + - - +
13A MET 3.4 9.9 + - - +
14A GLY 4.7 0.3 - - - +
15A ASN* 1.3 77.0 - - - +
17A LYS* 1.3 64.6 + - - +
32A CYS* 4.1 12.8 - - + -
33A ALA 3.4 11.2 - - - +
34A THR* 4.4 9.8 + - - +
118A VAL* 3.8 24.8 + - - +
119A VAL 4.4 0.7 - - - -
120A ASN* 3.1 49.4 + - + +
165A GLY* 5.1 0.4 - - - -
166A ALA* 4.9 0.2 - - - +
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Residues in contact with LYS 17 (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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14A GLY 2.7 26.8 + - - -
15A ASN* 3.8 10.3 - - - +
16A THR* 1.3 79.3 - - - +
18A PRO* 1.3 69.7 - - + +
19A VAL* 3.7 1.0 - - - +
32A CYS* 3.6 2.3 - - - +
33A ALA* 2.9 34.5 + - + +
41A TYR* 3.7 35.7 - - + +
57A LEU* 4.8 3.1 - - + -
58A ASP* 3.5 32.8 - - + +
96A VAL* 4.5 9.5 - - - +
120A ASN 3.7 3.1 - - - -
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Residues in contact with PRO 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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17A LYS* 1.3 91.1 - - + +
19A VAL* 1.3 63.0 + - - +
20A GLU* 3.6 16.6 - - - +
31A CYS 4.1 1.6 - - - +
56A MET 3.6 1.2 - - - +
57A LEU* 3.6 0.7 - - - -
58A ASP* 3.0 40.0 + - + +
59A GLY 5.0 2.0 - - - +
120A ASN* 3.1 35.9 - - - +
121A ASN* 3.9 11.2 - - - -
122A ALA* 4.1 4.3 - - + +
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Residues in contact with VAL 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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18A PRO* 1.3 80.2 - - - +
20A GLU* 1.3 74.4 + - - +
21A LEU* 5.0 2.2 - - + -
30A ILE* 3.5 5.7 - - - +
31A CYS* 2.9 45.6 + - - +
32A CYS 3.7 11.4 - - - +
33A ALA* 3.6 31.4 - - + -
43A VAL* 5.2 2.9 - - + -
47A LEU* 4.7 12.8 - - + -
55A ILE* 4.3 20.0 - - + -
56A MET 3.1 11.2 - - - +
57A LEU* 4.9 5.4 - - + -
88A MET* 6.4 1.3 - - + -
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Residues in contact with GLU 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 PRO* 3.6 13.4 - - - +
19A VAL* 1.3 95.9 + - - +
21A LEU* 1.3 64.9 + - - +
22A ILE* 4.0 14.5 + - + -
27A THR* 4.6 8.1 - - + +
29A ALA 3.4 5.8 - - - +
30A ILE* 4.3 9.2 - - + -
54A LYS 4.0 0.2 - - - +
55A ILE* 3.7 4.3 - - - +
56A MET* 2.9 56.9 + - + +
59A GLY 5.2 4.9 + - - -
122A ALA* 3.4 32.5 + - + +
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Residues in contact with LEU 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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19A VAL* 5.0 1.3 - - + -
20A GLU* 1.3 80.6 - - - +
22A ILE* 1.3 61.5 + - - +
27A THR* 3.2 6.8 - - - -
28A VAL* 2.8 38.7 + - + -
29A ALA* 2.8 22.0 + - + +
47A LEU* 3.6 41.7 - - + +
48A PHE* 6.5 0.2 - - + -
50A GLU* 3.5 32.3 - - + -
52A TYR* 4.0 28.3 - - + -
54A LYS 3.8 0.9 - - - -
55A ILE* 4.3 20.4 - - + -
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Residues in contact with ILE 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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20A GLU* 4.3 12.6 - - + -
21A LEU* 1.3 79.4 - - - +
23A LEU* 1.3 56.7 + - - +
25A GLY* 3.9 14.8 - - - +
26A LYS 3.3 19.3 - - - +
27A THR* 3.4 26.0 - - - +
52A TYR* 3.7 1.7 - - - +
53A ASP* 2.4 36.3 + - - +
54A LYS* 2.9 36.3 + - + +
56A MET* 4.1 22.4 - - + -
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Residues in contact with LEU 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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22A ILE* 1.3 73.4 - - - +
24A ASP* 1.3 91.5 + - - +
26A LYS* 2.7 26.4 + - - +
28A VAL* 3.5 22.2 - - + +
51A LYS* 3.2 54.7 - - + +
52A TYR* 3.9 11.4 - - - +
53A ASP* 3.4 17.7 - - + +
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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