Contacts of the strand formed by residues 21 - 27 (chain E) in PDB entry 2POZ
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 21 (chain E).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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10E ILE* 4.4 2.9 - - + -
11E TYR 3.2 7.6 - - - +
12E LEU* 3.8 8.1 - - + -
19E HIS 3.6 10.5 - - - +
20E PRO* 1.3 75.6 - - - +
22E LEU* 1.3 62.6 + - - +
36E GLU* 3.5 8.6 + - - +
37E ALA* 3.0 37.4 + - + +
39E ILE 4.1 12.5 + - - +
45E GLY 3.5 21.1 - - - +
48E ALA* 4.2 7.6 - - + -
49E ALA* 3.9 30.5 - - + +
52E ILE* 4.0 18.1 - - + +
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Residues in contact with LEU 22 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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10E ILE* 3.4 8.3 - - - +
11E TYR* 2.8 46.3 + - + -
13E LEU* 4.3 14.1 - - + -
20E PRO* 4.6 3.4 - - + -
21E VAL* 1.3 78.3 - - - +
23E VAL* 1.3 62.2 + - - +
35E GLY 3.5 3.8 - - - +
36E GLU* 3.5 41.5 - - + +
52E ILE* 4.7 2.9 - - - +
311E SER* 3.9 5.6 - - - +
313E LEU* 4.1 6.5 - - + -
346E VAL* 3.8 33.2 - - + -
370E LEU* 4.5 14.4 - - + -
375E ILE* 4.2 17.9 - - + -
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Residues in contact with VAL 23 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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8E VAL* 3.4 29.2 - - + -
9E ASN 3.3 6.1 - - - +
11E TYR* 5.1 1.3 - - - -
22E LEU* 1.3 76.0 - - - +
24E GLU* 1.3 67.0 + - - +
25E ILE* 4.4 5.8 - - + -
34E ALA* 3.4 4.7 - - - +
35E GLY* 2.9 42.3 + - - +
52E ILE* 3.7 27.1 - - + -
95E ALA* 3.5 34.1 - - + +
96E ILE* 4.2 4.3 - - + +
99E ALA* 4.4 7.2 - - + -
313E LEU* 5.2 0.3 - - - +
370E LEU* 5.3 1.4 - - - +
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Residues in contact with GLU 24 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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7E GLY 3.9 0.3 - - - +
8E VAL* 3.4 3.5 - - - -
9E ASN* 3.0 41.1 + - + +
11E TYR* 3.7 27.3 + - + -
23E VAL* 1.3 75.1 - - - +
25E ILE* 1.3 69.7 + - - +
26E SER* 4.0 12.5 + - - +
32E THR* 4.5 18.7 + - - +
33E GLY 3.2 9.9 - - - +
370E LEU* 4.3 16.3 - - + +
372E LYS* 3.5 30.9 - - - +
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Residues in contact with ILE 25 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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5E ILE* 3.6 37.2 - - + -
7E GLY 3.6 3.1 - - - +
8E VAL* 4.4 10.1 - - + -
23E VAL* 4.4 8.5 - - + -
24E GLU* 1.3 76.0 - - - +
26E SER* 1.3 66.4 + - - +
31E ILE 4.1 0.5 - - - +
32E THR* 3.2 7.1 - - - -
33E GLY 2.7 38.1 + - - +
60E LEU* 4.3 8.7 - - + -
96E ILE* 4.0 27.8 - - + +
99E ALA* 3.5 26.2 - - + -
100E LEU* 4.3 13.0 - - + +
103E ILE* 4.1 15.2 - - + +
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Residues in contact with SER 26 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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5E ILE* 3.4 8.7 - - - +
6E THR* 2.8 33.3 + - - -
7E GLY* 2.8 18.8 + - - -
9E ASN* 6.0 1.0 - - - -
24E GLU* 4.3 14.4 + - - +
25E ILE* 1.3 75.5 - - - +
27E THR* 1.3 63.3 + - - +
31E ILE 4.2 2.2 - - - -
32E THR* 4.3 12.7 - - - +
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Residues in contact with THR 27 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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3E LEU* 3.6 29.6 - - + +
4E LYS 3.1 13.0 - - - +
5E ILE* 4.7 2.7 - - + -
6E THR* 3.6 8.9 + - - -
26E SER* 1.3 79.7 - - - +
28E ASP* 1.3 59.5 + - - +
29E GLU 2.9 6.7 + - - -
30E GLY* 3.3 9.4 + - - -
31E ILE* 2.5 43.9 + - - +
32E THR* 5.3 0.4 - - - +
65E PRO* 4.4 9.9 - - + -
103E ILE* 3.8 22.7 - - + -
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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