Contacts of the strand formed by residues 21 - 27 (chain D) 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 D).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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10D ILE* 4.4 2.9 - - + -
11D TYR 3.2 10.5 - - - +
12D LEU* 4.0 8.5 - - + -
19D HIS 3.7 10.3 - - - +
20D PRO* 1.3 77.4 - - - +
22D LEU* 1.3 60.6 + - - +
36D GLU* 3.3 5.8 - - - +
37D ALA* 3.0 40.7 + - + +
39D ILE 4.0 13.2 + - - +
45D GLY* 3.6 20.4 - - - +
48D ALA* 4.1 6.3 - - + -
49D ALA* 4.1 20.2 - - + +
52D ILE* 3.8 26.1 - - + +
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Residues in contact with LEU 22 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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10D ILE* 3.5 7.1 - - - +
11D TYR* 2.7 48.6 + - + +
13D LEU* 3.9 24.9 - - + -
20D PRO* 4.8 1.6 - - + -
21D VAL* 1.3 76.8 - - - +
23D VAL* 1.3 62.7 + - - +
35D GLY 3.5 2.2 - - - +
36D GLU* 3.4 42.8 - - + +
52D ILE* 5.1 0.9 - - - -
311D SER* 3.6 8.5 - - - +
313D LEU* 3.7 11.4 - - + -
346D VAL* 4.0 27.4 - - + -
370D LEU* 4.8 11.0 - - + -
375D ILE* 4.1 13.9 - - + -
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Residues in contact with VAL 23 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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8D VAL* 3.6 28.3 - - + -
9D ASN 3.4 6.3 - - - +
10D ILE* 4.6 0.2 - - + -
11D TYR* 4.8 1.6 - - - -
22D LEU* 1.3 78.2 - - - +
24D GLU* 1.3 66.6 + - - +
25D ILE* 4.6 5.2 - - + -
34D ALA* 3.5 5.5 - - - +
35D GLY* 2.8 45.0 + - - +
52D ILE* 3.7 24.7 - - + -
95D ALA* 3.5 34.5 - - + +
96D ILE* 4.2 5.2 - - + +
99D ALA* 4.4 6.5 - - + -
313D LEU* 5.2 0.2 - - - +
370D LEU* 5.1 1.8 - - - +
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Residues in contact with GLU 24 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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7D GLY 3.8 0.3 - - - +
8D VAL* 3.4 3.5 - - - -
9D ASN* 2.9 36.6 + - + +
11D TYR* 3.7 19.3 + - + -
23D VAL* 1.3 76.1 - - - +
25D ILE* 1.3 64.6 + - - +
26D SER* 4.0 7.2 + - - +
32D THR* 4.6 20.6 + - + +
33D GLY 3.4 9.4 - - - +
370D LEU* 3.1 24.5 - - + +
372D LYS* 2.9 45.9 - - - +
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Residues in contact with ILE 25 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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5D ILE* 3.5 36.3 - - + -
7D GLY 3.6 3.1 - - - +
8D VAL* 4.4 11.9 - - + +
23D VAL* 4.6 8.3 - - + -
24D GLU* 1.3 75.2 - - - +
26D SER* 1.3 66.6 + - - +
31D ILE 4.2 0.5 - - - +
32D THR* 3.1 8.5 - - - -
33D GLY 2.9 33.0 + - - +
60D LEU* 4.2 8.1 - - + -
96D ILE* 4.0 20.9 - - + +
99D ALA* 3.5 25.4 - - + -
100D LEU* 3.8 20.9 - - + -
103D ILE* 4.0 16.3 - - + +
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Residues in contact with SER 26 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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5D ILE* 3.4 8.7 - - - +
6D THR* 2.7 37.6 + - - -
7D GLY* 2.8 20.6 + - - -
24D GLU* 4.0 8.0 + - - -
25D ILE* 1.3 71.9 - - - +
27D THR* 1.3 59.2 + - - +
32D THR* 3.5 21.6 - - - +
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Residues in contact with THR 27 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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3D LEU* 3.9 20.5 - - + +
4D LYS 3.3 12.8 - - - +
5D ILE* 4.3 5.4 - - + -
6D THR* 3.6 8.8 + - - -
26D SER* 1.3 80.6 - - - +
28D ASP* 1.3 61.9 + - - +
29D GLU 3.0 10.4 + - - -
30D GLY* 3.2 11.3 + - - -
31D ILE* 2.6 46.4 + - - +
32D THR* 4.9 0.6 - - - +
65D PRO* 4.1 13.0 - - + -
103D ILE* 4.0 16.4 - - + -
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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