Contacts of the strand formed by residues 5 - 12 (chain F) 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 ILE 5 (chain F).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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4F LYS* 1.3 73.8 - - - +
6F THR* 1.3 62.4 + - - +
7F GLY 3.9 11.2 - - - +
8F VAL* 4.2 7.9 - - + -
25F ILE* 3.8 28.5 - - + -
26F SER 3.5 11.0 - - - +
27F THR* 4.3 2.0 - - + +
60F LEU* 3.5 47.8 - - + +
61F ILE* 4.0 3.2 - - - +
62F GLY* 2.8 28.6 + - - -
63F LYS* 2.9 21.0 + - + +
65F PRO* 4.1 16.8 - - + -
71F LEU* 4.8 0.9 - - + -
100F LEU* 4.2 20.0 - - + -
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Residues in contact with THR 6 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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4F LYS* 3.4 8.3 + - + +
5F ILE* 1.3 78.0 - - - +
7F GLY* 1.3 58.7 + - - +
26F SER* 2.8 23.5 + - - -
27F THR 3.6 5.9 + - - -
28F ASP* 3.5 34.9 - - + +
61F ILE* 4.6 6.5 - - - +
384F THR* 3.7 26.1 - - - +
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Residues in contact with GLY 7 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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5F ILE* 3.7 3.5 - - - +
6F THR* 1.3 86.0 + - - +
8F VAL* 1.3 70.0 + - - +
9F ASN* 4.3 1.1 - - - -
24F GLU 4.4 0.2 - - - -
25F ILE* 3.5 0.3 - - - -
26F SER* 2.8 33.6 + - - +
61F ILE* 5.1 1.6 - - - -
383F CYS 3.2 12.1 - - - -
384F THR* 4.1 7.0 - - - -
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Residues in contact with VAL 8 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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5F ILE* 4.2 13.7 - - + -
7F GLY* 1.3 80.6 - - - +
9F ASN* 1.3 62.4 + - - +
10F ILE* 4.4 5.6 - - + -
23F VAL* 3.4 30.5 - - + -
24F GLU 3.4 4.7 - - - +
25F ILE* 4.3 8.3 - - + -
56F SER* 3.3 31.0 - - - +
60F LEU* 4.0 25.1 - - + -
61F ILE* 4.8 4.0 - - + -
381F ALA 4.0 0.2 - - - +
382F SER* 3.5 1.7 - - - -
383F CYS* 2.8 43.6 + - + +
384F THR* 5.0 0.2 - - - +
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Residues in contact with ASN 9 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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7F GLY 4.3 0.6 - - - -
8F VAL* 1.3 76.5 + - - +
10F ILE* 1.3 60.7 + - - +
11F TYR* 3.4 31.9 + - + +
23F VAL* 3.3 6.8 - - - +
24F GLU* 2.9 45.0 + - - +
26F SER* 5.7 0.8 + - - -
372F LYS* 4.8 0.5 + - - -
376F GLU* 5.3 2.1 - - - +
379F LEU* 3.7 12.0 - - + +
381F ALA 3.5 1.6 - - - -
382F SER* 2.8 33.7 + - - +
383F CYS 4.6 0.2 - - - +
384F THR* 5.9 2.4 - - - +
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Residues in contact with ILE 10 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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8F VAL* 4.4 4.0 - - + -
9F ASN* 1.3 79.6 - - - +
11F TYR* 1.3 59.5 - - - +
21F VAL* 4.6 2.5 - - + -
22F LEU 3.5 7.6 - - - +
23F VAL* 4.5 0.2 - - + -
49F ALA* 3.8 34.3 - - + +
52F ILE* 3.6 24.2 - - + +
53F LYS* 3.2 46.7 - - + +
56F SER* 4.5 1.6 - - - +
379F LEU* 3.6 2.4 - - - -
380F TRP* 2.6 37.0 + - + +
381F ALA* 2.8 22.4 + - + +
383F CYS* 4.3 14.8 - - - -
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Residues in contact with TYR 11 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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9F ASN* 3.4 36.6 + - + +
10F ILE* 1.3 74.5 - - - +
12F LEU* 1.3 60.2 + - - +
13F LEU* 3.6 19.5 - - + -
20F PRO 3.7 1.0 - - - +
21F VAL* 3.3 9.2 - - - +
22F LEU* 2.8 54.5 + - + +
23F VAL 4.6 0.4 - - - -
24F GLU* 3.5 15.4 + - + -
372F LYS* 2.9 24.1 + - - -
375F ILE* 3.2 52.9 - - + -
376F GLU* 3.8 10.0 + - - -
378F TYR 3.5 3.6 - - - +
379F LEU* 3.6 28.9 - - + +
380F TRP* 4.5 0.7 - - - -
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Residues in contact with LEU 12 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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11F TYR* 1.3 72.3 - - - +
13F LEU* 1.3 64.4 + - - +
19F HIS* 4.3 12.8 - - + +
20F PRO 3.9 0.4 - - - -
21F VAL* 3.8 25.4 - - + -
45F GLY* 3.8 14.6 - - - +
46F THR* 3.9 25.6 - - + +
49F ALA* 4.6 4.9 - - + -
378F TYR* 3.1 25.5 + - - +
380F TRP* 3.7 41.8 - - + +
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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