Contacts of the strand formed by residues 32 - 37 (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 THR 32 (chain F).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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24F GLU* 4.6 19.0 + - - +
25F ILE 3.2 8.1 - - - +
26F SER* 4.1 20.6 - - - +
30F GLY* 3.7 11.8 + - - +
31F ILE* 1.3 78.7 - - - +
33F GLY* 1.3 57.0 + - - +
103F ILE* 3.7 5.3 - - - +
106F LYS* 2.7 46.0 + - - +
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Residues in contact with GLY 33 (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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24F GLU* 3.4 5.1 - - - +
25F ILE 2.8 34.7 + - - -
32F THR* 1.3 76.1 - - - +
34F ALA* 1.3 61.0 + - - +
99F ALA* 3.5 13.9 - - - +
102F ASP* 3.4 7.6 - - - -
103F ILE* 3.5 20.4 - - - +
106F LYS* 5.5 0.2 - - - -
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Residues in contact with ALA 34 (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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23F VAL 3.4 7.9 - - - +
24F GLU* 5.4 0.2 - - + -
33F GLY* 1.3 74.4 - - - +
35F GLY* 1.3 59.7 + - - +
99F ALA* 3.4 11.2 + - - +
102F ASP* 2.9 11.7 + - - +
313F LEU* 3.9 19.5 - - + -
366F LEU* 3.1 25.3 - - - +
368F ALA 6.1 1.3 - - - +
370F LEU* 3.5 34.8 - - + -
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Residues in contact with GLY 35 (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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22F LEU* 3.4 4.2 - - - -
23F VAL* 2.9 38.1 + - - +
34F ALA* 1.3 75.8 - - - +
36F GLU* 1.3 60.7 + - - -
95F ALA 3.4 19.3 - - - -
98F GLN* 3.5 9.6 - - - -
313F LEU* 3.5 11.2 - - - +
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Residues in contact with GLU 36 (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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20F PRO* 3.7 10.7 - - - +
21F VAL 3.4 14.1 - - - +
22F LEU* 3.4 13.0 - - + +
35F GLY* 1.3 75.8 - - - +
37F ALA* 1.3 72.5 + - - +
38F GLY 3.7 1.6 + - - -
40F ALA* 4.7 1.4 - - - +
95F ALA* 3.6 6.3 - - - +
98F GLN* 2.9 33.3 + - - +
282F GLY* 3.8 1.7 - - - -
310F GLY* 3.3 9.2 - - - -
311F SER* 2.5 48.4 + - - -
313F LEU* 3.5 3.1 - - + +
314F ILE* 3.0 39.7 + - + +
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Residues in contact with ALA 37 (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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21F VAL* 2.9 34.4 + - + +
36F GLU* 1.3 83.7 - - - +
38F GLY* 1.3 57.7 + - - +
39F ILE 2.9 9.7 + - - +
40F ALA* 4.4 2.4 + - - +
48F ALA* 4.4 9.0 - - + -
52F ILE* 4.1 15.5 - - + -
91F ALA* 3.6 32.3 - - + +
95F ALA* 3.6 2.6 - - - +
282F GLY 3.9 0.2 - - - -
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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