Contacts of the helix formed by residues 19 - 29 (chain B) in PDB entry 2OOR
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 SER 19 (chain B).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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18B ILE* 1.3 76.7 - - - +
20B PRO* 1.4 69.3 - - - +
21B GLU* 3.7 9.2 + - - +
22B VAL* 3.2 26.7 + - - +
23B VAL* 2.9 28.2 + - - +
45B ILE* 4.2 3.6 - - - -
50B LEU* 4.1 5.8 - - - -
333B PRO* 4.0 31.2 + - - +
336B ALA* 3.8 2.8 - - - +
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Residues in contact with PRO 20 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
19B SER* 1.4 86.3 - - - +
21B GLU* 1.3 62.2 + - - +
23B VAL* 3.3 1.5 + - + -
24B LYS* 3.2 23.5 + - + +
45B ILE* 4.0 24.5 - - + -
49B ALA* 4.0 19.1 - - + +
50B LEU* 3.9 13.9 - - + -
53B ALA* 3.3 28.8 - - + +
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Residues in contact with GLU 21 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
19B SER* 3.3 9.4 + - - +
20B PRO* 1.3 80.0 - - - +
22B VAL* 1.3 63.7 + - + +
24B LYS* 3.5 15.0 + - + +
25B LYS* 3.4 30.5 + - + +
333B PRO* 5.8 3.8 - - - +
337B LYS* 4.8 23.2 - - - +
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Residues in contact with VAL 22 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
18B ILE* 4.2 4.3 - - + -
19B SER* 3.2 24.4 + - - +
21B GLU* 1.3 78.9 - - + +
23B VAL* 1.3 61.4 + - - +
25B LYS* 3.4 6.1 + - - +
26B LEU* 2.9 33.8 + - + +
72B TRP* 3.6 30.1 - - + -
333B PRO 4.7 1.1 - - - +
336B ALA* 3.9 26.5 - - + +
337B LYS* 3.9 14.1 - - + +
340B LEU* 4.0 23.1 - - + -
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Residues in contact with VAL 23 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
18B ILE* 3.6 22.4 - - + -
19B SER 2.9 21.5 + - - +
20B PRO 3.3 8.0 + - - +
22B VAL* 1.3 75.0 - - - +
24B LYS* 1.3 63.2 - - - +
26B LEU* 3.1 9.3 + - - +
27B VAL* 3.1 22.7 + - + +
33B VAL* 4.1 14.4 - - + -
35B VAL* 5.7 0.2 - - + -
50B LEU* 4.2 12.3 - - + -
53B ALA* 3.4 23.6 - - + +
54B GLY 3.8 3.4 - - - -
55B ALA* 3.5 31.9 - - + +
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Residues in contact with LYS 24 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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20B PRO* 3.2 15.5 + - + +
21B GLU* 3.5 16.2 - - - +
23B VAL* 1.3 76.9 - - - +
25B LYS* 1.3 62.9 + - + +
27B VAL* 3.4 9.4 - - - +
28B GLY* 3.3 17.3 + - - -
53B ALA* 3.6 26.0 - - + +
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Residues in contact with LYS 25 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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21B GLU* 3.4 21.4 + - + +
22B VAL 3.7 3.6 - - - +
23B VAL 3.2 0.4 - - - -
24B LYS* 1.3 79.8 - - + +
26B LEU* 1.3 56.6 + - - +
28B GLY* 3.2 4.3 + - - -
29B LEU* 3.0 38.5 + - + +
337B LYS* 5.9 5.2 - - - +
340B LEU* 3.7 33.0 - - + -
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Residues in contact with LEU 26 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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3B ILE* 4.3 17.5 - - + -
18B ILE* 3.8 25.8 - - + -
22B VAL 2.9 20.5 + - - +
23B VAL 3.1 1.1 + - - +
25B LYS* 1.3 76.2 - - - +
27B VAL* 1.3 59.3 + - - +
29B LEU* 3.2 9.7 + - + +
30B GLY 3.3 0.7 + - - -
31B PHE* 3.0 50.9 + - + +
33B VAL* 3.5 25.6 - - + -
72B TRP* 3.9 24.2 - - + -
340B LEU* 4.0 19.7 - - + -
343B LEU* 4.3 8.3 - - + -
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Residues in contact with VAL 27 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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23B VAL 3.1 14.1 + - - +
24B LYS* 3.4 16.8 - - - +
26B LEU* 1.3 75.1 - - - +
28B GLY* 1.3 62.0 + - - +
30B GLY* 3.0 19.6 + - - -
31B PHE 3.4 21.4 + - - +
32B GLU* 5.5 0.2 - - - -
33B VAL* 4.0 10.1 - - + +
53B ALA 4.8 4.3 - - - +
54B GLY* 3.9 28.5 - - - +
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Residues in contact with GLY 28 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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24B LYS 3.3 6.4 + - - -
25B LYS* 3.2 8.6 + - - -
27B VAL* 1.3 86.1 - - - +
29B LEU* 1.3 59.1 + - - +
30B GLY* 3.5 0.5 + - - -
349B LYS* 3.6 20.6 - - - -
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Residues in contact with LEU 29 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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25B LYS* 3.0 35.2 + - + +
26B LEU* 3.2 11.4 + - + +
28B GLY* 1.3 75.4 - - - +
30B GLY* 1.3 57.4 + - - +
31B PHE* 3.8 16.8 - - + -
340B LEU* 4.7 6.3 - - + -
343B LEU* 4.9 2.0 - - + -
344B THR* 4.1 33.9 - - + +
347B VAL* 3.6 51.0 - - + +
349B LYS* 4.7 18.0 - - + +
352B LYS* 4.5 10.7 - - - +
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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