Contacts of the helix formed by residues 28 - 40 (chain A) in PDB entry 2P0R
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 28 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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21A ILE* 3.6 24.9 - - - +
27A GLN* 1.3 75.0 - - - +
29A PHE* 1.3 67.5 + - - +
30A GLU* 3.6 8.1 + - - +
31A GLN* 2.8 50.7 + - - +
32A MET* 2.9 13.1 + - - +
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Residues in contact with PHE 29 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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21A ILE* 5.4 0.2 - - - +
28A SER* 1.3 71.5 - - - +
30A GLU* 1.3 85.5 + - + +
32A MET* 3.9 13.3 - - - +
33A ARG* 3.0 53.0 + - - +
120A ASP 6.1 0.4 - - - -
121A GLN* 4.1 9.4 - - + -
130A ILE* 3.8 42.5 - - + +
131A PHE* 4.0 4.9 - - - -
132A HIS* 3.2 52.9 - + + -
143A ASP* 3.9 23.5 + - - +
145A VAL* 3.9 4.2 - - + +
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Residues in contact with GLU 30 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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28A SER* 3.2 7.0 + - - +
29A PHE* 1.3 95.7 - - + +
31A GLN* 1.3 60.7 + - + +
33A ARG* 2.8 33.3 + - - +
34A GLN* 2.9 35.8 + - - +
132A HIS* 5.3 0.9 - - - -
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Residues in contact with GLN 31 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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21A ILE* 5.0 1.4 - - - +
26A GLY 4.7 1.4 - - - +
27A GLN* 3.2 32.9 + - + +
28A SER* 2.8 49.8 + - - +
30A GLU* 1.3 72.6 - - + +
32A MET* 1.3 59.8 + - - +
34A GLN* 3.0 6.5 + - - +
35A GLU* 2.9 30.4 + - - +
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Residues in contact with MET 32 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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23A HIS* 3.3 38.8 - - + -
25A SER* 3.6 7.0 - - - -
27A GLN* 3.3 40.1 - - + +
28A SER 2.9 16.5 + - - +
29A PHE* 3.9 3.4 - - - +
31A GLN* 1.3 75.9 - - - +
33A ARG* 1.3 63.5 + - - +
35A GLU* 3.6 7.7 + - - +
36A CYS* 3.2 28.4 + - - -
43A PHE* 3.9 15.5 - - + -
130A ILE* 4.0 11.9 - - + -
145A VAL* 3.8 28.5 - - + -
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Residues in contact with ARG 33 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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29A PHE* 3.0 45.3 + - - +
30A GLU* 2.8 35.4 + - - +
31A GLN 3.2 0.2 - - - -
32A MET* 1.3 76.3 - - - +
34A GLN* 1.3 70.5 + - - +
36A CYS* 3.4 4.4 + - - +
37A LEU* 3.1 37.6 + - + +
125A PRO 5.0 0.2 + - - -
126A GLY* 2.9 44.1 + - - +
128A ALA* 3.7 5.2 - - + +
130A ILE* 3.6 26.8 - - + +
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Residues in contact with GLN 34 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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30A GLU* 2.9 20.3 + - - +
31A GLN* 3.0 6.5 + - - +
33A ARG* 1.3 93.4 + - - +
35A GLU* 1.3 60.9 + - - +
37A LEU* 3.3 26.7 + - - +
38A GLN* 2.9 38.5 + - - +
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Residues in contact with GLU 35 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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31A GLN 2.9 15.9 + - - +
32A MET* 3.7 9.4 - - - +
34A GLN* 1.3 75.4 - - - +
36A CYS* 1.3 61.2 + - - +
38A GLN* 3.3 6.7 + - - +
39A ARG* 2.9 59.1 + - - +
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Residues in contact with CYS 36 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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32A MET 3.2 14.5 + - - +
33A ARG* 3.6 9.2 - - - +
34A GLN 3.3 0.2 - - - -
35A GLU* 1.3 83.0 - - - +
37A LEU* 1.3 55.3 + - - +
39A ARG* 4.8 0.4 - - - -
40A GLY* 2.6 30.3 + - - -
41A THR* 2.9 34.4 + - - +
42A LEU 4.0 3.8 - - - -
43A PHE* 3.5 42.0 - - - -
128A ALA* 3.7 11.4 - - + -
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Residues in contact with LEU 37 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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33A ARG* 3.1 30.8 + - - +
34A GLN* 3.6 30.3 - - - +
35A GLU 3.3 0.2 - - - -
36A CYS* 1.3 78.3 - - - +
38A GLN* 1.3 62.8 + - - +
40A GLY* 3.4 11.1 + - - -
41A THR 5.2 0.2 - - - -
126A GLY* 3.6 34.1 - - - +
127A TYR 3.6 25.6 - - - +
128A ALA* 4.1 4.3 - - + -
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Residues in contact with GLN 38 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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34A GLN* 2.9 25.1 + - - +
35A GLU* 3.7 6.3 - - - +
37A LEU* 1.3 79.7 - - - +
39A ARG* 1.3 63.0 + - + +
40A GLY* 4.2 0.7 - - - -
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Residues in contact with ARG 39 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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35A GLU* 2.9 46.5 + - - +
36A CYS* 4.2 2.2 - - - +
38A GLN* 1.3 73.7 - - + +
40A GLY* 1.3 60.8 - - - +
41A THR* 3.4 26.6 + - + +
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Residues in contact with GLY 40 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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36A CYS 2.6 15.7 + - - -
37A LEU* 3.7 9.2 - - - -
38A GLN 3.2 3.0 - - - -
39A ARG* 1.3 76.6 - - - +
41A THR* 1.3 58.8 + - - +
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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