Contacts of the helix formed by residues 45 - 57 (chain E) in PDB entry 2CNW
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 GLY 45 (chain E).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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40E LEU* 3.4 13.6 + - - +
43E ASP 3.2 3.4 - - - -
44E VAL* 1.3 80.7 - - - +
46E LEU* 1.3 62.7 + - - -
47E SER* 3.5 3.6 - - - -
48E ALA 4.4 0.4 - - - -
49E THR* 2.6 32.0 + - - -
234E GLN* 3.4 26.9 - - - +
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Residues in contact with LEU 46 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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8B ARG* 4.0 15.7 - - - +
36B ARG* 3.2 62.8 - - + +
39B MET* 3.8 28.0 - - + -
40B ASP* 3.3 23.4 + - - +
36E GLU* 5.9 2.5 - - - +
40E LEU* 3.9 18.6 - - + +
45E GLY* 1.3 71.0 - - - -
47E SER* 1.3 66.5 + - - +
49E THR* 3.4 1.9 + - - -
50E GLU* 3.0 32.8 + - + +
234E GLN* 4.8 0.2 + - - -
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Residues in contact with SER 47 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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40B ASP* 5.3 0.4 + - - -
45E GLY* 4.8 2.1 - - - -
46E LEU* 1.3 80.5 + - - +
48E ALA* 1.3 64.7 + - - +
50E GLU* 3.7 12.1 - - - +
51E GLU* 3.2 37.8 + - - +
234E GLN* 5.3 3.1 + - - -
237E LEU* 5.6 4.7 - - - +
268E PRO* 5.0 7.6 - - - +
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Residues in contact with ALA 48 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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44E VAL* 3.7 27.4 - - + +
45E GLY 4.0 1.0 + - - -
47E SER* 1.3 78.2 + - - +
49E THR* 1.3 59.7 + - - +
51E GLU* 3.7 8.7 + - - +
52E ILE* 3.0 35.1 + - - +
267E ILE* 4.2 9.2 - - + -
268E PRO* 4.0 22.4 - - + -
271E ARG* 4.3 11.0 + - - +
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Residues in contact with THR 49 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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36E GLU* 3.7 32.3 - - + +
39E LEU* 3.6 30.2 - - + +
40E LEU* 3.6 12.0 - - + +
44E VAL* 3.5 14.5 - - - +
45E GLY 2.6 24.6 + - - -
46E LEU* 3.8 2.9 - - - -
47E SER 3.3 0.2 - - - -
48E ALA* 1.3 75.5 - - - +
50E GLU* 1.3 67.0 + - - +
52E ILE* 2.9 16.2 + - - +
53E LEU* 2.9 21.4 + - + +
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Residues in contact with GLU 50 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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8B ARG* 5.6 0.9 + - - -
36B ARG* 3.1 30.0 + - - +
46E LEU* 3.0 22.2 + - + +
47E SER* 3.7 14.7 - - - +
49E THR* 1.3 74.6 - - - +
51E GLU* 1.3 58.1 + - + +
53E LEU* 3.3 10.6 + - + +
54E GLN* 2.8 58.6 + - - +
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Residues in contact with GLU 51 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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47E SER* 3.2 28.4 + - - +
48E ALA 3.9 2.9 - - - +
49E THR 3.2 1.2 - - - -
50E GLU* 1.3 81.1 - - + +
52E ILE* 1.3 63.4 + - - +
54E GLN* 4.1 12.1 - - - +
55E GLU* 3.0 37.0 + - - +
271E ARG* 2.6 44.4 + - - +
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Residues in contact with ILE 52 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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35E LEU* 4.7 7.0 - - + -
39E LEU* 4.0 31.4 - - + -
44E VAL* 4.3 6.1 - - + -
48E ALA 3.0 26.6 + - - +
49E THR 2.9 7.4 + - - +
51E GLU* 1.3 76.5 - - - +
53E LEU* 1.3 61.6 + - - +
55E GLU* 3.3 3.8 + - - +
56E VAL* 2.9 40.0 + - + +
68E VAL* 4.8 7.4 - - + -
71E LYS* 4.1 24.5 - - + +
72E LEU* 3.7 29.8 - - + -
75E MET* 5.3 0.4 - - + -
267E ILE* 4.3 15.0 - - + -
271E ARG* 5.1 7.2 - - - +
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Residues in contact with LEU 53 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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32E LEU* 3.4 23.7 - - + +
35E LEU* 3.3 33.7 - - + -
36E GLU* 3.6 39.9 - - + +
39E LEU* 4.5 3.1 - - + -
49E THR* 2.9 24.6 + - + +
50E GLU* 3.7 9.4 - - + +
52E ILE* 1.3 76.2 - - - +
54E GLN* 1.3 52.3 + - - +
56E VAL* 3.1 7.3 + - - +
57E ARG* 2.5 59.3 + - - +
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Residues in contact with GLN 54 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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50E GLU* 2.8 47.0 + - - +
51E GLU* 4.5 10.4 - - - +
53E LEU* 1.3 74.8 - - - +
55E GLU* 1.3 63.1 + - + +
56E VAL 3.3 0.5 + - - -
57E ARG* 3.5 37.4 + - - +
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Residues in contact with GLU 55 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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51E GLU* 3.0 24.2 + - - +
52E ILE 3.3 1.8 + - - -
54E GLN* 1.3 77.1 - - + +
56E VAL* 1.3 61.3 + - - +
57E ARG 5.0 0.9 - - - -
71E LYS* 2.8 34.8 + - - -
271E ARG* 3.3 18.2 + - - -
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Residues in contact with VAL 56 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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32E LEU* 3.7 21.3 - - + -
35E LEU* 5.2 0.2 - - + -
52E ILE* 2.9 26.8 + - + +
53E LEU* 3.5 5.6 - - - +
55E GLU* 1.3 80.2 - - - +
57E ARG* 1.3 65.6 + - - +
60E GLY* 4.2 15.8 + - - -
61E ARG* 4.8 5.6 + - + +
64E LEU* 4.8 17.9 - - + -
67E ALA* 5.0 10.1 - - + +
68E VAL* 3.7 33.9 - - + +
71E LYS* 4.6 10.5 - - + -
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Residues in contact with ARG 57 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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28E LEU* 5.2 9.2 - - + -
29E GLU* 4.9 8.7 - - - -
32E LEU* 3.4 33.7 - - + +
53E LEU* 2.5 41.3 + - - +
54E GLN* 3.7 38.7 - - - +
55E GLU 5.0 0.7 - - - -
56E VAL* 1.3 76.6 - - - +
60E GLY* 3.4 22.3 + - - -
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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