Contacts of the helix formed by residues 38 - 48 (chain E) in PDB entry 2PWZ
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 VAL 38 (chain E).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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9E ALA* 4.0 23.3 - - + +
14E GLN* 4.9 5.2 - - - +
36E ALA* 3.1 7.1 + - + -
37E PRO* 1.3 79.0 - - + +
39E THR* 1.3 60.0 + - - +
40E PRO* 3.4 0.9 - - - -
41E GLY* 2.8 22.4 + - - -
42E VAL* 3.1 21.9 + - + -
217G LYS* 3.7 48.0 + - + +
220G GLY* 3.9 17.3 - - - +
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Residues in contact with THR 39 (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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8E ALA* 4.3 5.4 - - + -
9E ALA* 3.7 7.2 - - - +
32E LEU* 4.0 27.5 - - + +
33E TYR 4.0 1.8 - - - -
34E ASP* 3.1 29.8 - - + +
36E ALA 2.8 16.6 + - - -
37E PRO 3.2 0.2 - - - -
38E VAL* 1.3 76.7 - - - +
40E PRO* 1.3 71.7 - - - +
42E VAL* 3.2 19.9 + - + +
43E ALA* 3.3 9.9 + - - +
57E GLY* 3.9 3.3 - - - -
58E PHE 3.6 20.6 - - - +
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Residues in contact with PRO 40 (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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37E PRO 3.3 15.5 - - - +
38E VAL 3.6 0.7 - - - -
39E THR* 1.3 92.6 - - - +
41E GLY* 1.3 53.6 + - - +
43E ALA* 3.6 4.3 + - - +
44E VAL* 3.1 31.2 + - + +
57E GLY* 3.7 27.1 + - - +
58E PHE* 4.3 0.4 - - - -
59E SER* 3.9 21.5 - - - +
216G ALA* 4.0 10.3 - - + +
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Residues in contact with GLY 41 (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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38E VAL 2.8 9.5 + - - -
40E PRO* 1.3 73.4 - - - +
42E VAL* 1.3 60.7 + - - +
43E ALA 3.4 0.4 - - - -
44E VAL* 3.7 2.1 - - - +
45E ASP* 3.0 27.9 + - - +
213G VAL* 4.1 2.1 - - - +
216G ALA* 3.2 34.9 + - - -
217G LYS* 3.6 16.7 - - - +
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Residues in contact with VAL 42 (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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8E ALA 4.5 4.5 - - - +
9E ALA* 4.9 3.4 - - - -
14E GLN* 3.9 35.0 - - + +
17E ALA* 5.3 0.4 - - + -
32E LEU* 3.9 16.8 - - + -
38E VAL* 3.1 27.8 + - + +
39E THR* 3.2 15.0 + - + +
41E GLY* 1.3 74.6 - - - +
43E ALA* 1.3 58.1 + - - +
45E ASP* 3.2 8.9 - - - +
46E LEU* 3.1 28.9 + - + +
217G LYS* 4.4 6.7 - - - +
225G LEU* 3.8 24.2 - - + -
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Residues in contact with ALA 43 (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* 3.9 10.9 - - + +
39E THR 3.3 2.8 + - - -
40E PRO 3.7 3.8 - - - +
42E VAL* 1.3 76.9 - - - +
44E VAL* 1.3 59.7 + - + +
46E LEU 3.4 0.5 + - - -
47E SER* 2.8 29.9 + - - -
55E ILE* 3.5 18.5 - - + +
56E LYS* 3.5 13.9 - - - +
57E GLY* 3.3 36.3 - - - +
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Residues in contact with VAL 44 (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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40E PRO 3.1 22.0 + - - +
41E GLY 4.0 2.2 - - - +
42E VAL 3.4 0.6 - - - -
43E ALA* 1.3 71.5 - - + +
45E ASP* 1.3 67.8 + - - +
47E SER* 2.6 26.2 + - - +
48E HIS* 3.4 18.0 - - - +
212G GLU* 4.1 29.4 - - + +
213G VAL* 4.1 13.5 - - + -
216G ALA* 3.7 19.3 - - + -
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Residues in contact with ASP 45 (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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41E GLY 3.0 15.3 + - - +
42E VAL* 3.2 13.4 - - - +
44E VAL* 1.3 78.2 - - - +
46E LEU* 1.3 61.5 + - - +
48E HIS* 3.2 11.1 + - - +
213G VAL* 4.0 15.6 - - + +
217G LYS* 3.6 8.3 + - - -
223G ALA* 3.7 6.2 - - - -
224G THR* 2.9 30.0 + - - -
225G LEU* 3.2 16.5 + - - +
226G SER* 2.6 51.3 + - - -
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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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17E ALA* 3.7 34.5 - - + +
18E LEU* 3.7 23.1 - - + -
21E LYS* 3.0 30.4 - - + -
32E LEU* 4.2 4.9 - - + -
42E VAL* 3.1 18.6 + - + +
43E ALA 3.8 3.8 - - - +
45E ASP* 1.3 77.9 - - - +
47E SER* 1.3 59.3 + - - +
48E HIS 3.1 0.2 - - - -
49E ILE* 3.2 32.7 + - + +
55E ILE* 3.9 21.1 - - + -
225G LEU* 3.7 32.8 - - + -
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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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21E LYS* 4.3 4.8 + - - +
43E ALA 2.8 17.0 + - - -
44E VAL* 2.6 27.1 + - - +
46E LEU* 1.3 73.7 - - - +
48E HIS* 1.3 64.9 + - - +
49E ILE 3.1 6.4 + - - +
55E ILE* 3.7 22.0 - - - +
156G THR* 3.2 23.0 - - - +
157G PHE* 5.2 0.2 - - - -
205G ARG* 5.7 1.0 + - - -
212G GLU* 5.1 0.9 + - - -
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Residues in contact with HIS 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* 3.4 15.1 + - - +
45E ASP 3.2 9.6 + - - +
46E LEU 3.1 1.6 - - - -
47E SER* 1.3 84.1 - - - +
49E ILE* 1.3 59.8 + - - +
50E PRO* 3.7 0.2 - - - +
149G LEU* 5.2 0.2 - - + -
152G ILE* 3.5 22.2 - - - +
153G ARG* 3.2 32.5 + - + +
156G THR* 3.1 17.3 + - - -
157G PHE* 3.8 15.3 - + - -
205G ARG* 5.0 0.7 - - - -
209G ALA* 3.4 36.8 - - + -
212G GLU* 2.8 27.6 + - - -
213G VAL* 3.7 18.6 - - + +
226G SER* 4.4 8.8 + - - -
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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