Contacts of the helix formed by residues 34 - 47 (chain A) in PDB entry 2CZY
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 34 (chain A).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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33A HIS* 1.3 76.9 - - + +
35A GLU* 1.3 56.3 + - - +
37A ALA* 3.9 6.3 - - - +
38A LEU* 3.0 45.0 + - + +
48B MET* 5.1 6.4 - - + +
52B VAL* 4.3 22.2 - - + -
56B GLY* 6.1 2.2 - - - -
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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 PRO 6.0 0.2 - - - +
33A HIS* 3.0 6.3 - - + +
34A VAL* 1.3 78.2 - - - +
36A ASP* 1.3 65.3 + - - +
38A LEU* 3.4 14.9 + - + +
39A THR* 3.2 27.4 + - - +
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Residues in contact with ASP 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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31A PRO* 3.5 31.6 + - - +
32A VAL* 4.0 4.0 - - - -
33A HIS 2.8 12.3 + - - +
35A GLU* 1.3 78.9 - - - +
37A ALA* 1.3 61.4 + - - +
39A THR* 3.2 25.5 - - - +
40A TYR* 3.2 11.8 + - - +
96A PHE* 3.0 32.3 - - + -
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Residues in contact with ALA 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 HIS 3.0 13.1 + - - +
34A VAL* 4.1 4.9 - - - +
36A ASP* 1.3 75.9 - - - +
38A LEU* 1.3 65.0 + - - +
40A TYR* 3.5 7.5 + - - +
41A LEU* 3.2 27.3 + - + +
96A PHE* 4.5 4.9 - - + -
48B MET* 4.7 10.1 - - + -
49B LEU* 4.3 22.9 - - + +
52B VAL* 4.1 25.4 - - + -
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Residues in contact with LEU 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 VAL* 3.0 40.4 + - + +
35A GLU* 3.6 19.3 - - + +
37A ALA* 1.3 76.1 - - - +
39A THR* 1.3 63.8 + - - +
41A LEU* 3.2 9.5 + - + +
42A ASP* 3.2 22.9 + - - +
52B VAL* 4.0 16.1 - - + +
56B GLY 3.6 23.6 - - - +
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Residues in contact with THR 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* 3.2 16.1 + - - +
36A ASP* 3.2 21.5 - - - +
38A LEU* 1.3 78.5 - - - +
40A TYR* 1.3 59.5 + - + +
42A ASP* 3.0 9.3 + - - +
43A GLN* 2.7 52.8 + - - +
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Residues in contact with TYR 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 ASP* 3.2 15.8 + - - +
37A ALA* 3.5 9.2 - - - +
38A LEU 3.2 0.2 - - - -
39A THR* 1.3 84.7 - - + +
41A LEU* 1.3 53.4 + - + +
43A GLN* 3.2 8.7 + - + +
44A VAL* 2.7 45.2 + - + +
58A PHE* 3.5 37.7 - + - -
83A PHE* 3.7 13.1 - + - -
88A ASP 4.7 1.8 - - - -
89A LEU* 2.6 47.4 + - + +
92A GLY* 4.0 12.3 - - - -
93A PHE* 3.4 28.1 - + + +
96A PHE* 5.2 9.0 - + + -
49B LEU* 5.0 7.9 - - + -
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Residues in contact with LEU 41 (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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37A ALA* 3.2 13.7 + - + +
38A LEU* 3.2 9.5 + - + +
39A THR 3.2 0.6 - - - -
40A TYR* 1.3 79.5 - - + +
42A ASP* 1.3 58.9 + - - +
44A VAL* 3.2 3.7 + - + +
45A LYS* 3.0 29.3 + - - +
55A TYR* 3.5 33.6 - - + +
58A PHE* 4.2 29.6 - - + -
59A LEU* 4.6 4.3 - - + -
49B LEU* 5.0 2.7 - - + +
52B VAL* 3.8 18.4 - - + +
53B ALA* 3.7 37.9 - - + +
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Residues in contact with ASP 42 (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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38A LEU* 3.2 11.1 + - - +
39A THR* 3.0 12.4 + - - +
41A LEU* 1.3 79.2 - - - +
43A GLN* 1.3 59.4 + - - +
45A LYS* 3.6 11.0 + - - +
46A ILE* 2.9 44.3 + - + +
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Residues in contact with GLN 43 (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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39A THR* 2.7 36.6 + - - +
40A TYR* 3.5 10.0 - - + +
42A ASP* 1.3 77.7 - - - +
44A VAL* 1.3 59.5 + - + +
46A ILE* 4.5 7.7 - - - +
47A ARG* 3.2 62.3 + - - +
88A ASP* 5.4 8.1 - - - +
89A LEU* 5.6 2.4 - - + +
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Residues in contact with VAL 44 (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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40A TYR* 2.7 41.2 + - + +
41A LEU* 3.7 7.0 - - - +
43A GLN* 1.3 77.3 - - + +
45A LYS* 1.3 63.5 + - - +
46A ILE 3.5 0.2 - - - -
47A ARG* 4.8 2.2 - - - -
48A PHE* 3.3 30.7 + - + +
54A THR* 5.3 0.2 - - + -
55A TYR* 4.1 21.9 - - + -
58A PHE* 5.1 10.3 - - + -
83A PHE* 3.9 27.1 - - + -
89A LEU* 3.4 26.0 - - + -
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Residues in contact with LYS 45 (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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41A LEU 3.0 13.6 + - - +
42A ASP* 3.9 13.2 - - - +
43A GLN 3.3 0.2 - - - -
44A VAL* 1.3 76.9 - - - +
46A ILE* 1.3 61.5 + - + +
48A PHE 3.2 4.3 - - - +
49A GLY* 3.0 26.9 + - - -
55A TYR* 3.3 47.1 - - + +
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Residues in contact with ILE 46 (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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42A ASP* 2.9 33.1 + - + +
43A GLN* 4.5 7.6 - - - +
45A LYS* 1.3 73.1 - - + +
47A ARG* 1.3 84.5 + - - +
48A PHE 3.0 1.3 - - - -
49A GLY* 3.0 14.5 + - - +
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Residues in contact with ARG 47 (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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43A GLN* 3.2 44.7 + - - +
44A VAL* 4.6 3.6 - - - +
46A ILE* 1.3 105.2 - - - +
48A PHE* 1.3 68.5 + - + +
49A GLY 3.5 0.7 + - - -
50A SER* 5.3 2.3 + - - -
86A HIS* 5.1 19.6 + - + +
89A LEU* 5.4 9.6 - - + -
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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