Contacts of the helix formed by residues 29 - 47 (chain A) in PDB entry 2GZY
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 CYS 29 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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26A ALA 3.3 12.4 + - - +
27A PRO 3.2 1.0 - - - -
28A TRP* 1.3 80.4 - - + +
30A GLY* 1.3 67.7 + - - +
31A PRO* 3.7 19.3 - - - -
32A CYS* 3.3 27.9 + - - +
33A LYS* 3.5 10.9 - - - +
72A ILE* 3.6 38.4 - - + -
73A PRO* 3.9 4.0 - - - -
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Residues in contact with GLY 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 TRP 3.7 4.6 + - - -
29A CYS* 1.3 68.6 - - - +
31A PRO* 1.3 66.0 - - - +
33A LYS* 2.8 36.0 + - - +
34A MET* 3.0 23.4 + - - +
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Residues in contact with PRO 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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29A CYS* 3.7 11.0 - - - -
30A GLY* 1.3 87.2 - - - +
32A CYS* 1.3 56.2 + - - +
34A MET* 3.6 12.2 - - + +
35A ILE* 2.9 33.1 + - - +
73A PRO* 3.8 23.6 - - + +
89A GLY* 5.6 0.7 - - - -
90A PHE* 4.6 16.0 - - + +
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Residues in contact with CYS 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 ASP* 4.8 0.6 - - - +
25A TRP* 3.7 20.1 - - + -
26A ALA 3.5 19.5 - - - +
29A CYS* 3.3 27.7 + - - +
30A GLY 3.1 1.4 + - - -
31A PRO* 1.3 75.0 - - - +
33A LYS* 1.3 61.6 + - + +
35A ILE* 3.5 12.0 - - - +
36A ALA* 3.4 18.9 + - - +
54A LYS* 4.5 6.4 + - - -
72A ILE* 3.6 11.2 - - - -
73A PRO* 3.5 33.7 - - - -
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Residues in contact with LYS 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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25A TRP* 5.1 7.4 - - + -
27A PRO* 2.8 34.5 + - + +
28A TRP* 4.5 6.5 + - - +
29A CYS 3.5 13.8 + - - +
30A GLY* 2.8 15.7 + - - +
32A CYS* 1.3 76.5 - - + +
34A MET* 1.3 66.7 + - + +
36A ALA* 3.2 21.5 + - - +
37A PRO* 3.3 7.3 - - - +
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Residues in contact with MET 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 GLY* 3.0 27.1 + - - +
31A PRO* 3.2 11.6 + - + +
33A LYS* 1.3 79.6 - - + +
35A ILE* 1.3 59.6 + - - +
37A PRO* 3.4 18.2 - - - +
38A VAL* 3.9 2.1 - - - +
90A PHE* 3.6 26.6 - - + -
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Residues in contact with ILE 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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23A ASP* 4.7 4.0 - - - +
31A PRO 2.9 15.6 + - - +
32A CYS* 3.5 20.0 - - - +
34A MET* 1.3 75.4 - - - +
36A ALA* 1.3 63.5 + - - +
37A PRO* 3.5 0.4 - - - -
38A VAL* 3.0 18.4 + - + -
39A LEU* 2.9 36.5 + - + +
73A PRO* 4.3 12.1 - - + -
75A LEU* 3.9 32.5 - - + -
89A GLY 4.0 12.1 - - - +
90A PHE* 3.8 11.0 - - + -
91A LYS* 3.7 29.6 - - + +
96A LEU* 4.9 3.1 - - + -
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Residues in contact with ALA 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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3A ILE* 5.3 0.2 - - - +
32A CYS 3.4 13.2 + - - +
33A LYS* 3.2 17.9 + - - +
35A ILE* 1.3 75.4 - - - +
37A PRO* 1.4 60.9 - - + +
39A LEU* 3.1 6.8 + - - +
40A GLU* 3.0 35.5 + - + +
54A LYS* 4.2 20.1 - - - +
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Residues in contact with PRO 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 LYS 3.3 13.9 - - - +
34A MET* 3.4 14.4 - - - +
36A ALA* 1.4 89.8 - - + +
38A VAL* 1.3 57.0 + - + +
40A GLU* 3.3 17.2 + - + +
41A GLU* 2.9 33.4 + - + +
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Residues in contact with VAL 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 MET 3.9 5.4 - - - +
35A ILE* 3.0 14.3 + - + +
37A PRO* 1.3 77.7 - - + +
39A LEU* 1.3 58.3 + - - +
41A GLU* 3.2 9.1 + - - +
42A LEU* 3.0 27.7 + - - +
90A PHE* 3.8 22.0 - - + -
91A LYS 3.6 20.6 - - - +
92A PRO* 3.8 0.9 - - + -
93A LYS* 3.5 40.2 - - + +
96A LEU* 4.0 14.1 - - + -
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Residues in contact with LEU 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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3A ILE* 3.9 13.6 - - + +
21A LEU* 3.6 31.6 - - + -
23A ASP* 3.4 36.6 - - + +
35A ILE* 2.9 29.6 + - + +
36A ALA* 3.5 7.2 - - - +
38A VAL* 1.3 76.8 - - - +
40A GLU* 1.3 56.2 + - - +
42A LEU* 3.3 4.6 + - + -
43A ASP* 2.8 24.3 + - - +
52A ILE* 3.5 18.8 - - + +
54A LYS* 3.6 13.7 - - - +
75A LEU* 4.2 8.7 - - + -
96A LEU* 4.2 16.2 - - + -
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Residues in contact with GLU 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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3A ILE* 4.0 15.3 - - + -
36A ALA* 3.0 21.9 + - + +
37A PRO* 3.3 18.7 + - + +
39A LEU* 1.3 73.8 - - - +
41A GLU* 1.3 59.2 + - - +
43A ASP* 3.3 9.0 + - + +
44A GLN* 2.9 40.8 + - + +
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Residues in contact with GLU 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 PRO* 2.9 18.8 + - + +
38A VAL* 3.2 11.2 + - - +
40A GLU* 1.3 74.5 - - - +
42A LEU* 1.3 57.5 + - - +
44A GLN* 2.8 29.5 + - - +
45A GLU* 2.9 37.5 + - - +
93A LYS* 2.8 50.8 + - + +
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Residues in contact with LEU 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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21A LEU* 5.8 1.6 - - + -
38A VAL* 3.0 18.2 + - + +
39A LEU* 3.3 11.6 + - + +
41A GLU* 1.3 76.3 - - - +
43A ASP* 1.3 57.4 + - - +
45A GLU* 4.4 3.4 - - + +
46A MET* 2.8 64.5 + - + +
47A GLY* 3.1 4.7 + - - -
50A LEU* 4.6 2.4 - - + +
52A ILE* 3.9 14.5 - - + +
93A LYS* 4.4 12.6 - - + +
96A LEU* 3.8 30.7 - - + -
97A GLN* 4.0 22.0 - - + +
100A VAL* 4.0 20.9 - - + -
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Residues in contact with ASP 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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1A MET 2.8 58.8 + - - +
2A ALA* 3.2 19.6 + - - +
3A ILE* 3.8 25.3 + - + +
39A LEU 2.8 16.1 + - - +
40A GLU* 3.6 7.1 - - + +
41A GLU 3.3 0.2 - - - -
42A LEU* 1.3 75.9 - - - +
44A GLN* 1.3 63.8 + - - +
47A GLY* 3.0 25.1 + - - +
52A ILE* 3.7 7.2 + - + +
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Residues in contact with GLN 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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1A MET 5.0 1.8 - - - +
40A GLU* 2.9 33.2 + - + +
41A GLU* 2.8 32.8 + - - +
43A ASP* 1.3 81.8 - - - +
45A GLU* 1.3 64.2 + - + +
47A GLY 4.8 0.5 + - - -
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Residues in contact with GLU 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 GLU* 2.9 22.4 + - - +
42A LEU* 4.1 5.2 - - + +
44A GLN* 1.3 81.1 - - + +
46A MET* 1.3 74.6 + - + +
49A LYS* 4.9 8.3 - - - -
93A LYS* 2.8 37.4 + - - +
97A GLN* 6.0 2.2 - - + -
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Residues in contact with MET 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 LEU* 2.8 28.6 + - + +
45A GLU* 1.3 83.4 - - + +
47A GLY* 1.3 51.1 + - - +
48A ASP* 2.7 18.4 + - - -
49A LYS* 2.9 19.9 + - + +
50A LEU* 2.9 32.8 + - + +
97A GLN* 3.9 35.9 - - + +
100A VAL* 3.5 28.3 - - + -
101A ASN* 4.1 13.0 - - + -
104A LEU* 4.3 14.4 - - + -
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Residues in contact with GLY 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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1A MET* 2.9 33.9 + - - +
2A ALA 5.5 0.3 - - - +
42A LEU 3.1 3.0 + - - -
43A ASP* 3.0 33.5 + - - +
44A GLN 4.8 0.2 + - - -
46A MET* 1.3 71.4 - - - +
48A ASP* 1.3 55.3 + - - -
50A LEU* 3.3 17.0 - - - -
51A LYS* 5.6 0.2 - - - -
52A ILE* 5.2 2.9 - - - -
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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