Contacts of the helix formed by residues 29 - 46 (chain A) in PDB entry 1ZP2
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 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 THR* 4.2 24.2 + - - +
27A CYS 5.1 0.2 - - - -
28A LEU* 1.3 74.9 - - - +
30A LYS* 1.3 64.9 - - - +
31A ASP* 3.1 20.6 + - - +
32A THR* 2.9 21.2 + - - -
33A ILE* 3.0 28.5 + - - +
224A PHE* 5.0 4.5 - - - -
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Residues in contact with LYS 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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29A SER* 1.3 75.0 - - - +
31A ASP* 1.3 59.0 + - - +
33A ILE* 3.8 10.9 + - + +
34A TYR* 3.0 27.2 + - - +
224A PHE* 4.4 27.8 - - + -
228A GLU* 6.1 0.4 - - - +
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Residues in contact with ASP 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 SER* 3.0 9.8 + - - +
30A LYS* 1.3 78.0 - - - +
32A THR* 1.3 57.3 + - - +
33A ILE 3.2 0.2 - - - -
34A TYR* 3.0 10.6 + - - +
35A GLN* 2.7 54.3 + - - +
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Residues in contact with THR 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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26A THR 3.9 6.6 + - - -
27A CYS* 4.7 0.2 - - - -
28A LEU 3.5 4.6 + - - +
29A SER* 2.9 28.6 + - - -
31A ASP* 1.3 80.7 - - - +
33A ILE* 1.3 64.6 + - - +
35A GLN* 3.4 10.7 + - - -
36A TRP* 3.1 10.0 + - - +
61A ARG* 2.7 41.8 + - - +
168A ALA 2.6 28.5 - - - +
169A SER* 3.4 17.3 - - - +
170A SER* 3.6 3.2 + - - +
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Residues in contact with ILE 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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28A LEU* 3.7 19.3 - - + -
29A SER 3.0 21.5 + - - +
30A LYS* 3.8 9.2 - - + +
32A THR* 1.3 75.8 - - - +
34A TYR* 1.3 65.0 + - - +
36A TRP* 3.6 4.2 + - - +
37A LYS* 3.3 29.4 + - + +
168A ALA* 3.6 26.0 - - + +
221A ILE* 5.8 2.9 - - + +
224A PHE* 4.3 26.9 - - + +
225A GLU* 5.7 5.4 - - + +
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Residues in contact with TYR 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 LYS 3.0 19.7 + - - +
31A ASP* 3.0 13.5 + - - +
33A ILE* 1.3 76.5 - - - +
35A GLN* 1.3 57.4 + - + +
37A LYS* 2.7 36.4 + - + +
38A VAL* 2.9 27.6 + - + +
75A LEU* 3.4 28.7 - - + -
76A GLU* 4.5 10.2 + - - -
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Residues in contact with GLN 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 ASP* 2.7 37.8 + - + +
32A THR* 3.4 14.1 + - - +
34A TYR* 1.3 73.7 - - + +
36A TRP* 1.3 62.2 + - - +
38A VAL* 3.2 12.3 + - - +
39A VAL* 3.1 27.0 + - - +
57A ILE* 4.0 8.3 - - + -
60A LEU* 4.8 5.6 - - + -
61A ARG* 3.8 15.7 + - - +
64A MET* 4.6 22.8 - - - +
75A LEU* 4.0 30.9 - - + +
79A VAL* 4.8 0.3 - - - +
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Residues in contact with TRP 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 THR 3.1 9.1 + - - +
33A ILE 3.8 2.2 - - - +
35A GLN* 1.3 75.8 - - - +
37A LYS* 1.3 59.2 + - - +
39A VAL* 3.2 6.9 + - + -
40A GLN* 3.0 73.7 + - + +
50A GLN* 3.9 26.2 - - - -
53A LEU* 3.9 22.0 - - + -
54A ALA 4.3 2.5 - - - -
57A ILE* 3.4 42.2 - - + -
61A ARG* 3.9 1.5 - - - +
164A ASN* 3.6 24.6 + - + -
165A ASP* 4.6 5.1 + - - +
167A TYR* 3.2 28.9 - + + +
168A ALA* 3.4 32.8 - - + -
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Residues in contact with LYS 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 ILE* 3.3 20.4 + - + +
34A TYR* 2.7 27.3 + - + +
36A TRP* 1.3 73.2 - - - +
38A VAL* 1.3 57.5 + - + +
40A GLN* 3.1 22.8 + - + +
41A THR* 2.8 38.1 + - - +
225A GLU* 5.4 5.7 + - - +
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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 TYR* 2.9 54.2 + - + +
35A GLN* 3.5 6.1 - - - +
37A LYS* 1.3 75.2 - - - +
39A VAL* 1.3 62.5 + - - +
41A THR* 3.3 7.4 + - - -
42A PHE* 3.1 24.6 + - - +
75A LEU* 3.8 13.2 - - + -
76A GLU* 5.0 4.9 - - + +
79A VAL* 3.8 19.7 - - + -
107A TRP* 3.6 27.3 - - + +
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Residues in contact with VAL 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 GLN 3.1 16.2 + - - +
36A TRP* 3.2 13.7 + - + +
38A VAL* 1.3 72.7 - - - +
40A GLN* 1.3 65.5 + - - +
42A PHE* 3.6 1.2 + - - +
43A GLY* 2.9 21.8 + - - -
53A LEU* 4.0 25.8 - - + +
56A ALA* 4.2 6.3 - - + -
57A ILE* 3.7 23.6 - - + +
60A LEU* 4.3 6.3 - - + -
79A VAL* 3.6 25.8 - - + -
82A CYS* 6.2 0.7 - - + -
83A ILE* 3.8 24.3 - - + +
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Residues in contact with GLN 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 TRP* 3.0 69.0 + - + +
37A LYS* 3.3 29.6 - - + +
39A VAL* 1.3 76.5 - - - +
41A THR* 1.3 60.2 - - - +
43A GLY* 3.1 0.9 + - - -
44A ASP* 2.6 42.1 + - - +
50A GLN* 5.7 0.4 + - - -
53A LEU* 4.4 13.4 - - + +
164A ASN 6.1 0.4 - - - -
165A ASP* 5.9 1.2 + - - -
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Residues in contact with THR 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 LYS* 2.8 24.6 + - - +
38A VAL* 3.4 11.5 - - - -
40A GLN* 1.3 79.1 - - - +
42A PHE* 1.3 66.1 + - - +
43A GLY 2.8 0.3 + - - -
44A ASP* 3.0 15.2 + - - +
45A ARG* 3.3 10.0 + - - +
106A LEU* 4.1 23.6 - - + -
107A TRP* 5.5 5.8 - - + +
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Residues in contact with PHE 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 VAL 3.1 7.7 + - - +
39A VAL 4.3 1.6 - - - +
41A THR* 1.3 79.6 - - - +
43A GLY* 1.3 59.1 + - - +
45A ARG* 3.4 6.4 - - + +
46A LEU* 3.0 43.7 - - + +
79A VAL* 4.3 3.4 - - + -
80A ALA* 3.6 26.5 - - - -
83A ILE* 3.7 33.0 - - + -
99A ILE* 3.6 31.0 - - + -
102A GLU* 4.0 4.5 - - + -
103A ALA* 3.8 25.4 - - + -
106A LEU* 3.9 19.3 - - + -
107A TRP* 3.4 31.0 - + + -
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Residues in contact with GLY 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 VAL 2.9 18.9 + - - -
40A GLN 3.5 0.7 - - - -
41A THR 2.8 1.4 + - - -
42A PHE* 1.3 75.1 - - - +
44A ASP* 1.3 58.1 + - - +
45A ARG 2.9 10.2 + - - -
46A LEU* 3.1 11.6 + - - -
47A ARG 3.2 7.6 + - - -
48A LEU* 3.2 23.4 + - - +
53A LEU* 3.6 20.6 - - - -
83A ILE* 4.7 2.7 - - - +
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Residues in contact with ASP 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 GLN* 2.6 40.4 + - - +
41A THR* 3.0 7.0 + - - +
43A GLY* 1.3 72.1 - - - +
45A ARG* 1.3 61.5 + - - +
47A ARG* 3.5 17.9 + - - +
48A LEU 4.9 3.9 - - - +
53A LEU* 4.3 12.8 - - - +
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Residues in contact with ARG 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 THR* 3.3 8.4 + - - +
42A PHE* 3.4 14.6 - - + +
43A GLY 2.9 0.6 - - - -
44A ASP* 1.3 76.9 - - - +
46A LEU* 1.3 62.5 + - + +
47A ARG* 2.9 17.7 + - - +
102A GLU* 2.8 87.4 + - + +
105A ASP* 3.2 20.4 + - - +
106A LEU* 3.3 37.5 - - + +
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Residues in contact with LEU 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 PHE* 3.0 55.2 - - + +
43A GLY 3.1 2.6 + - - -
45A ARG* 1.3 80.2 - - + +
47A ARG* 1.3 70.7 + - - +
48A LEU* 3.0 28.8 + - + +
83A ILE* 5.2 1.3 - - + -
94A VAL* 3.6 33.8 - - + +
98A THR* 4.4 13.9 - - + +
99A ILE* 4.1 15.7 - - + -
102A GLU* 4.3 11.9 - - + -
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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