Contacts of the helix formed by residues 28 - 40 (chain A) in PDB entry 3CR2
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 LYS 28 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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21A GLU* 3.9 38.7 + - + +
22A GLY* 4.1 8.5 - - - -
23A ASP 5.1 0.2 - - - +
26A LYS 3.6 2.0 + - - -
27A LEU* 1.3 74.9 - - - +
29A LYS* 1.3 63.5 + - - +
30A SER* 3.3 24.0 - - - +
31A GLU* 2.9 24.8 + - + +
32A LEU* 2.9 24.9 + - - +
57A MET* 3.7 3.1 - - - -
66A GLY 5.0 0.4 - - - -
67A GLU* 3.6 27.8 + - + +
92A CA 4.3 1.1 - - - -
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Residues in contact with LYS 29 (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 LYS* 1.3 74.1 - - - +
30A SER* 1.3 58.2 + - - +
32A LEU* 3.4 3.1 + - - +
33A LYS* 3.0 29.5 + - - +
50A GLN* 4.1 8.2 - - - +
53A VAL* 3.7 23.2 - - + +
54A ASP* 2.7 41.9 + - - +
57A MET* 3.5 33.8 - - + +
66A GLY* 4.9 6.6 + - - +
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Residues in contact with SER 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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21A GLU* 4.2 11.6 - - - -
28A LYS* 3.3 21.1 - - - +
29A LYS* 1.3 76.2 - - - +
31A GLU* 1.3 67.0 + - - +
33A LYS* 3.6 8.6 + - - +
34A GLU* 3.1 32.4 + - - +
53A VAL* 5.6 0.4 - - - -
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Residues in contact with GLU 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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17A TYR* 2.9 37.7 - - - +
18A SER 3.3 0.7 - - - +
20A ARG* 3.9 13.5 - - + +
21A GLU* 2.7 31.0 + - + +
26A LYS 3.0 4.7 - - - +
27A LEU* 3.3 7.3 - - + -
28A LYS* 2.9 31.8 + - + +
30A SER* 1.3 78.0 + - - +
32A LEU* 1.3 66.4 + - - +
34A GLU* 3.3 4.6 + - - -
35A LEU* 3.0 24.4 + - - +
92A CA 2.4 30.4 - - - -
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Residues in contact with LEU 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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27A LEU* 4.2 25.4 - - + +
28A LYS 2.9 11.9 + - - +
29A LYS* 3.5 10.3 - - - +
31A GLU* 1.3 76.7 - - - +
33A LYS* 1.3 61.6 + - - +
35A LEU* 3.2 8.3 + - + +
36A ILE* 3.0 38.2 + - + +
53A VAL* 5.0 4.0 - - + +
56A VAL* 4.1 8.5 - - + -
57A MET* 3.8 43.1 - - + +
60A LEU* 3.9 32.1 - - + -
68A CYS* 4.9 1.8 - - + -
76A PHE* 4.6 7.0 - - + -
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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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29A LYS 3.0 17.2 + - - +
30A SER* 3.8 9.4 - - - +
32A LEU* 1.3 75.2 - - - +
34A GLU* 1.3 77.0 + - - +
36A ILE* 3.3 5.5 + - - +
37A ASN* 2.8 52.9 + - - +
47A ILE* 4.0 27.4 - - + -
48A LYS* 5.9 1.9 - - - +
53A VAL* 3.9 26.2 - - + +
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Residues in contact with GLU 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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17A TYR* 3.6 5.6 - - + -
20A ARG* 3.3 30.7 - - - +
30A SER* 3.1 21.9 + - - +
31A GLU 3.8 1.8 - - - +
33A LYS* 1.3 96.9 + - - +
35A LEU* 1.3 67.0 + - - +
37A ASN* 4.3 9.5 - - - +
38A ASN* 2.8 40.9 + - - +
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Residues in contact with LEU 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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13A VAL* 4.2 19.7 - - + +
14A PHE* 4.7 0.7 - - - -
17A TYR* 3.5 39.9 - - + -
27A LEU* 4.2 13.7 - - + -
31A GLU 3.0 13.4 + - - +
32A LEU* 3.2 11.9 + - + +
34A GLU* 1.3 77.4 - - - +
36A ILE* 1.3 59.6 + - + +
39A GLU* 2.8 42.8 + - + +
40A LEU* 4.1 20.6 - - + -
73A PHE* 3.8 37.9 - - + -
76A PHE* 4.7 3.1 - - + -
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Residues in contact with ILE 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 LEU* 3.0 24.9 + - + +
33A LYS 3.6 6.5 - - - +
35A LEU* 1.3 77.5 - - + +
37A ASN* 1.3 69.2 + - - +
40A LEU* 3.1 34.0 + - + +
41A SER* 4.5 0.7 - - - -
44A LEU* 4.0 25.8 - - + +
45A GLU 4.6 4.0 - - - +
47A ILE* 3.7 33.4 - - + -
56A VAL* 3.9 25.1 - - + -
76A PHE* 3.9 30.1 - - + -
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Residues in contact with ASN 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* 2.8 33.4 + - - +
34A GLU* 3.3 9.0 + - - +
36A ILE* 1.3 84.0 - - - +
38A ASN* 1.3 68.5 + - - +
41A SER* 3.8 18.1 - - - +
46A GLU* 3.7 23.8 - - + +
47A ILE* 2.8 54.7 - - - +
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Residues in contact with ASN 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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17A TYR* 3.0 31.2 + - - +
20A ARG* 4.4 6.7 - - - +
34A GLU* 2.8 31.0 + - - +
37A ASN* 1.3 87.3 - - - +
39A GLU* 1.3 70.8 + - - +
40A LEU 3.8 0.4 - - - -
41A SER* 4.8 7.5 + - - -
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Residues in contact with GLU 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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13A VAL* 3.8 19.9 - - + +
16A GLN* 4.9 4.2 - - - +
17A TYR* 2.5 44.0 + - + +
35A LEU* 2.8 23.5 + - + +
38A ASN* 1.3 86.7 - - - +
40A LEU* 1.3 66.3 + - + +
41A SER 3.6 2.2 - - - -
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Residues in contact with LEU 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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35A LEU* 3.7 19.0 + - + -
36A ILE* 3.1 20.4 + - + +
39A GLU* 1.3 87.6 - - + +
41A SER* 1.3 57.5 + - - +
42A HIS 3.2 3.1 - - - -
43A PHE* 3.1 28.4 + - + +
44A LEU* 2.8 48.2 + - + +
76A PHE* 3.9 18.4 - - + -
80A ILE* 3.8 35.0 - - + -
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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