Contacts of the helix formed by residues 20 - 37 (chain A) in PDB entry 2NSC
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 GLY 20 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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1A MET* 4.7 5.5 - - - +
18A VAL 4.1 1.0 + - - -
19A PHE* 1.3 73.6 - - - +
21A ALA* 1.3 65.8 + - - -
22A GLU 3.2 3.9 + - - -
23A GLU* 2.9 16.6 + - - +
24A ILE* 3.1 26.1 + - - +
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Residues in contact with ALA 21 (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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20A GLY* 1.3 71.6 - - - -
22A GLU* 1.3 62.5 + - - +
24A ILE* 3.6 10.5 + - - +
25A ALA* 3.1 23.0 + - - +
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Residues in contact with GLU 22 (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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20A GLY 3.2 1.2 - - - -
21A ALA* 1.3 77.5 - - - +
23A GLU* 1.3 62.9 + - + +
25A ALA* 3.3 7.7 + - - +
26A GLN* 2.9 54.8 + - - +
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Residues in contact with GLU 23 (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 45.4 + - - +
19A PHE* 3.4 12.9 - - + -
20A GLY* 2.9 28.3 + - - +
22A GLU* 1.3 74.5 - - + +
24A ILE* 1.3 60.2 + - - +
26A GLN* 3.4 14.9 + - - +
27A ALA* 2.9 30.5 + - - +
70A LEU* 3.6 15.2 - - + +
73A LEU* 4.2 13.3 - - + +
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Residues in contact with ILE 24 (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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19A PHE* 3.9 25.4 - - + +
20A GLY 3.1 20.6 + - - +
21A ALA* 3.7 9.2 - - - +
23A GLU* 1.3 74.2 - - - +
25A ALA* 1.3 59.4 + - - +
27A ALA* 3.2 3.6 + - - +
28A GLU* 2.8 50.8 + - + +
66A THR* 4.1 8.5 - - + +
70A LEU* 4.2 14.6 - - + -
94A LEU* 4.7 17.9 - - + -
95A LYS 6.1 1.3 - - - +
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Residues in contact with ALA 25 (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 ALA 3.1 17.8 + - - +
22A GLU* 3.7 10.5 - - - +
24A ILE* 1.3 77.1 - - - +
26A GLN* 1.3 57.2 + - - +
28A GLU* 3.3 15.6 + - - +
29A ASP* 3.0 35.6 + - - +
51A LYS* 4.6 6.4 + - - +
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Residues in contact with GLN 26 (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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22A GLU* 2.9 49.0 + - - +
23A GLU* 3.6 13.6 - - - +
25A ALA* 1.3 74.3 - - - +
27A ALA* 1.3 56.9 + - - +
29A ASP* 3.3 12.9 + - - +
30A LYS* 3.1 38.9 + - - +
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Residues in contact with ALA 27 (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 GLU 2.9 20.2 + - - +
24A ILE 3.6 3.8 - - - +
26A GLN* 1.3 69.7 - - - +
28A GLU* 1.3 61.1 + - - +
30A LYS* 3.1 9.7 + - - +
31A ALA* 2.9 27.5 + - - +
66A THR* 3.7 25.9 - - + +
69A PHE* 4.1 12.3 - - + +
70A LEU* 3.7 24.2 - - + +
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Residues in contact with GLU 28 (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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24A ILE* 2.8 37.3 + - - +
25A ALA* 3.5 16.7 + - - +
27A ALA* 1.3 72.0 - - - +
29A ASP* 1.3 56.7 + - - +
31A ALA* 3.1 5.5 + - - +
32A VAL* 3.0 32.6 + - - +
51A LYS* 4.4 14.2 + - + +
55A LYS* 2.5 40.3 + - - -
62A PHE* 3.7 7.9 - - + -
66A THR* 3.7 27.3 - - + +
94A LEU* 6.4 0.2 - - - -
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Residues in contact with ASP 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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25A ALA* 3.0 20.5 + - - +
26A GLN* 3.4 14.2 - - - +
28A GLU* 1.3 73.4 - - - +
30A LYS* 1.3 64.4 + - - +
32A VAL* 3.4 8.0 + - - +
33A ARG* 3.1 42.9 + - - +
51A LYS* 3.4 23.8 + - - +
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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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26A GLN* 3.1 28.7 + - - +
27A ALA* 3.1 8.4 + - - +
29A ASP* 1.3 74.7 - - - +
31A ALA* 1.3 58.4 + - - +
33A ARG* 3.2 24.3 + - - +
34A TYR* 2.8 30.7 + - - +
69A PHE* 3.7 50.5 + - + -
72A ASP* 5.3 5.3 - - - +
73A LEU* 4.5 17.2 - - - +
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Residues in contact with ALA 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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27A ALA 2.9 12.2 + - - +
28A GLU* 3.2 11.2 - - - +
30A LYS* 1.3 77.3 - - - +
32A VAL* 1.3 61.6 + - - +
34A TYR* 3.6 1.5 - - - +
35A LEU* 3.0 32.9 + - - +
62A PHE* 3.8 17.3 - - + -
65A TYR* 4.0 31.0 - - + -
66A THR* 4.3 1.6 - - - +
69A PHE* 3.9 10.9 - - + -
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Residues in contact with VAL 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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28A GLU 3.0 19.1 + - - +
29A ASP* 3.7 9.4 - - - +
30A LYS 3.3 0.2 - - - -
31A ALA* 1.3 74.0 - - - +
33A ARG* 1.3 64.7 + - - +
35A LEU* 3.3 1.9 + - - +
36A ASN* 3.0 42.8 + - - +
49A ILE 4.1 6.3 - - - +
51A LYS* 3.6 45.3 - - + +
54A LEU* 4.0 12.8 - - + -
62A PHE* 3.9 11.2 - - + -
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Residues in contact with ARG 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 ASP* 3.1 31.5 + - - +
30A LYS* 3.3 35.2 - - - +
32A VAL* 1.3 77.8 - - - +
34A TYR* 1.3 61.7 + - - +
36A ASN* 3.5 5.6 + - - +
37A GLN* 3.2 44.2 + - + +
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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 2.8 19.7 + - - +
31A ALA 3.6 3.6 - - - +
33A ARG* 1.3 73.6 - - - +
35A LEU* 1.3 72.5 + - + +
37A GLN* 3.4 17.2 + - - +
38A ARG* 3.2 70.8 + - - +
65A TYR* 3.6 38.7 - + - -
69A PHE* 3.7 26.7 - + + -
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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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31A ALA* 3.0 21.3 + - + +
32A VAL 3.8 3.1 - - - +
34A TYR* 1.3 86.3 - - + +
36A ASN* 1.3 57.5 + - - +
38A ARG* 3.1 3.2 + - + -
39A VAL* 2.8 53.6 + - + +
54A LEU* 4.1 20.4 - - + -
58A LEU* 3.5 30.3 - - + -
62A PHE* 4.1 18.8 - - + -
65A TYR* 3.9 36.1 - - + +
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Residues in contact with ASN 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 VAL* 3.0 32.3 + - - +
33A ARG* 4.0 5.4 - - - +
35A LEU* 1.3 76.9 - - - +
37A GLN* 1.3 60.1 + - - +
38A ARG 3.3 0.6 + - - -
39A VAL* 4.2 7.1 - - - +
46A LYS* 5.2 3.6 - - - +
47A GLY* 3.2 43.5 + - - +
48A ARG 3.3 0.9 + - - -
49A ILE* 2.9 63.3 + - - +
54A LEU* 4.2 3.1 - - - +
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Residues in contact with GLN 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 ARG* 3.2 34.0 + - + +
34A TYR* 3.6 13.6 - - - +
35A LEU 3.2 1.0 - - - -
36A ASN* 1.3 79.4 - - - +
38A ARG* 1.3 82.8 + - - +
46A LYS* 5.5 7.0 - - - +
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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