Contacts of the helix formed by residues 30 - 42 (chain A) in PDB entry 3NSI
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 30 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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29A LEU* 1.3 77.1 - - - +
31A GLN* 1.3 66.7 + - - +
32A ALA* 4.1 10.3 - - + +
33A GLU* 3.0 29.7 + - + +
34A LEU* 2.9 20.4 + - - +
66A LYS 5.3 1.8 - - - +
67A ASP 3.4 5.6 - - - +
68A CYS* 2.0 45.1 - - - +
70A VAL* 4.3 1.8 - - - -
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Residues in contact with GLN 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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30A CYS* 1.3 73.4 - - - +
32A ALA* 1.3 56.4 + - - +
34A LEU* 3.2 7.7 + - - +
35A LYS* 2.8 30.5 + - - +
61A VAL* 5.8 3.0 - - - +
62A LEU* 2.8 38.9 - - - +
65A ASN* 3.3 38.0 - - + +
66A LYS* 4.1 1.8 - - - -
67A ASP* 2.8 39.3 + - - +
70A VAL* 3.7 20.7 - - - +
74A GLU* 3.8 13.6 + - - +
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Residues in contact with ALA 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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30A CYS* 3.1 7.5 - - + +
31A GLN* 1.3 78.2 - - - +
33A GLU* 1.3 57.1 + - + +
35A LYS* 3.5 11.0 + - - +
36A GLU* 3.0 27.5 + - - +
62A LEU 4.5 4.4 + - - -
65A ASN 5.0 0.6 + - - -
66A LYS* 4.7 24.7 - - + +
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Residues in contact with GLU 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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19A TYR* 4.0 18.1 - - + +
22A ARG* 4.3 22.4 + - - +
23A CYS* 4.7 14.0 - - - +
28A LYS 4.6 1.4 - - - +
29A LEU* 3.7 26.1 - - + +
30A CYS* 3.0 40.6 + - + +
32A ALA* 1.3 78.5 - - + +
34A LEU* 1.3 60.2 + - - +
36A GLU* 3.3 11.0 + - - +
37A LEU* 2.8 30.1 + - - +
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Residues in contact with LEU 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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29A LEU* 4.5 14.0 - - + +
30A CYS 2.9 11.6 + - - +
31A GLN* 3.5 14.6 - - - +
33A GLU* 1.3 76.3 - - - +
35A LYS* 1.3 57.5 + - - +
37A LEU* 3.2 7.1 + - + +
38A LEU* 2.9 47.1 + - + +
62A LEU* 4.0 22.4 - - + -
70A VAL* 4.1 20.2 - - + -
74A GLU* 5.1 4.7 - - + +
75A TYR* 4.0 26.7 - - + -
78A SER* 3.7 33.2 - - - +
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Residues in contact with LYS 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 GLN 2.8 19.7 + - - +
32A ALA* 3.8 8.5 - - - +
34A LEU* 1.3 72.9 - - - +
36A GLU* 1.3 62.2 + - - +
38A LEU* 3.4 3.0 + - - +
39A GLN* 2.9 71.8 + - - +
59A MET* 4.2 10.1 - - + +
62A LEU* 4.0 30.9 - - + +
63A ASP* 3.0 35.8 + - - +
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Residues in contact with GLU 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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19A TYR* 3.9 4.3 - - + -
22A ARG* 2.7 46.2 + - - -
32A ALA 3.0 17.4 + - - +
33A GLU* 3.5 9.3 - - - +
35A LYS* 1.3 80.7 - - - +
37A LEU* 1.3 64.2 + - - +
39A GLN* 3.8 4.6 - - - +
40A LYS* 2.8 69.7 + - + +
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Residues in contact with LEU 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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15A THR* 3.9 11.2 - - + +
16A PHE* 4.8 1.1 - - - -
19A TYR* 3.6 49.8 - - + -
29A LEU* 4.2 10.5 - - + -
33A GLU 2.8 13.8 + - - +
34A LEU* 3.3 9.4 - - + +
36A GLU* 1.3 76.3 - - - +
38A LEU* 1.3 66.6 + - + +
41A GLU* 2.7 40.8 + - + +
75A TYR* 3.5 33.0 - - + -
5B LEU* 3.8 27.6 - - + -
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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 LEU* 2.9 26.9 + - + +
35A LYS 3.8 2.9 - - - +
37A LEU* 1.3 79.4 - - + +
39A GLN* 1.3 58.5 + - - +
42A LEU* 2.9 39.9 + - + +
58A PHE* 4.2 13.7 - - + -
59A MET* 4.8 8.5 - - + -
62A LEU* 3.7 30.3 - - + -
78A SER* 4.0 19.5 - - - +
79A LEU* 3.6 31.4 - - + -
82A LEU* 3.7 24.8 - - + +
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Residues in contact with GLN 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 LYS* 2.9 53.8 + - - +
36A GLU* 4.0 4.9 - - - +
38A LEU* 1.3 75.2 - - - +
40A LYS* 1.3 60.4 + - + +
42A LEU 5.4 0.4 - - - -
43A ALA* 3.4 26.0 - - - +
59A MET* 3.6 29.9 - - + +
63A ASP* 5.3 2.4 + - - -
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Residues in contact with LYS 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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19A TYR* 3.9 14.1 - - - +
22A ARG* 5.8 0.2 - - - +
36A GLU* 2.8 54.7 + - + +
39A GLN* 1.3 81.8 - - + +
41A GLU* 1.3 66.9 + - - +
42A LEU 3.4 0.4 - - - -
43A ALA* 4.0 10.4 + - - +
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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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15A THR* 4.0 14.0 + - + +
18A GLU* 4.6 8.5 - - - +
19A TYR* 2.6 33.4 + - - +
37A LEU* 2.7 36.6 + - + +
40A LYS* 1.3 77.7 - - - +
42A LEU* 1.3 58.8 + - + +
43A ALA 3.6 0.7 - - - -
3B ARG 4.5 16.2 + - - +
4B PRO* 5.3 4.3 - - - +
5B LEU* 3.6 27.1 - - + +
6B GLU* 3.3 25.5 + - - +
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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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38A LEU* 2.9 30.9 + - + +
39A GLN* 5.4 0.2 - - - -
41A GLU* 1.3 80.9 - - - +
43A ALA* 1.3 63.7 - - - +
44A THR 3.2 2.9 - - - -
45A TRP* 3.1 44.3 + - + +
79A LEU* 4.0 14.8 - - + -
82A LEU* 3.4 34.5 - - + +
5B LEU* 4.3 11.4 - - + +
6B GLU* 3.6 37.7 - - + +
9B VAL* 4.6 8.1 - - + -
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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