Contacts of the helix formed by residues 36 - 49 (chain A) in PDB entry 3NSB
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 ASP 36 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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34A VAL* 3.7 1.0 - - - +
35A SER* 1.3 78.5 + - - +
37A PRO* 1.3 77.4 - - - +
38A ASP* 3.5 5.9 + - - +
39A ALA* 2.9 23.0 + - + +
40A LYS* 2.9 23.6 + - - +
230A PHE* 3.4 35.0 - - + -
231A GLY* 3.3 28.2 + - - -
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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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35A SER 3.1 9.4 - - - +
36A ASP* 1.3 90.9 - - - +
38A ASP* 1.3 67.1 + - - +
40A LYS* 3.2 14.5 + - + +
41A LYS* 3.2 29.7 + - - +
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Residues in contact with ASP 38 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
36A ASP* 3.3 10.8 + - - +
37A PRO* 1.3 82.4 - - - +
39A ALA* 1.3 62.9 + - - +
41A LYS* 3.1 36.8 + - - +
42A PHE* 3.2 24.2 + - + -
229A ILE 3.4 11.4 - - - +
230A PHE 4.8 0.4 - - - -
231A GLY* 3.8 20.3 - - - +
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Residues in contact with ALA 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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34A VAL* 3.5 13.9 - - + -
36A ASP* 2.9 19.3 + - - +
38A ASP* 1.3 75.3 - - - +
40A LYS* 1.3 58.2 + - - +
42A PHE* 3.2 2.6 + - - +
43A TYR* 2.9 35.8 + - + -
229A ILE* 3.1 22.8 + - + +
230A PHE* 3.4 31.6 - - + -
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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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34A VAL* 3.4 32.1 - - + +
35A SER* 3.8 16.3 + - - +
36A ASP 2.9 16.5 + - - +
37A PRO* 3.3 13.9 - - + +
39A ALA* 1.3 78.2 - - - +
41A LYS* 1.3 57.0 + - + +
43A TYR* 3.3 5.6 + - - +
44A ALA* 2.9 31.6 + - - +
1000A LI1 4.7 8.3 - - + +
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Residues in contact with LYS 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* 3.4 17.5 - - - +
38A ASP* 3.1 29.9 + - - +
40A LYS* 1.3 77.9 - - + +
42A PHE* 1.3 59.6 + - + +
44A ALA* 3.6 4.5 - - - +
45A ILE* 3.0 37.4 + - + +
99A LEU* 4.4 28.1 - - + +
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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 ASP* 3.2 26.4 + - + -
39A ALA 3.2 6.4 + - - +
41A LYS* 1.3 82.7 - - + +
43A TYR* 1.3 55.1 + - - +
46A THR* 2.6 36.4 + - - -
96A ASP* 3.3 43.2 - - - +
99A LEU* 3.9 18.2 - - + -
100A LEU* 3.6 37.5 - - + -
223A LEU* 3.9 12.3 - - + -
224A LEU* 4.2 7.2 - - + -
228A ALA 4.7 1.3 - - - -
229A ILE* 3.5 45.3 - - + -
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Residues in contact with TYR 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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27A PHE 3.9 9.6 - - - -
30A LYS* 2.7 41.0 + - + +
31A GLY* 3.4 34.5 - - - +
34A VAL* 3.8 26.0 - - + +
39A ALA* 2.9 28.2 + - + +
40A LYS* 3.8 5.4 - - - +
42A PHE* 1.3 74.7 - - - +
44A ALA* 1.3 61.1 + - - +
46A THR* 4.5 0.2 - - - -
47A THR* 2.8 38.0 + - - +
224A LEU* 3.6 36.5 + - + -
229A ILE* 3.7 20.3 - - + +
230A PHE* 5.2 3.3 - + - -
1000A LI1 4.2 13.5 - - + -
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Residues in contact with ALA 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 LYS 2.9 18.6 + - - +
41A LYS* 3.6 5.6 - - - +
43A TYR* 1.3 77.7 - - - +
45A ILE* 1.3 63.5 + - + +
47A THR* 4.1 0.9 - - - -
48A LEU* 3.0 28.3 + - - +
1000A LI1 3.4 27.2 - - + +
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Residues in contact with ILE 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 LYS* 3.0 17.8 + - + +
42A PHE* 4.8 0.4 - - - -
44A ALA* 1.3 79.7 - - + +
46A THR* 1.3 62.8 + - - +
48A LEU* 3.4 5.4 + - - +
49A VAL* 3.3 24.3 + - + +
92A LEU* 3.2 44.2 - - + +
95A LEU* 3.6 31.9 - - + -
96A ASP* 3.3 27.8 - - - +
99A LEU* 3.6 24.0 - - + -
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Residues in contact with THR 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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27A PHE* 3.6 8.7 - - + -
42A PHE 2.6 22.8 + - - -
43A TYR 4.1 0.4 - - - -
45A ILE* 1.3 74.4 - - - +
47A THR* 1.3 59.1 + - - +
49A VAL* 3.9 5.2 + - + +
50A PRO* 2.9 21.9 - - - +
93A LEU* 6.4 1.3 - - + -
96A ASP* 2.9 22.0 + - - +
216A LYS 5.1 1.9 - - - +
219A PHE* 5.5 1.6 - - + -
220A GLY* 3.6 26.9 - - - -
223A LEU* 3.5 11.6 - - + +
224A LEU* 3.5 29.9 - - + +
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Residues in contact with THR 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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24A THR* 3.9 30.2 - - + +
27A PHE* 3.3 27.0 + - + +
28A LEU* 4.2 10.3 - - + +
43A TYR* 2.8 25.4 + - - -
46A THR* 1.3 73.9 - - - +
48A LEU* 1.3 65.0 + - - +
49A VAL 3.2 0.4 - - - -
50A PRO* 3.2 15.9 - - - +
51A ALA* 3.3 10.2 + - - +
1000A LI1 3.7 33.0 - - + +
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Residues in contact with LEU 48 (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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44A ALA 3.0 19.0 + - - +
45A ILE* 3.7 5.6 - - - +
47A THR* 1.3 79.3 - - - +
49A VAL* 1.3 62.2 + - - +
51A ALA* 3.2 5.9 + - + +
52A ILE* 3.0 42.8 + - + +
92A LEU* 3.7 24.5 - - + -
1000A LI1 4.1 26.4 - - + +
1003A LI1 3.9 26.9 - - + -
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Residues in contact with VAL 49 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
45A ILE* 3.3 19.0 + - + +
46A THR* 4.0 5.6 - - + +
48A LEU* 1.3 78.6 - - - +
50A PRO* 1.3 66.9 - - + +
53A ALA* 3.1 22.7 + - - +
89A THR* 3.4 24.4 - - - +
92A LEU* 3.8 26.7 - - + -
93A LEU* 4.2 22.0 - - + +
96A ASP* 5.6 0.2 - - - +
216A LYS* 3.5 39.9 - - + +
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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