Contacts of the helix formed by residues 35 - 47 (chain S) in PDB entry 2ZJQ
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 35 (chain S).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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3S LEU* 4.8 2.2 - - - +
17S SER* 3.1 16.6 + - - +
18S MET* 3.1 18.3 - - + +
34S LEU* 1.3 99.5 - - - +
36S ARG* 1.3 78.0 + - - +
37S LYS* 2.7 9.7 + - - +
38S ALA* 2.4 45.1 + - + +
39S PHE 3.6 5.2 + - - -
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Residues in contact with ARG 36 (chain S).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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17S SER* 3.2 45.1 - - - +
18S MET* 2.9 12.8 - - - +
19S ILE* 3.4 23.8 - - + +
35S ASP* 1.3 86.0 + - - +
37S LYS* 1.3 76.9 + - - +
38S ALA 2.6 13.2 + - - -
39S PHE 3.0 3.6 + - - -
40S ASP* 2.2 43.5 + - - +
1049X C 5.8 1.6 + - - -
1050X G 4.9 21.2 + - - -
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Residues in contact with LYS 37 (chain S).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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17S SER* 5.7 1.1 - - - -
35S ASP* 2.7 12.0 + - - +
36S ARG* 1.3 96.4 - - - +
38S ALA* 1.3 52.6 + - - +
40S ASP* 2.5 32.4 + - - +
41S ARG* 2.8 26.8 + - + +
1050X G 3.7 24.5 + - - +
1051X U 2.9 31.5 + - - -
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Residues in contact with ALA 38 (chain S).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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1S MET* 5.0 19.3 - - + +
2S GLU 5.9 0.4 - - - +
34S LEU* 6.3 0.7 - - + -
35S ASP* 2.4 36.0 + - + +
36S ARG 2.6 0.8 + - - -
37S LYS* 1.3 69.2 - - - +
39S PHE* 1.3 52.3 + - - +
40S ASP 2.9 4.0 - - - -
41S ARG* 3.1 6.7 + - - +
42S ALA* 2.7 37.1 + - - +
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Residues in contact with PHE 39 (chain S).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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1S MET* 5.0 7.7 - - - +
19S ILE* 4.0 17.9 - - + -
34S LEU* 3.5 31.4 - - + +
35S ASP 3.6 2.0 + - - +
36S ARG 3.0 4.0 + - - +
38S ALA* 1.3 77.5 - - - +
40S ASP* 1.3 59.8 + - - +
42S ALA* 3.5 9.0 - - + -
43S PHE* 3.0 66.0 + + + +
66S VAL* 4.5 7.9 - - + -
69S VAL* 4.2 9.6 - - + -
78S PRO* 5.2 9.9 - - + -
81S VAL* 3.4 34.1 - - + -
83S PHE* 3.7 32.3 - + - -
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Residues in contact with ASP 40 (chain S).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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19S ILE* 3.5 13.8 - - - +
36S ARG* 2.2 54.3 + - - +
37S LYS* 2.5 30.4 + - + +
39S PHE* 1.3 83.8 - - - +
41S ARG* 1.3 57.0 + - - +
44S ARG* 4.2 13.5 + - - +
78S PRO* 6.4 1.8 - - - -
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Residues in contact with ARG 41 (chain S).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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37S LYS* 2.8 22.8 + - + +
38S ALA* 3.9 5.2 + - - +
40S ASP* 1.3 73.9 - - - +
42S ALA* 1.3 66.8 + - - +
44S ARG* 3.6 5.8 - - - +
45S GLN* 3.6 26.0 + - + +
1051X U 5.6 6.1 - - - -
1052X C 6.0 1.8 + - - -
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Residues in contact with ALA 42 (chain S).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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1S MET* 3.9 25.6 - - + -
38S ALA 2.7 18.5 + - - +
39S PHE* 3.5 10.8 - - + -
40S ASP 3.3 0.2 - - - -
41S ARG* 1.3 75.0 - - - +
43S PHE* 1.3 68.2 + - - +
44S ARG 2.6 6.1 + - - -
45S GLN* 2.7 23.6 + - - +
46S GLN* 3.7 4.1 + - - +
52S PHE* 5.9 0.9 - - + -
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Residues in contact with PHE 43 (chain S).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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136J GLU* 3.2 44.5 - - + +
138J TYR* 4.9 4.3 - + + -
1S MET* 5.5 0.4 - - - -
39S PHE* 3.0 46.5 + + + +
42S ALA* 1.3 76.7 - - - +
44S ARG* 1.3 57.9 + - - +
46S GLN* 4.9 1.8 - - - +
47S SER* 2.6 67.1 + - - +
48S THR* 3.4 12.6 - - + -
66S VAL* 3.7 28.3 - - + -
69S VAL* 4.4 15.0 - - + -
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Residues in contact with ARG 44 (chain S).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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136J GLU* 3.7 19.6 - - - +
39S PHE 4.5 0.8 + - - -
40S ASP 4.2 13.2 + - - +
41S ARG* 3.6 11.6 - - - +
42S ALA 2.6 4.2 + - - +
43S PHE* 1.3 77.9 - - - +
45S GLN* 1.3 86.3 + - - +
47S SER* 4.2 2.8 + - - -
1051X U 5.7 3.2 + - - -
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Residues in contact with GLN 45 (chain S).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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41S ARG* 3.6 20.2 + - + +
42S ALA* 2.7 13.6 + - - +
44S ARG* 1.3 117.1 - - - +
46S GLN* 1.3 69.2 + - + +
47S SER* 3.1 4.2 + - - -
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Residues in contact with GLN 46 (chain S).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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1S MET* 5.7 0.2 - - - +
42S ALA 3.7 5.7 + - - +
43S PHE* 5.4 2.0 - - - -
45S GLN* 1.3 81.4 - - + +
47S SER* 1.3 71.2 + - - +
49S THR* 3.4 20.4 + - - +
50S GLY* 3.0 31.7 - - - +
51S LEU* 2.7 32.7 + - - +
52S PHE* 3.4 28.4 - - - +
66S VAL* 6.1 0.4 - - + -
132S GLN* 5.3 6.4 - - - +
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Residues in contact with SER 47 (chain S).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
136J GLU* 4.5 6.3 + - - -
138J TYR* 5.0 7.1 - - - -
43S PHE* 2.6 50.2 + - - -
44S ARG 4.6 3.4 - - - -
45S GLN 3.9 7.0 - - - -
46S GLN* 1.3 85.3 - - - +
48S THR* 1.3 71.6 + - - +
49S THR* 2.9 9.4 + - - -
50S GLY* 3.3 6.6 + - - -
66S VAL* 3.8 12.8 - - - +
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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