Contacts of the helix formed by residues 38 - 53 (chain A) in PDB entry 2JNU
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 ALA 38 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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29A THR* 5.1 4.0 - - + -
32A LEU* 3.0 36.9 - - - +
33A LYS* 4.4 7.6 - - + -
36A PHE* 3.5 8.5 - - + -
37A SER* 1.3 75.0 - - - +
39A GLU* 1.3 63.5 + - - +
40A ASN 3.0 2.5 + - - -
41A VAL* 3.1 10.6 - - + +
42A THR* 2.9 31.7 + - + +
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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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36A PHE* 5.1 10.8 - - + +
37A SER* 2.8 35.5 + - - +
38A ALA* 1.3 77.0 - - - +
40A ASN* 1.3 81.4 + - - +
42A THR* 3.4 10.6 - - - +
43A PHE* 2.9 32.1 + - - +
72A PHE* 3.7 2.9 - - - -
79A SER* 3.7 29.8 - - - +
80A PRO* 4.0 6.3 - - + +
81A VAL* 3.5 29.8 - - + +
82A ASN* 4.7 5.5 + - - +
109A ILE* 5.9 0.2 - - - +
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Residues in contact with ASN 40 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
32A LEU* 3.6 10.5 - - - +
37A SER* 2.6 34.4 + - - -
39A GLU* 1.3 96.1 + - - +
41A VAL* 1.3 85.1 + - - +
43A PHE* 3.1 2.4 + - - +
44A TRP 2.9 24.8 + - - -
81A VAL* 4.6 0.4 - - - -
109A ILE* 3.1 35.6 - - + +
112A LEU* 5.3 12.0 - - + +
113A MET* 3.1 24.1 - - + +
117A SER* 5.2 2.2 + - - -
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Residues in contact with VAL 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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19A LEU* 5.1 2.4 - - + +
25A LEU* 4.6 12.1 - - + -
28A PHE* 3.4 26.7 - - + -
29A THR* 4.2 19.1 - - + +
32A LEU* 3.6 17.0 - - + -
38A ALA* 3.1 18.6 - - + +
40A ASN* 1.3 97.1 + - - +
42A THR* 1.3 62.2 + - - +
44A TRP* 3.3 7.0 + - - +
45A LYS* 2.8 34.2 + - + +
113A MET* 3.3 21.1 - - + -
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Residues in contact with THR 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 ALA* 2.9 31.4 + - + +
39A GLU* 3.4 11.7 - - - +
41A VAL* 1.3 76.5 - - - +
43A PHE* 1.3 61.9 + - - +
45A LYS* 3.5 17.3 - - - +
46A ALA* 2.8 26.3 + - - +
72A PHE* 3.4 24.2 - - + -
79A SER* 5.9 0.2 - - - -
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Residues in contact with PHE 43 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
39A GLU 2.9 21.3 + - - +
40A ASN 3.4 3.1 - - - +
42A THR* 1.3 76.4 - - - +
44A TRP* 1.3 60.3 + - - +
46A ALA* 3.0 5.2 + - - +
47A CYS* 2.8 55.1 + - - -
68A ILE* 3.8 16.6 - - + -
72A PHE* 3.7 28.3 - + + -
73A LEU* 3.6 32.1 - - + -
81A VAL* 3.7 13.7 - - + -
83A ILE* 4.5 0.9 - - + -
102A PHE* 4.8 4.0 - + + -
105A GLN* 3.6 35.9 - - + -
106A GLN* 4.2 0.9 - - - -
109A ILE* 3.6 26.7 - - + -
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Residues in contact with TRP 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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19A LEU* 3.6 51.1 - - + -
20A GLN* 4.7 14.6 - - - -
25A LEU* 4.7 4.7 - - + -
40A ASN 2.9 11.8 + - - +
41A VAL 3.5 8.5 - - - +
43A PHE* 1.3 79.2 - - - +
45A LYS* 1.3 65.1 + - + +
47A CYS* 3.4 2.1 + - - +
48A GLU* 2.8 52.6 + - + +
106A GLN* 3.4 56.5 + - + +
107A LEU* 5.3 2.8 - - - +
109A ILE* 3.9 7.6 - - + -
110A PHE* 3.4 29.6 - + + +
113A MET* 4.0 9.0 - - + -
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Residues in contact with LYS 45 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
25A LEU* 3.4 44.6 - - + +
29A THR* 4.3 12.3 - - + -
41A VAL* 2.8 25.0 + - + +
42A THR* 3.5 18.8 - - - +
44A TRP* 1.3 86.4 - - + +
46A ALA* 1.3 51.8 - - - +
48A GLU* 3.4 18.8 + - - +
49A ARG* 2.7 34.3 + - - +
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Residues in contact with ALA 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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42A THR 2.8 18.3 + - - +
43A PHE* 3.0 10.9 + - - +
45A LYS* 1.3 77.0 - - - +
47A CYS* 1.3 58.7 + - - +
49A ARG* 3.2 10.2 - - - +
50A PHE 2.8 22.2 + - - -
64A GLU* 5.7 1.1 - - - +
68A ILE* 3.3 36.7 - - + +
72A PHE* 4.0 11.7 - - + -
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Residues in contact with CYS 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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43A PHE* 2.8 54.7 + - - +
44A TRP 3.8 0.4 - - - +
46A ALA* 1.3 73.6 - - - +
48A GLU* 1.3 59.9 + - - +
50A PHE* 3.1 10.1 + - - +
51A GLN* 2.9 29.6 + - - +
68A ILE* 4.6 2.5 - - - -
102A PHE* 3.6 24.9 - - + -
106A GLN* 3.2 35.6 - - + +
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Residues in contact with GLU 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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25A LEU* 5.9 1.0 - - - +
44A TRP* 2.8 39.7 + - + +
45A LYS* 3.5 20.0 + - - +
47A CYS* 1.3 75.5 - - - +
49A ARG* 1.3 66.5 + - - +
51A GLN* 3.2 20.1 - - + +
52A GLN* 2.9 33.8 + - - +
106A GLN* 4.1 5.5 + - - +
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Residues in contact with ARG 49 (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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45A LYS 2.7 22.0 + - - +
46A ALA* 3.2 11.2 - - - +
48A GLU* 1.3 80.7 + - - +
50A PHE* 1.3 62.2 + - - +
52A GLN* 3.3 28.1 + - - +
53A ILE* 3.4 14.8 - - + +
60A GLN* 5.8 4.2 - - - +
64A GLU* 3.3 32.2 + - - +
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Residues in contact with PHE 50 (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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46A ALA 2.8 13.6 + - - +
47A CYS* 3.1 13.7 + - - +
49A ARG* 1.3 74.8 - - - +
51A GLN* 1.3 57.2 + - - +
52A GLN 3.1 4.5 - - - -
53A ILE* 3.1 27.8 + - + +
61A LEU* 3.1 49.9 - - + +
64A GLU* 3.7 20.4 - - + -
65A ALA* 3.6 13.5 - - + -
68A ILE* 4.1 3.4 - - + -
93A VAL* 5.6 0.2 - - + -
97A PRO* 4.1 6.3 - - + -
98A ARG 3.0 40.2 - - - -
99A PRO* 3.8 8.4 - - + +
101A MET* 4.2 5.8 - - + -
102A PHE* 3.7 31.6 - + + -
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Residues in contact with GLN 51 (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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47A CYS 2.9 12.2 + - - +
48A GLU* 3.2 23.6 - - + +
50A PHE* 1.3 74.4 - - - +
52A GLN* 1.3 63.4 + - - +
53A ILE 3.2 6.4 + - - +
99A PRO* 3.7 27.6 - - - +
106A GLN* 3.2 33.8 + - - +
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Residues in contact with GLN 52 (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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48A GLU* 2.9 24.4 + - - +
49A ARG* 3.3 22.9 + - - +
50A PHE 3.1 0.2 - - - -
51A GLN* 1.3 79.2 - - - +
53A ILE* 1.3 71.6 + - - +
54A PRO* 3.5 8.8 - - - +
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Residues in contact with ILE 53 (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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49A ARG* 3.4 18.6 - - + +
50A PHE* 3.1 10.4 + - - +
51A GLN 3.7 3.2 - - - +
52A GLN* 1.3 84.8 - - - +
54A PRO* 1.3 84.5 - - + +
55A ALA 3.5 2.1 + - - -
57A ASP* 3.8 2.7 - - + +
60A GLN* 3.7 44.9 - - + +
61A LEU* 3.6 17.7 - - + -
64A GLU* 3.7 34.3 - - + +
99A PRO* 3.6 18.4 - - - +
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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