Contacts of the helix formed by residues 38 - 55 (chain A) in PDB entry 2JAJ
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 38 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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36A GLU* 3.6 3.0 + - + +
37A VAL* 1.3 70.0 - - - +
39A VAL* 1.3 64.5 + - - +
40A ALA* 3.3 10.4 + - - +
41A ARG* 3.2 27.8 + - + +
42A ALA* 3.0 22.0 + - - +
263A GLU* 2.9 28.0 + - - +
266A LYS* 5.2 0.4 - - - +
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Residues in contact with VAL 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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20A LEU* 3.9 20.5 - - + +
21A PRO 4.4 0.2 - - - +
22A GLU* 3.7 42.2 - - - +
24A LEU* 5.1 1.8 - - + -
25A GLY* 3.5 35.0 - - - +
37A VAL* 3.6 10.0 + - + +
38A ASP* 1.3 74.0 + - - +
40A ALA* 1.3 56.6 - - - +
42A ALA* 3.3 7.8 + - - +
43A GLU* 2.9 28.7 + - + +
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Residues in contact with ALA 40 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
38A ASP* 3.3 9.3 + - - +
39A VAL* 1.3 80.2 - - - +
41A ARG* 1.4 55.0 + - - +
43A GLU* 3.4 8.0 + - - +
44A ARG* 3.1 26.3 + - - +
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Residues in contact with ARG 41 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
38A ASP* 3.2 28.7 + - - +
40A ALA* 1.4 72.6 - - - +
42A ALA* 1.3 59.9 + - - +
44A ARG* 3.2 7.5 + - + +
45A GLN* 2.9 45.8 + - + +
260A SER* 5.8 1.0 - - - -
262A SER* 2.7 32.3 + - - -
263A GLU* 2.8 39.5 + - + +
266A LYS* 5.6 0.8 - - - +
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Residues in contact with ALA 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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20A LEU* 3.7 9.2 - - + +
24A LEU* 5.3 0.7 - - + -
37A VAL* 4.8 4.5 - - + -
38A ASP 3.0 13.2 + - - +
39A VAL* 3.4 12.8 - - - +
41A ARG* 1.3 77.0 - - - +
43A GLU* 1.3 56.7 + - - +
45A GLN* 3.8 4.1 - - - +
46A HIS* 2.8 32.1 + - - +
263A GLU* 3.8 21.4 - - + +
264A LEU* 3.8 27.4 - - + +
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Residues in contact with GLU 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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20A LEU* 3.9 17.9 - - + +
39A VAL* 2.9 13.6 + - + +
40A ALA* 3.5 12.1 - - - +
42A ALA* 1.3 75.1 - - - +
44A ARG* 1.3 60.2 + - - +
46A HIS* 3.3 2.3 + - - +
47A GLN* 2.7 47.3 + - + +
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Residues in contact with ARG 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 ALA 3.1 12.3 + - - +
41A ARG* 3.6 11.9 - - + +
42A ALA 3.2 0.2 - - - -
43A GLU* 1.3 79.7 - - - +
45A GLN* 1.3 65.4 + - + +
47A GLN* 2.7 40.6 + - - +
48A LEU* 2.9 56.6 + - + +
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Residues in contact with GLN 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 ARG* 2.9 46.8 + - + +
42A ALA* 3.8 4.2 - - - +
44A ARG* 1.3 73.2 - - + +
46A HIS* 1.3 63.1 + - - +
48A LEU* 3.2 14.3 + - + +
49A TYR* 3.0 22.9 + - - +
259A VAL* 5.4 0.5 - - - +
260A SER* 3.8 37.0 - - - +
261A MET* 3.7 8.3 - - + +
262A SER* 2.9 31.6 + - - -
263A GLU* 3.1 28.5 + - - +
264A LEU* 4.4 2.1 + - + +
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Residues in contact with HIS 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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17A VAL* 4.4 9.1 - - + +
18A ARG 3.4 34.3 + - - -
19A ALA* 4.3 7.9 - - - -
20A LEU* 4.0 13.8 + - + +
42A ALA 2.8 22.0 + - - +
43A GLU* 3.8 4.2 + - - +
45A GLN* 1.3 72.2 - - - +
47A GLN* 1.3 61.8 + - - +
49A TYR* 3.2 9.2 + + - +
50A VAL* 2.9 56.7 + - + +
63A GLU* 5.9 0.4 - - - -
74A VAL* 3.4 24.1 - - + +
261A MET* 5.4 4.4 - - - +
264A LEU* 4.7 4.7 - - + -
274A CYS* 4.3 20.7 + - + -
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Residues in contact with GLN 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 GLU* 2.7 35.6 + - - +
44A ARG* 2.7 45.4 + - - +
46A HIS* 1.3 76.3 - - - +
48A LEU* 1.4 58.7 + - - +
50A VAL* 3.4 6.7 + - - +
51A GLY* 2.9 26.0 + - - -
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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 ARG* 2.9 51.7 + - + +
45A GLN* 3.2 13.2 + - + +
47A GLN* 1.4 76.5 - - - +
49A TYR* 1.3 61.3 + - - +
51A GLY* 3.3 3.5 + - - -
52A VAL* 3.1 26.9 + - + +
259A VAL* 5.5 3.1 - - + -
260A SER* 6.2 2.5 - - - -
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Residues in contact with TYR 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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17A VAL* 4.4 2.0 - - + -
45A GLN 3.0 12.9 + - - +
46A HIS* 3.4 13.9 - + - +
48A LEU* 1.3 72.1 - - - +
50A VAL* 1.3 74.6 + - + +
52A VAL* 3.2 16.7 + - - +
53A LEU* 3.2 32.4 + - + +
222A ILE* 3.3 15.0 - - + +
234A LEU* 4.7 8.2 - - + +
259A VAL* 4.1 23.2 - - + +
261A MET* 3.8 20.6 - - + -
271A LEU* 2.7 37.2 + - + -
274A CYS* 3.5 29.6 - - + -
275A SER* 2.7 28.8 + - - -
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Residues in contact with VAL 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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17A VAL* 4.0 17.5 - - + -
46A HIS* 2.9 48.2 + - + +
47A GLN* 3.8 6.5 - - - +
49A TYR* 1.3 80.4 - - + +
51A GLY* 1.3 62.4 + - - +
53A LEU* 3.3 6.0 + - - +
54A GLY* 3.0 23.3 + - - -
61A VAL* 4.3 16.6 - - + -
63A GLU* 3.8 33.9 - - - +
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Residues in contact with GLY 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 GLN 2.9 15.7 + - - -
48A LEU* 3.3 5.8 + - - -
49A TYR 3.3 0.2 - - - -
50A VAL* 1.3 76.0 - - - +
52A VAL* 1.3 56.0 + - - +
55A SER* 2.8 36.6 + - - -
56A LYS* 2.9 10.3 + - - +
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Residues in contact with VAL 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 LEU 3.1 15.6 + - - +
49A TYR* 3.2 8.2 + - - +
51A GLY* 1.3 75.4 - - - +
53A LEU* 1.3 59.1 + - - +
56A LYS* 3.9 12.8 - - + +
57A LEU* 2.8 40.6 + - + +
234A LEU* 3.7 36.3 - - + -
257A ILE* 4.0 30.5 - - + -
259A VAL* 4.3 10.3 - - + -
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Residues in contact with LEU 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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15A ALA* 4.4 8.1 - - + -
17A VAL* 4.4 7.0 - - + -
49A TYR* 3.2 42.0 + - + +
50A VAL* 3.3 6.5 + - - +
52A VAL* 1.3 80.6 - - - +
54A GLY* 1.3 58.3 + - - +
57A LEU* 3.5 5.2 - - + +
58A GLY 3.4 5.2 + - - -
59A LEU* 3.0 42.9 + - + +
61A VAL* 4.2 9.6 - - + -
222A ILE* 5.0 4.7 - - + -
224A LEU* 4.0 26.2 - - + -
234A LEU* 4.3 16.8 - - + -
275A SER* 4.0 19.1 - - - +
277A LEU* 4.4 7.6 - - + -
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Residues in contact with GLY 54 (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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50A VAL 3.0 10.2 + - - -
53A LEU* 1.3 79.1 - - - +
55A SER* 1.3 62.2 + - - +
58A GLY* 3.4 17.7 - - - -
59A LEU 3.4 19.0 - - - +
61A VAL* 3.4 14.8 - - - +
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Residues in contact with SER 55 (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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50A VAL 4.2 0.6 + - - -
51A GLY* 2.8 27.0 + - - -
54A GLY* 1.3 74.5 - - - +
56A LYS* 1.3 64.9 + - - +
57A LEU 3.5 0.2 + - - -
58A GLY* 3.6 5.0 + - - -
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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