Contacts of the helix formed by residues 38 - 55 (chain B) 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 B).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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36B GLU* 3.9 3.4 + - - +
37B VAL* 1.3 70.9 - - - +
39B VAL* 1.3 55.8 + - - +
40B ALA* 3.4 11.6 + - - +
41B ARG* 3.4 30.9 + - + +
42B ALA* 3.1 23.0 + - - +
263B GLU* 2.7 27.9 + - - +
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Residues in contact with VAL 39 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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20B LEU* 3.7 22.7 - - + -
22B GLU* 3.8 24.7 - - + +
24B LEU* 5.1 2.5 - - + -
25B GLY* 3.7 31.6 - - - +
37B VAL* 3.1 10.3 + - + +
38B ASP* 1.3 68.9 + - - +
40B ALA* 1.3 55.1 + - - +
42B ALA* 3.0 8.3 + - - +
43B GLU* 2.7 47.3 + - - +
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Residues in contact with ALA 40 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
38B ASP* 3.3 9.3 + - - +
39B VAL* 1.3 75.6 - - - +
41B ARG* 1.3 66.7 + - - +
43B GLU* 3.9 9.4 - - - +
44B ARG* 3.1 23.0 + - - +
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Residues in contact with ARG 41 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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38B ASP* 3.4 24.4 + - - +
39B VAL 3.3 0.2 - - - -
40B ALA* 1.3 77.3 - - - +
42B ALA* 1.3 57.6 + - - +
44B ARG* 3.2 7.5 + - + +
45B GLN* 2.8 48.0 + - + +
240B GLU* 6.3 0.2 - - - +
260B SER* 5.7 1.2 + - - -
262B SER* 2.8 31.9 + - - -
263B GLU* 3.5 33.1 + - + +
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Residues in contact with ALA 42 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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20B LEU* 3.9 8.9 - - + +
24B LEU* 5.5 0.7 - - + -
37B VAL* 4.8 3.8 - - + -
38B ASP 3.1 13.3 + - - +
39B VAL* 3.0 13.1 + - - +
41B ARG* 1.3 75.7 - - - +
43B GLU* 1.3 59.8 + - - +
45B GLN* 3.3 4.4 + - - +
46B HIS* 2.8 31.4 + - - +
263B GLU* 3.6 20.1 - - + +
264B LEU* 4.0 26.9 - - + +
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Residues in contact with GLU 43 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
20B LEU* 3.5 37.8 - - + +
22B GLU* 4.8 6.8 + - - +
39B VAL* 2.7 39.8 + - - +
40B ALA* 4.1 8.0 - - - +
42B ALA* 1.3 71.9 - - - +
44B ARG* 1.3 56.6 + - - +
46B HIS* 3.7 3.6 - - - +
47B GLN* 2.7 50.1 + - - +
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Residues in contact with ARG 44 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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40B ALA 3.1 19.3 + - - +
41B ARG* 3.5 7.9 - - + +
42B ALA 3.1 0.2 - - - -
43B GLU* 1.3 78.5 - - - +
45B GLN* 1.3 64.2 - - + +
47B GLN* 2.3 42.1 + - - +
48B LEU* 3.0 54.2 + - + +
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Residues in contact with GLN 45 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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41B ARG* 2.8 40.8 + - + +
42B ALA* 3.7 3.6 - - - +
44B ARG* 1.3 75.2 - - + +
46B HIS* 1.3 64.3 + - - +
48B LEU* 3.4 12.7 + - + +
49B TYR* 3.1 21.1 + - - +
259B VAL* 5.3 0.2 - - - +
260B SER* 3.5 43.2 - - - +
261B MET* 3.7 8.3 - - - +
262B SER* 2.9 30.9 + - - +
263B GLU* 3.1 32.7 + - - +
264B LEU* 4.3 1.5 + - + -
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Residues in contact with HIS 46 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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17B VAL* 4.4 6.8 - - + +
18B ARG 3.3 31.8 + - - -
19B ALA* 4.4 7.1 - - - -
20B LEU* 4.4 8.8 + - + +
42B ALA 2.8 21.7 + - - +
43B GLU* 3.7 8.3 - - - +
45B GLN* 1.3 73.1 - - - +
47B GLN* 1.3 61.9 + - - +
49B TYR* 2.9 25.9 + + + +
50B VAL* 2.9 36.5 + - + +
74B VAL* 3.5 21.8 - - + +
261B MET* 4.9 5.9 - - + +
264B LEU* 4.7 4.7 - - + -
274B CYS* 4.3 27.5 + - + +
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Residues in contact with GLN 47 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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43B GLU* 2.7 43.0 + - - +
44B ARG* 2.3 41.7 + - - +
46B HIS* 1.3 83.4 + - + +
48B LEU* 1.3 58.7 + - - +
50B VAL* 3.7 8.6 + - + +
51B GLY* 2.9 24.3 + - - -
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Residues in contact with LEU 48 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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44B ARG* 3.0 47.5 + - + +
45B GLN* 3.7 11.7 - - + +
47B GLN* 1.3 75.3 - - - +
49B TYR* 1.3 58.5 + - - +
51B GLY* 3.2 3.3 + - - -
52B VAL* 2.9 33.9 + - + +
259B VAL* 5.6 2.2 - - + -
260B SER* 6.0 6.7 - - - +
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Residues in contact with TYR 49 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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17B VAL* 4.6 1.6 - - + -
45B GLN 3.1 12.9 + - - +
46B HIS* 2.9 14.3 + + - +
48B LEU* 1.3 71.4 - - - +
50B VAL* 1.3 67.9 + - + +
52B VAL* 2.8 27.8 + - - +
53B LEU* 3.3 29.6 + - + +
222B ILE* 3.1 15.1 - - + +
234B LEU* 4.6 7.6 - - + +
259B VAL* 4.0 13.8 - - + +
261B MET* 3.5 23.1 - - + -
271B LEU* 2.7 48.4 + - + -
274B CYS* 3.7 27.6 - - + -
275B SER* 2.8 24.5 + - - -
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Residues in contact with VAL 50 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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17B VAL* 3.8 13.9 - - + -
46B HIS* 2.9 49.6 + - + +
47B GLN* 3.9 7.6 - - - +
49B TYR* 1.3 78.8 - - + +
51B GLY* 1.3 58.2 + - - +
52B VAL 3.3 0.2 + - - -
53B LEU* 3.3 8.6 + - - +
54B GLY* 2.9 27.6 + - - -
61B VAL* 3.9 28.9 - - + -
63B GLU* 4.2 21.1 - - - +
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Residues in contact with GLY 51 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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47B GLN 2.9 17.7 + - - -
48B LEU* 3.4 6.5 - - - -
49B TYR 3.1 0.4 + - - -
50B VAL* 1.3 76.4 - - - +
52B VAL* 1.3 61.4 + - - +
55B SER* 3.0 33.3 + - - -
56B LYS* 3.0 9.0 + - - +
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Residues in contact with VAL 52 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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48B LEU* 2.9 17.4 + - + +
49B TYR 2.8 15.6 + - - +
51B GLY* 1.3 71.5 - - - +
53B LEU* 1.3 55.2 + - - +
56B LYS* 3.3 10.8 - - + +
57B LEU* 2.7 37.4 + - + +
234B LEU* 3.5 36.8 - - + -
257B ILE* 3.8 35.0 - - + -
258B PRO 5.4 0.4 - - - +
259B VAL* 4.0 11.7 - - + -
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Residues in contact with LEU 53 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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15B ALA* 4.0 20.6 - - + -
17B VAL* 4.5 6.3 - - + -
49B TYR* 3.8 34.8 - - + +
50B VAL* 3.3 7.5 + - - +
52B VAL* 1.3 77.4 - - - +
54B GLY* 1.3 57.9 + - - +
57B LEU* 4.2 4.9 - - + -
58B GLY 3.4 3.0 + - - -
59B LEU* 2.8 39.6 + - + +
61B VAL* 4.4 7.9 - - + -
222B ILE* 4.9 5.6 - - + -
224B LEU* 3.9 24.2 - - + -
234B LEU* 3.8 25.6 - - + -
275B SER* 4.1 10.8 - - - +
277B LEU* 4.6 8.5 - - + -
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Residues in contact with GLY 54 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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50B VAL* 2.9 14.2 + - - -
53B LEU* 1.3 79.1 - - - +
55B SER* 1.3 60.8 + - - +
58B GLY* 3.5 13.5 - - - -
59B LEU 3.3 20.5 - - - +
61B VAL* 3.6 13.9 - - - -
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Residues in contact with SER 55 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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50B VAL 4.4 0.2 + - - -
51B GLY* 3.0 20.2 + - - -
54B GLY* 1.3 74.8 - - - +
56B LYS* 1.3 69.4 + - - +
58B GLY* 4.4 2.5 + - - -
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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