Contacts of the helix formed by residues 30 - 50 (chain A) in PDB entry 2JQK
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 TYR 30 (chain A).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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25A ASP* 4.3 15.3 + - - -
28A GLY* 3.0 28.8 + - - -
29A ASN* 1.3 88.9 - - - +
31A GLU* 1.3 60.0 + - - +
32A GLU* 3.4 2.3 + - - -
33A ALA* 3.7 5.1 - - - +
34A LEU* 2.7 38.0 + - - +
75A LEU* 3.3 35.8 - - + +
78A TYR* 4.4 23.4 + + - -
79A LEU* 3.8 34.8 - - + -
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Residues in contact with GLU 31 (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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30A TYR* 1.3 81.6 - - - +
32A GLU* 1.3 71.6 + - - +
34A LEU* 3.6 7.5 - - + +
35A GLN* 3.4 38.0 + - - +
79A LEU* 4.4 11.1 - - + +
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Residues in contact with GLU 32 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
24A GLU* 3.7 8.7 - - + +
29A ASN* 2.7 52.8 + - + +
30A TYR 3.5 5.9 + - - -
31A GLU* 1.3 88.9 + - - +
33A ALA* 1.3 61.5 + - - +
35A GLN* 3.6 5.3 + - - +
36A LEU* 2.7 42.7 + - + +
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Residues in contact with ALA 33 (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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21A ALA* 3.5 15.5 - - - +
24A GLU* 3.4 28.0 - - + -
25A ASP* 4.2 3.1 - - - +
29A ASN 3.9 12.6 - - - +
30A TYR* 3.3 7.3 + - - +
31A GLU 3.3 0.6 - - - -
32A GLU* 1.3 80.5 - - - +
34A LEU* 1.3 54.7 + - - +
36A LEU* 3.8 4.6 - - - -
37A TYR* 2.8 49.3 + - + -
75A LEU* 4.8 1.8 - - + -
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Residues in contact with LEU 34 (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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30A TYR 2.7 22.6 + - - +
31A GLU* 3.6 7.6 - - + +
33A ALA* 1.3 74.7 - - - +
35A GLN* 1.3 66.2 + - + +
37A TYR* 3.3 15.8 + - - +
38A GLN* 3.3 30.3 + - - +
72A ALA* 2.8 50.7 - - + +
75A LEU* 4.8 4.7 - - + +
76A LYS* 3.5 37.7 - - + +
79A LEU* 4.6 7.4 - - + -
126B LEU* 5.0 0.2 - - + -
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Residues in contact with GLN 35 (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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31A GLU* 3.4 33.1 + - - +
32A GLU* 4.0 5.8 - - - +
34A LEU* 1.3 82.0 - - + +
36A LEU* 1.3 62.6 + - + +
38A GLN* 3.6 9.6 + - - +
39A HIS* 3.1 53.1 + - + +
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Residues in contact with LEU 36 (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 LEU* 3.6 27.8 - - + +
20A LYS* 4.2 17.0 - - + -
21A ALA* 3.6 18.6 - - + -
24A GLU* 3.3 26.0 - - - +
32A GLU* 2.7 32.6 + - + +
33A ALA* 4.1 3.1 - - - -
35A GLN* 1.3 74.9 - - + +
37A TYR* 1.3 58.0 + - - +
39A HIS* 4.3 6.7 - - - +
40A ALA* 2.7 38.6 + - - +
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Residues in contact with TYR 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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18A ALA* 5.4 0.7 - - - -
21A ALA* 3.5 26.5 - - + -
22A ALA* 3.3 12.8 - - - +
25A ASP* 3.1 40.6 + - - +
33A ALA* 2.8 34.9 + - + +
34A LEU* 3.4 11.0 - - - +
36A LEU* 1.3 77.6 - - - +
38A GLN* 1.3 54.5 + - - +
40A ALA* 3.8 2.3 - - + +
41A VAL* 2.8 41.3 + - - +
68A TYR* 3.4 51.3 - + + +
69A LEU* 5.9 0.2 - - - -
71A ARG* 3.5 15.3 + - + -
72A ALA* 4.0 15.5 - - + -
75A LEU* 4.1 9.9 - - + -
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Residues in contact with GLN 38 (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 LEU* 3.3 39.0 + - - +
35A GLN* 4.1 10.6 - - - +
37A TYR* 1.3 75.7 - - - +
39A HIS* 1.3 63.3 + - + +
41A VAL* 3.8 5.4 - - - +
42A GLN* 2.9 38.5 + - + +
69A LEU* 5.1 5.6 - - + -
72A ALA* 4.3 10.1 - - + -
76A LYS* 5.9 1.0 - - - +
123B LEU* 4.0 2.3 - - + +
126B LEU* 3.2 52.9 + - + +
127B GLY* 3.3 8.8 + - - -
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Residues in contact with HIS 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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17A LEU* 4.3 19.6 - - + +
35A GLN* 3.1 39.6 + - + +
36A LEU* 3.8 5.1 - - - +
38A GLN* 1.3 82.9 - - + +
40A ALA* 1.3 63.6 + - - +
42A GLN* 3.1 28.7 + - - +
43A TYR* 3.3 20.4 + - + -
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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
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14A ALA* 4.0 3.9 - - - +
17A LEU* 3.1 15.1 - - - +
18A ALA* 3.0 44.2 - - + +
21A ALA* 5.0 0.2 - - + -
36A LEU 2.7 22.6 + - - +
37A TYR* 3.8 5.2 - - + +
39A HIS* 1.3 73.7 - - - +
41A VAL* 1.3 63.6 + - + +
43A TYR* 3.2 14.4 + - - +
44A PHE* 3.3 16.3 + - - -
68A TYR* 6.1 0.4 - - + -
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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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37A TYR 2.8 25.5 + - - +
38A GLN 3.9 2.0 - - - +
40A ALA* 1.3 76.8 - - + +
42A GLN* 1.3 63.7 + - - +
44A PHE* 3.1 17.5 + - - +
45A LEU* 3.2 11.1 + - - +
65A CYS* 3.2 35.2 - - + +
68A TYR* 3.6 34.3 - - + -
69A LEU* 4.0 14.1 - - + +
123B LEU* 3.5 27.9 - - + +
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Residues in contact with GLN 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 GLN* 2.9 25.2 + - + +
39A HIS* 3.1 21.5 + - - +
41A VAL* 1.3 78.6 - - - +
43A TYR* 1.3 60.1 + - + +
45A LEU* 3.7 1.6 + - - +
46A HIS* 3.0 28.9 + - - +
49A LYS* 5.2 1.9 + - - -
123B LEU* 3.3 29.6 + - + +
124B LYS* 6.1 0.4 - - - +
127B GLY* 5.4 8.3 + - - -
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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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10A ASN* 3.0 52.0 - - - +
13A LYS* 3.6 26.4 + - + +
14A ALA* 3.7 17.0 - - + -
17A LEU* 3.7 19.3 - - + -
39A HIS* 3.3 24.9 + - + -
40A ALA 3.2 9.6 + - - +
42A GLN* 1.3 78.5 - - + +
44A PHE* 1.3 65.5 + - - +
46A HIS* 3.4 5.2 - + + +
47A VAL* 3.1 29.5 + - - +
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Residues in contact with PHE 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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11A LEU* 5.8 4.7 - - + -
14A ALA* 4.1 17.5 - - + -
15A ILE* 4.7 15.5 - - + -
18A ALA* 4.0 23.3 - - + -
40A ALA 3.3 16.9 + - - -
41A VAL* 3.1 15.6 + - - +
43A TYR* 1.3 78.3 - - - +
45A LEU* 1.3 50.8 - - - +
47A VAL* 2.9 17.6 - - + +
48A VAL* 2.7 30.7 - - - +
61A ILE* 3.1 36.6 - - + -
64A LYS* 4.0 27.6 - - + -
65A CYS* 3.7 16.4 - - - -
68A TYR* 4.6 10.5 - + - -
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Residues in contact with LEU 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 VAL 3.2 10.9 + - - +
42A GLN 4.3 2.5 - - - +
44A PHE* 1.3 77.4 - - - +
46A HIS* 1.3 59.9 + - - +
48A VAL* 3.6 7.2 - - + +
49A LYS* 2.9 54.0 + - + +
61A ILE* 4.2 21.1 - - + -
62A ARG* 5.1 5.6 - - + -
65A CYS* 4.7 8.7 - - - -
116B ASP* 5.5 5.6 - - + +
119B ILE* 4.7 8.5 - - + -
120B GLU* 3.4 48.0 - - + +
123B LEU* 4.0 17.3 - - + -
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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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10A ASN* 3.3 26.0 + - - -
42A GLN 3.0 20.9 + - - +
43A TYR* 3.4 10.5 - + - +
44A PHE 3.2 0.2 - - - -
45A LEU* 1.3 78.3 - - - +
47A VAL* 1.3 63.8 + - - +
49A LYS* 3.5 16.8 + - - +
50A TYR* 3.2 47.9 + + + +
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Residues in contact with VAL 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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10A ASN* 3.5 34.8 - - + +
11A LEU* 4.0 39.3 - - + +
14A ALA* 5.7 0.4 - - + -
43A TYR 3.1 7.4 + - - +
44A PHE* 2.9 31.9 - - + +
46A HIS* 1.3 79.0 - - + +
48A VAL* 1.3 55.6 + - + +
50A TYR* 3.1 2.7 - - - +
51A GLU* 2.6 49.9 + - + +
61A ILE* 5.6 1.6 - - + -
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Residues in contact with VAL 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 PHE 2.7 26.2 - - - +
45A LEU* 3.6 11.7 - - + +
46A HIS 3.3 0.6 - - - -
47A VAL* 1.3 80.1 - - + +
49A LYS* 1.3 62.1 + - + +
50A TYR 3.5 0.3 + - - -
51A GLU 3.5 20.9 + - - +
52A ALA* 3.7 9.2 - - - +
58A LYS* 3.7 39.8 - - + +
61A ILE* 3.3 38.6 - - + -
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Residues in contact with LYS 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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42A GLN 5.2 2.0 + - - -
45A LEU* 2.9 45.8 + - + +
46A HIS* 3.5 22.2 + - - +
47A VAL 3.2 0.2 - - - -
48A VAL* 1.3 78.0 - - + +
50A TYR* 1.3 83.5 + - + +
51A GLU 3.9 0.2 + - - -
120B GLU* 5.3 8.3 + - + +
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Residues in contact with TYR 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 HIS* 3.2 37.6 + + + +
47A VAL* 3.1 4.4 + - - +
49A LYS* 1.3 101.7 - - + +
51A GLU* 1.3 77.8 + - - +
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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