Contacts of the helix formed by residues 24 - 45 (chain A) in PDB entry 1OZJ
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 ASN 24 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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22A GLU 4.2 3.1 - - - +
23A GLN* 1.3 89.8 + - - +
25A GLY* 1.3 52.5 + - - +
26A GLN* 3.8 7.8 + - - +
27A GLU* 2.5 56.8 + - + +
28A GLU 3.2 1.3 + - - -
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Residues in contact with GLY 25 (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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23A GLN* 3.1 12.4 + - - -
24A ASN* 1.3 69.5 - - - +
26A GLN* 1.3 62.8 + - - +
28A GLU* 3.2 19.4 - - - +
29A LYS* 3.4 7.4 + - - +
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Residues in contact with GLN 26 (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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24A ASN* 2.7 10.8 + - - +
25A GLY* 1.3 72.0 - - - +
27A GLU* 1.3 62.6 + - - +
29A LYS* 3.0 23.1 + - - +
30A TRP* 3.1 11.7 + - + +
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Residues in contact with GLU 27 (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 GLY 4.5 7.0 - - - +
22A GLU 5.4 0.7 - - - +
23A GLN 3.4 13.5 - - - +
24A ASN* 2.5 32.6 + - + +
26A GLN* 1.3 74.9 - - - +
28A GLU* 1.3 60.3 + - - +
30A TRP* 3.0 26.4 + - - +
31A CYS* 3.2 21.4 + - - -
80A ARG* 2.8 31.9 + - - -
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Residues in contact with GLU 28 (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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16A LEU* 5.3 9.2 - - - +
20A LYS* 3.3 48.9 - - - +
21A GLY 4.1 10.0 + - - +
23A GLN* 3.9 22.2 + - - +
24A ASN 3.2 4.6 + - - +
25A GLY* 3.2 14.4 - - - +
26A GLN 3.1 0.4 - - - -
27A GLU* 1.3 80.6 - - - +
29A LYS* 1.3 62.2 + - - +
30A TRP 3.3 0.2 + - - -
31A CYS* 3.5 5.5 + - - +
32A GLU* 3.4 16.6 + - - +
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Residues in contact with LYS 29 (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 GLY 3.4 5.9 + - - +
26A GLN* 3.0 17.9 + - - +
28A GLU* 1.3 77.4 - - - +
30A TRP* 1.3 64.7 + - - +
32A GLU* 3.4 34.5 + - - +
33A LYS* 3.0 63.9 + - - +
36A LYS* 4.9 4.6 - - - +
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Residues in contact with TRP 30 (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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26A GLN* 3.1 9.8 + - + +
27A GLU* 3.0 25.7 + - - +
29A LYS* 1.3 74.5 - - - +
31A CYS* 1.3 79.6 + - - +
33A LYS* 2.8 12.6 + - - +
34A ALA* 2.8 43.9 + - + -
77A VAL* 3.1 41.9 + - + +
78A SER* 3.7 19.7 - - - -
80A ARG* 3.3 49.1 - - + +
87A ILE* 3.8 37.5 - - + -
90A ARG* 5.6 8.3 - - - -
91A LEU* 5.3 3.1 - - + -
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Residues in contact with CYS 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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16A LEU* 4.2 3.6 - - + -
20A LYS 3.2 29.8 - - - +
21A GLY* 3.8 14.8 - - - -
27A GLU* 3.2 20.5 + - - -
28A GLU* 3.8 8.3 - - - +
30A TRP* 1.3 95.8 - - - +
32A GLU* 1.3 57.0 + - - +
34A ALA* 3.3 5.8 + - - +
35A VAL* 2.9 35.3 + - - +
91A LEU* 4.1 15.4 - - + +
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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
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8A THR* 3.4 31.5 + - + +
12A VAL* 4.5 1.3 - - + -
13A LYS* 5.6 4.1 - - - +
16A LEU* 3.9 31.5 - - + +
28A GLU 3.4 9.5 + - - +
29A LYS* 3.4 38.2 + - + +
30A TRP 3.0 0.8 - - - -
31A CYS* 1.3 76.5 - - - +
33A LYS* 1.3 56.0 + - - +
35A VAL* 3.2 2.5 + - - +
36A LYS* 2.8 54.7 + - + +
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Residues in contact with LYS 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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29A LYS* 3.0 51.7 - - - +
30A TRP* 2.8 12.3 + - - +
32A GLU* 1.3 77.6 - - - +
34A ALA* 1.3 58.7 + - - +
36A LYS* 3.2 17.4 + - - +
37A SER* 2.9 31.2 + - - -
77A VAL* 4.0 13.7 - - + -
78A SER* 4.8 20.4 - - - +
1006C C 3.2 32.8 + - - +
1007C T 5.2 1.4 + - - +
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Residues in contact with ALA 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 TRP* 2.8 28.7 + - + +
31A CYS* 3.5 13.5 - - - +
33A LYS* 1.3 78.7 - - - +
35A VAL* 1.3 60.3 + - - +
37A SER* 3.6 1.0 + - - -
38A LEU 3.2 8.3 + - - -
77A VAL* 3.6 25.5 - - + +
87A ILE* 4.7 1.6 - - + -
88A TYR* 2.7 32.1 + - + +
91A LEU* 4.2 10.8 - - + -
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Residues in contact with VAL 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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12A VAL* 3.7 30.5 - - + +
15A LEU* 4.3 13.9 - - + -
16A LEU* 3.7 18.6 - - + -
31A CYS 2.9 22.1 + - - +
32A GLU 3.7 3.1 - - - +
34A ALA* 1.3 72.4 - - - +
36A LYS* 1.3 60.6 + - - +
37A SER 3.1 0.2 - - - -
38A LEU* 3.1 6.0 + - + +
39A VAL* 2.8 41.4 + - + +
51A LEU* 6.2 0.4 - - + -
88A TYR* 4.8 1.8 - - - -
91A LEU* 4.0 17.9 - - + -
92A TRP* 4.1 18.8 - - + -
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Residues in contact with LYS 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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7A PHE 5.8 0.9 - - - -
8A THR* 3.3 45.0 + - + +
9A PRO* 5.2 3.8 - - + -
12A VAL* 4.0 17.0 - - + -
29A LYS* 4.9 4.8 - - - +
32A GLU* 2.8 33.9 + - + +
33A LYS* 3.4 24.7 - - - +
35A VAL* 1.3 76.5 - - - +
37A SER* 1.3 62.9 + - - +
39A VAL* 3.8 1.9 - - - +
40A LYS* 3.1 25.6 + - - +
1006C C 5.4 3.0 + - - -
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Residues in contact with SER 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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33A LYS 2.9 16.3 + - - -
34A ALA 3.7 5.8 - - - -
36A LYS* 1.3 77.6 - - - +
38A LEU* 1.3 65.2 + - - +
40A LYS* 3.5 9.9 + - - +
41A LYS* 3.4 45.4 + - - +
75A LEU* 4.9 1.7 - - - +
76A GLN 5.2 0.3 + - - -
77A VAL* 4.5 13.8 - - - +
88A TYR* 4.5 2.7 + - - -
1007C T 3.7 23.5 + - - -
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Residues in contact with LEU 38 (chain A).
Click here for Legend to table.
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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34A ALA 3.2 4.9 + - - +
35A VAL* 3.1 8.8 + - + +
37A SER* 1.3 81.5 + - - +
39A VAL* 1.3 61.6 + - + +
41A LYS* 3.2 6.6 + - + +
42A LEU* 3.1 39.4 + - + +
51A LEU* 4.0 14.6 - - + -
67A ILE* 3.3 36.3 - - + -
88A TYR* 3.6 46.0 + - + +
92A TRP* 3.9 19.7 - - + -
122A VAL* 4.0 17.9 - - + +
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Residues in contact with VAL 39 (chain A).
Click here for Legend to table.
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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9A PRO* 5.4 3.8 - - + -
11A ILE* 4.1 15.3 - - + -
12A VAL* 3.9 21.3 - - + -
15A LEU* 4.1 12.6 - - + -
35A VAL* 2.8 32.4 + - + +
36A LYS 3.8 3.6 - - - +
38A LEU* 1.3 72.4 - - + +
40A LYS* 1.3 66.5 + - - +
42A LEU* 3.1 4.5 + - - +
43A LYS* 2.9 31.5 + - + +
48A LEU* 4.0 37.9 - - + +
51A LEU* 5.0 3.4 - - + -
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Residues in contact with LYS 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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36A LYS 3.1 16.0 + - - +
37A SER* 3.6 10.5 - - - +
39A VAL* 1.3 83.2 - - - +
41A LYS* 1.3 69.7 + - + +
43A LYS* 3.3 20.3 - - - +
44A LYS* 3.3 36.7 + - - +
2012D C 4.9 1.4 + - - -
2013D T 3.5 27.5 + - - -
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Residues in contact with LYS 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 SER* 3.4 29.2 + - - +
38A LEU* 3.2 6.8 + - + +
39A VAL 3.2 0.8 - - - -
40A LYS* 1.3 82.4 - - + +
42A LEU* 1.3 65.2 + - - +
44A LYS* 3.4 12.0 + - + +
45A THR* 3.2 26.2 + - - +
67A ILE* 3.9 33.1 - - + +
68A PRO* 5.0 10.1 - - + -
75A LEU* 3.3 34.6 - - - +
1007C T 6.1 3.3 - - - -
1008C A 4.0 10.1 + - - -
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Residues in contact with LEU 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 LEU* 3.1 25.4 + - + +
39A VAL* 3.8 3.8 - - - +
41A LYS* 1.3 73.9 - - - +
43A LYS* 1.3 60.8 + - - +
45A THR* 3.6 2.9 - - - -
46A GLY* 2.8 9.0 + - - -
47A GLN* 2.7 40.0 + - + +
48A LEU* 3.5 19.1 + - + +
51A LEU* 3.4 43.7 - - + -
65A ILE* 3.7 23.8 - - + -
66A THR 3.8 8.7 - - - +
67A ILE* 3.3 28.0 - - + -
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Residues in contact with LYS 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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9A PRO* 5.2 8.0 - - - +
11A ILE* 4.9 7.3 - - - +
39A VAL* 2.9 23.0 + - + +
40A LYS* 3.3 15.5 - - - +
41A LYS 3.2 0.2 - - - -
42A LEU* 1.3 78.6 - - - +
44A LYS* 1.3 63.1 + - + +
46A GLY* 3.1 13.9 + - - -
48A LEU* 3.7 30.5 - - + +
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Residues in contact with LYS 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 LYS* 3.3 43.3 + - - +
41A LYS* 3.8 12.4 - - + +
42A LEU 3.3 0.4 - - - -
43A LYS* 1.3 78.9 - - + +
45A THR* 1.3 61.5 + - + +
46A GLY 3.4 0.7 - - - -
2012D C 5.7 8.3 + - - -
2013D T 5.2 5.7 + - - -
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Residues in contact with THR 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 LYS 3.2 16.9 + - - +
42A LEU* 3.5 2.8 + - - -
43A LYS 3.1 0.4 - - - -
44A LYS* 1.3 83.5 - - + +
46A GLY* 1.3 62.9 + - - +
47A GLN* 2.7 40.8 + - - +
66A THR 5.6 0.7 - - - +
68A PRO* 6.3 4.0 - - + -
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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