Contacts of the helix formed by residues 25 - 45 (chain B) 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 GLY 25 (chain B).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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24B ASN* 1.3 80.2 - - - +
26B GLN* 1.3 63.7 + - - -
28B GLU* 3.4 13.6 + - - +
29B LYS* 3.8 4.0 + - - +
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Residues in contact with GLN 26 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
24B ASN 3.7 0.4 + - - -
25B GLY* 1.3 71.3 + - - -
27B GLU* 1.3 59.9 + - - +
28B GLU 3.2 0.9 - - - -
29B LYS* 3.5 35.8 - - - +
30B TRP* 3.0 28.8 + - + +
80B ARG* 5.3 9.2 - - - +
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Residues in contact with GLU 27 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
23B GLN* 2.9 48.8 - - + +
24B ASN 3.5 1.5 + - - +
25B GLY 3.1 0.4 - - - -
26B GLN* 1.3 80.2 - - - +
28B GLU* 1.3 52.6 + - - +
30B TRP* 3.6 16.6 - - - +
31B CYS* 2.7 49.1 + - - -
80B ARG* 2.8 38.2 + - - +
90B ARG* 5.6 6.1 - - - -
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Residues in contact with GLU 28 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
16B LEU* 5.6 6.9 - - - +
19B LYS* 3.4 24.3 + - - +
22B GLU* 3.8 6.7 - - - +
23B GLN 3.4 4.8 + - - +
24B ASN* 3.0 36.9 + - + +
25B GLY 3.4 13.0 + - - +
27B GLU* 1.3 78.2 - - - +
29B LYS* 1.3 63.7 + - - +
31B CYS* 3.5 4.4 + - - +
32B GLU* 3.2 20.3 + - - +
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Residues in contact with LYS 29 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
25B GLY 3.8 3.6 + - - +
26B GLN* 3.5 38.3 + - - +
27B GLU 3.4 0.2 - - - -
28B GLU* 1.3 79.5 - - - +
30B TRP* 1.3 58.1 + - - +
32B GLU* 3.2 16.6 + - - +
33B LYS* 3.0 52.4 + - + +
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Residues in contact with TRP 30 (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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26B GLN* 3.0 22.0 + - + +
27B GLU* 3.6 25.6 - - - +
28B GLU 3.2 0.2 - - - -
29B LYS* 1.3 75.7 - - - +
31B CYS* 1.3 72.4 + - - +
33B LYS* 3.0 7.3 + - - +
34B ALA* 2.8 33.6 + - + +
77B VAL* 3.1 46.1 + - + +
78B SER* 4.1 14.1 - - - -
80B ARG* 3.6 47.1 - - + +
87B ILE* 3.6 41.7 - - + -
90B ARG* 5.8 9.0 - - - -
91B LEU* 5.8 3.6 - - + -
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Residues in contact with CYS 31 (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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16B LEU* 4.5 3.8 - - + -
19B LYS* 3.9 26.7 - - - +
23B GLN* 5.1 2.5 - - - -
27B GLU* 2.7 47.0 + - - +
28B GLU* 3.7 5.2 - - - +
29B LYS 3.4 0.2 - - - -
30B TRP* 1.3 91.1 - - - +
32B GLU* 1.3 59.6 + - - +
34B ALA* 3.5 4.1 + - - +
35B VAL* 3.0 32.4 + - - +
91B LEU* 4.3 19.5 - - + -
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Residues in contact with GLU 32 (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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9B PRO* 4.5 16.8 - - - +
12B VAL* 4.3 8.4 - - + +
13B LYS* 5.0 5.9 - - - +
16B LEU* 3.9 30.6 - - + +
28B GLU 3.2 8.9 + - - +
29B LYS* 3.2 19.0 + - - +
30B TRP 3.0 0.4 - - - -
31B CYS* 1.3 77.7 - - - +
33B LYS* 1.3 67.5 + - - +
35B VAL* 3.0 4.0 + - - +
36B LYS* 2.9 41.3 + - - +
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Residues in contact with LYS 33 (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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29B LYS* 3.0 48.9 + - + +
30B TRP* 3.4 9.4 - - - +
32B GLU* 1.3 76.4 - - - +
34B ALA* 1.3 56.7 + - - +
36B LYS* 2.9 35.9 + - - +
37B SER* 2.8 34.2 + - - +
77B VAL* 3.8 12.1 - - + -
78B SER* 5.2 11.0 - - - +
2007D C 4.5 16.1 + - - +
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Residues in contact with ALA 34 (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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30B TRP* 2.8 38.3 + - + +
31B CYS* 3.7 7.0 - - - +
33B LYS* 1.3 74.0 - - - +
35B VAL* 1.3 61.8 + - - +
37B SER* 3.6 2.8 + - - -
38B LEU 3.3 9.0 + - - -
77B VAL* 3.4 26.1 - - + +
87B ILE* 4.7 2.7 - - + -
88B TYR* 2.8 35.1 + - + +
91B LEU* 4.9 3.1 - - + -
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Residues in contact with VAL 35 (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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12B VAL* 4.2 17.3 - - + +
15B LEU* 4.2 22.4 - - + -
16B LEU* 3.6 20.2 - - + -
31B CYS 3.0 15.0 + - - +
32B GLU 3.0 8.1 + - - +
34B ALA* 1.3 74.1 - - - +
36B LYS* 1.3 62.2 + - - +
38B LEU* 3.3 6.5 + - + +
39B VAL* 2.9 45.1 + - + +
88B TYR* 4.8 1.6 - - - -
91B LEU* 3.7 23.6 - - + -
92B TRP* 4.3 13.2 - - + +
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Residues in contact with LYS 36 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
9B PRO* 4.4 20.4 - - + -
12B VAL* 3.9 26.9 - - + -
32B GLU* 2.9 40.7 + - + +
33B LYS* 3.4 47.5 - - - +
35B VAL* 1.3 75.2 - - - +
37B SER* 1.3 66.4 + - - +
39B VAL* 3.3 2.5 + - - +
40B LYS* 2.9 27.1 + - - +
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Residues in contact with SER 37 (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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33B LYS* 2.8 19.3 + - - +
34B ALA* 3.8 7.0 - - - -
36B LYS* 1.3 77.1 - - - +
38B LEU* 1.3 64.6 + - - +
40B LYS* 3.3 11.1 + - - +
41B LYS* 3.2 41.8 + - - +
76B GLN 5.9 0.4 - - - -
77B VAL* 4.0 15.2 - - - +
88B TYR* 4.6 3.1 - - - -
2008D T 3.4 22.6 + - - -
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Residues in contact with LEU 38 (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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34B ALA 3.3 3.4 + - - +
35B VAL 3.3 8.0 + - - +
36B LYS 3.2 0.2 - - - -
37B SER* 1.3 80.1 - - - +
39B VAL* 1.3 57.8 + - + +
41B LYS* 3.0 9.2 + - + +
42B LEU* 2.8 50.4 + - + +
51B LEU* 4.8 6.7 - - + -
67B ILE* 3.5 34.1 - - + -
88B TYR* 3.5 47.2 + - + +
92B TRP* 3.8 24.7 - - + -
122B VAL* 4.2 13.7 - - + -
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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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11B ILE* 4.1 8.5 - - + -
12B VAL* 4.2 13.2 - - + -
15B LEU* 4.0 27.6 - - + -
35B VAL* 2.9 28.4 + - + +
36B LYS* 3.8 5.8 - - - +
38B LEU* 1.3 77.4 - - + +
40B LYS* 1.3 65.4 + - - +
42B LEU* 4.1 6.7 - - + +
43B LYS* 2.8 44.6 + - - +
48B LEU* 3.5 27.4 - - + -
51B LEU* 5.9 1.1 - - + -
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Residues in contact with LYS 40 (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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36B LYS 2.9 14.7 + - - +
37B SER* 3.4 14.4 - - - +
39B VAL* 1.3 79.6 - - - +
41B LYS* 1.3 61.4 + - + +
43B LYS* 3.5 8.9 - - - +
44B LYS* 3.2 51.1 + - - +
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Residues in contact with LYS 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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37B SER* 3.4 27.4 - - - +
38B LEU* 3.0 9.2 + - - +
40B LYS* 1.3 80.1 - - + +
42B LEU* 1.3 65.7 + - - +
43B LYS 3.2 1.3 - - - -
44B LYS* 3.5 17.3 + - + +
45B THR* 3.4 24.1 + - - +
67B ILE* 3.6 35.9 - - + +
68B PRO* 4.9 9.0 - - + -
75B LEU* 3.4 36.4 - - - +
88B TYR* 5.5 0.6 + - - -
2008D T 6.1 3.1 - - - -
2009D A 4.6 5.8 + - - -
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Residues in contact with LEU 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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38B LEU* 2.8 36.1 + - + +
39B VAL* 4.1 5.2 - - + +
41B LYS* 1.3 70.3 - - - +
43B LYS* 1.3 56.3 + - - +
45B THR* 3.1 3.6 + - - -
46B GLY 2.7 31.5 + - - -
47B GLN* 2.9 22.9 + - + +
48B LEU* 3.7 18.4 - - + +
51B LEU* 3.6 29.2 - - + -
65B ILE* 3.5 33.9 - - + -
66B THR 3.8 9.2 - - - +
67B ILE* 3.5 24.7 - - + -
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Residues in contact with LYS 43 (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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10B PRO* 5.5 4.9 - - - +
11B ILE* 4.4 8.7 - - - +
39B VAL* 2.8 38.4 + - + +
40B LYS* 3.5 8.7 - - - +
42B LEU* 1.3 75.8 - - - +
44B LYS* 1.3 66.6 + - + +
46B GLY* 2.8 15.1 + - - -
48B LEU* 3.7 24.4 - - + +
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Residues in contact with LYS 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 LYS* 3.2 42.3 + - - +
41B LYS* 3.6 16.4 - - + +
42B LEU 3.3 0.2 - - - -
43B LYS* 1.3 81.5 - - + +
45B THR* 1.3 62.8 + - + +
46B GLY 3.5 0.3 + - - -
1012C A 5.8 1.8 + - - -
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Residues in contact with THR 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 LYS 3.4 13.6 + - - +
42B LEU* 3.1 9.0 + - - +
44B LYS* 1.3 79.5 - - + +
46B GLY* 1.3 62.6 + - - +
47B GLN* 2.6 39.8 + - - +
66B THR 5.3 2.7 - - - +
68B PRO* 6.4 2.2 - - + -
119B GLU* 6.2 0.4 - - - +
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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
------------------------------------------------------------
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