Contacts of the helix formed by residues 12 - 35 (chain Z) in PDB entry 1OCR
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 PRO 12 (chain Z).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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9X PHE* 6.4 1.6 - - + -
10Z THR 4.6 0.4 - - - +
11Z SER* 1.3 87.1 - - - +
13Z LYS* 1.3 56.7 + - - +
15Z GLN* 3.1 15.5 + - + +
16Z ALA* 2.8 29.2 + - - +
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Residues in contact with LYS 13 (chain Z).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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11Z SER* 3.2 7.4 - - - +
12Z PRO* 1.3 78.7 - - - +
14Z GLU* 1.3 67.5 + - + +
16Z ALA* 2.9 20.2 + - + +
17Z ILE* 3.0 35.0 + - + +
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Residues in contact with GLU 14 (chain Z).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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473N TRP* 4.0 1.0 - - - -
18Y LYS* 3.6 21.4 + - - +
19Y TRP* 3.5 38.9 + - + -
9Z PRO 3.5 9.4 - - - +
10Z THR* 3.5 13.7 - - + -
11Z SER* 3.0 38.3 + - - +
13Z LYS* 1.3 81.2 - - + +
15Z GLN* 1.3 63.7 + - - +
17Z ILE* 3.2 9.9 + - + +
18Z GLY* 2.9 19.1 + - - -
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Residues in contact with GLN 15 (chain Z).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
406N ASN* 5.3 5.1 - - - +
409N TRP* 3.2 34.1 + - + +
470N PHE* 3.6 20.3 - - + -
473N TRP* 4.5 1.1 - - + -
474N GLU* 4.1 16.9 + - + +
10Z THR* 3.0 34.9 + - + -
11Z SER 3.0 14.3 + - - +
12Z PRO* 3.4 14.0 - - + +
14Z GLU* 1.3 76.0 - - - +
16Z ALA* 1.3 54.7 + - - +
18Z GLY* 2.9 2.8 + - - +
19Z LEU* 2.8 36.3 + - - +
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Residues in contact with ALA 16 (chain Z).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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12Z PRO 2.8 13.0 + - - +
13Z LYS* 3.2 13.5 - - + +
15Z GLN* 1.3 73.6 - - - +
17Z ILE* 1.3 57.6 + - + +
19Z LEU* 3.6 6.8 + - - +
20Z SER* 2.9 33.6 + - - -
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Residues in contact with ILE 17 (chain Z).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
19Y TRP* 3.9 23.3 - - + -
13Z LYS* 3.0 35.1 + - + +
14Z GLU* 3.4 13.9 - - + +
16Z ALA* 1.3 76.1 - - + +
18Z GLY* 1.3 60.3 + - - +
20Z SER* 3.2 6.0 + - - -
21Z VAL* 2.8 46.0 + - + +
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Residues in contact with GLY 18 (chain Z).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
470N PHE* 4.0 6.3 - - - -
473N TRP* 3.9 19.7 - - - -
22Y LEU* 4.0 17.1 - - - +
14Z GLU 2.9 10.7 + - - -
15Z GLN 2.9 6.5 + - - -
17Z ILE* 1.3 76.1 - - - +
19Z LEU* 1.3 60.8 + - - +
21Z VAL* 3.5 2.1 + - - +
22Z THR* 2.9 31.2 + - - -
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Residues in contact with LEU 19 (chain Z).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
409N TRP* 4.0 19.3 - - + -
467N LEU* 4.5 2.9 - - + -
470N PHE* 3.7 28.1 - - + -
88Q PHE* 3.8 27.6 - - + -
15Z GLN 2.8 14.9 + - - +
16Z ALA* 3.8 7.6 - - - +
18Z GLY* 1.3 76.8 - - - +
20Z SER* 1.3 65.1 + - - +
22Z THR* 3.3 3.0 + - - -
23Z PHE* 3.0 58.8 + - + +
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Residues in contact with SER 20 (chain Z).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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16Z ALA* 2.9 21.6 + - - +
17Z ILE* 3.5 7.6 - - - -
19Z LEU* 1.3 77.1 - - - +
21Z VAL* 1.3 66.8 + - - +
23Z PHE* 3.5 3.9 + - - +
24Z LEU* 3.0 37.5 + - - +
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Residues in contact with VAL 21 (chain Z).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
22Y LEU* 3.6 31.6 - - + +
23Y ALA* 6.1 0.4 - - - -
26Y THR* 3.5 23.1 - - + +
17Z ILE* 2.8 34.8 + - + +
18Z GLY 3.8 1.6 - - - +
20Z SER* 1.3 72.6 - - - +
22Z THR* 1.3 64.7 + - - +
24Z LEU* 3.2 8.7 + - - +
25Z SER* 2.9 22.5 + - - -
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Residues in contact with THR 22 (chain Z).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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466N MET 3.6 26.7 - - - +
469N VAL* 3.9 23.4 - - + +
470N PHE* 4.2 14.1 - - + +
473N TRP* 5.5 1.2 - - - +
22Y LEU* 4.1 10.7 - - - +
26Y THR* 4.4 4.1 + - - -
18Z GLY 2.9 22.7 + - - -
19Z LEU* 3.5 6.3 - - - -
21Z VAL* 1.3 75.7 - - - +
23Z PHE* 1.3 67.9 + - + +
25Z SER* 2.6 24.7 + - - +
26Z PHE* 3.3 15.4 + - + -
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Residues in contact with PHE 23 (chain Z).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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463N THR* 4.4 13.0 - - + -
466N MET* 3.7 37.2 - - + -
467N LEU* 3.9 17.3 - - + -
470N PHE* 5.6 0.7 - - + -
88Q PHE* 3.8 24.0 - + - -
91Q PHE* 3.6 40.4 - + + -
19Z LEU* 3.0 43.6 + - + +
20Z SER* 3.9 5.2 - - - +
22Z THR* 1.3 82.7 - - + +
24Z LEU* 1.3 63.3 + - + +
26Z PHE* 2.9 4.3 + - - +
27Z LEU* 2.8 37.3 + - + +
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Residues in contact with LEU 24 (chain Z).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
20Z SER* 3.0 28.7 + - - +
21Z VAL* 3.5 7.2 - - + +
23Z PHE* 1.3 80.7 - - + +
25Z SER* 1.3 59.6 + - - +
26Z PHE 3.0 0.3 + - - -
27Z LEU* 4.3 8.1 - - + +
28Z LEU* 2.9 62.6 + - + +
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Residues in contact with SER 25 (chain Z).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
26Y THR* 3.4 46.0 + - - -
30Y GLY* 4.2 14.6 + - - +
33Y PHE* 5.5 1.0 - - - -
21Z VAL* 2.9 10.9 + - - -
22Z THR* 2.6 21.7 + - - +
24Z LEU* 1.3 75.8 - - - +
26Z PHE* 1.3 66.4 + - - +
29Z PRO* 3.5 21.4 - - - +
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Residues in contact with PHE 26 (chain Z).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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28N MET* 3.7 22.0 - - - -
462N LEU* 4.7 0.4 - - + -
465N VAL* 4.1 13.0 - - + -
466N MET* 3.3 37.0 - - + -
469N VAL* 3.7 33.4 - - + -
29Y PHE* 4.2 15.9 - - + -
30Y GLY* 5.2 1.8 - - - -
33Y PHE* 3.5 66.3 - + + -
22Z THR* 3.3 26.6 + - + -
23Z PHE 2.9 2.3 + - - +
25Z SER* 1.3 87.7 - - - +
27Z LEU* 1.3 64.2 + - + +
28Z LEU 3.7 0.2 - - - -
29Z PRO* 4.4 1.3 - - - +
30Z ALA* 4.0 9.0 + - - +
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Residues in contact with LEU 27 (chain Z).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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462N LEU* 4.3 11.2 - - + -
466N MET* 4.1 20.2 - - + -
91Q PHE* 4.5 12.3 - - + -
95Q LEU* 3.9 43.3 - - + -
33Y PHE* 5.8 1.1 - - + -
23Z PHE* 2.8 28.2 + - + +
24Z LEU* 4.2 7.6 - - + +
26Z PHE* 1.3 78.6 - - + +
28Z LEU* 1.3 64.1 + - + +
30Z ALA* 4.2 2.5 - - + +
31Z GLY* 2.9 28.2 + - - -
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Residues in contact with LEU 28 (chain Z).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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24Z LEU* 2.9 47.6 + - + +
25Z SER* 5.6 0.2 - - - -
27Z LEU* 1.3 72.1 - - + +
29Z PRO* 1.4 74.7 - - + +
31Z GLY* 3.0 2.5 + - - -
32Z TRP* 2.9 25.1 + - - +
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Residues in contact with PRO 29 (chain Z).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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30Y GLY 6.3 0.9 - - - -
33Y PHE* 6.5 0.7 - - + -
34Y ALA* 4.2 25.1 - - + -
37Y PHE* 5.6 0.7 - - - -
38Y PHE* 4.3 13.3 - - + -
24Z LEU 3.9 2.0 - - - +
25Z SER* 3.5 24.7 - - - +
26Z PHE 4.4 2.2 - - - +
27Z LEU 4.0 0.7 - - - -
28Z LEU* 1.4 92.7 - - + +
30Z ALA* 1.3 61.2 + - - +
32Z TRP* 3.4 7.0 + - + +
33Z VAL* 3.3 27.2 + - - +
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Residues in contact with ALA 30 (chain Z).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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33Y PHE* 4.2 5.4 - - + -
34Y ALA* 5.9 0.6 - - - +
37Y PHE* 3.8 45.2 - - + -
26Z PHE 4.0 16.0 + - - +
27Z LEU* 3.7 3.9 + - + +
28Z LEU 3.2 0.6 - - - -
29Z PRO* 1.3 77.2 - - - +
31Z GLY* 1.3 66.9 + - - +
33Z VAL* 3.5 1.8 + - - +
34Z LEU* 2.9 33.8 + - + +
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Residues in contact with GLY 31 (chain Z).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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98Q TRP* 3.7 26.3 - - - -
27Z LEU 2.9 19.0 + - - -
28Z LEU* 3.0 1.5 + - - -
30Z ALA* 1.3 73.7 - - - +
32Z TRP* 1.3 60.6 + - - +
34Z LEU* 4.5 1.3 - - - -
35Z TYR* 2.8 36.1 + - - +
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Residues in contact with TRP 32 (chain Z).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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38Y PHE* 4.0 24.5 - + + -
41Y ARG* 3.6 27.6 - - - -
28Z LEU 2.9 11.5 + - - +
29Z PRO* 3.6 10.8 - - + +
31Z GLY* 1.3 78.4 - - - +
33Z VAL* 1.3 85.7 + - + +
35Z TYR* 4.5 1.1 - - - -
36Z HIS* 2.9 57.6 + + - -
40Z TYR* 3.4 16.8 - - - -
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Residues in contact with VAL 33 (chain Z).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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37Y PHE* 3.5 33.9 - - + +
38Y PHE* 3.7 37.9 - - + -
40Y VAL* 5.8 2.7 - - + -
41Y ARG* 4.1 15.3 - - + +
29Z PRO 3.3 14.3 + - - +
30Z ALA 3.9 5.4 - - - +
32Z TRP* 1.3 86.3 - - + +
34Z LEU* 1.3 66.1 + - + +
36Z HIS* 3.1 14.4 + - - -
37Z LEU* 3.3 15.0 + - + -
40Z TYR* 3.6 11.5 - - + -
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Residues in contact with LEU 34 (chain Z).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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36N LEU* 4.5 19.5 - - + -
39N ALA* 5.5 7.0 - - + -
47N LEU* 5.0 6.5 - - + -
459N PHE* 6.0 5.4 - - + -
98Q TRP* 4.5 8.5 - - + -
99Q GLU* 5.7 6.1 - - + +
103Q VAL* 3.6 46.2 - - + +
37Y PHE* 4.4 19.1 - - + -
30Z ALA* 2.9 23.6 + - + +
31Z GLY* 3.9 3.1 - - - +
33Z VAL* 1.3 75.9 - - + +
35Z TYR* 1.3 66.3 + - - +
37Z LEU* 3.2 35.8 + - + +
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Residues in contact with TYR 35 (chain Z).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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98Q TRP* 4.5 9.4 - + + -
102Q TYR* 3.1 64.0 - + + +
103Q VAL* 4.3 3.8 - - - +
31Z GLY 2.8 22.9 + - - +
32Z TRP* 3.6 5.2 - - - +
34Z LEU* 1.3 74.9 - - - +
36Z HIS* 1.3 88.5 + + + +
37Z LEU 3.4 2.4 + - - -
38Z ASP* 4.6 7.3 + - - +
39Z ASN* 4.8 1.9 - - - +
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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