Contacts of the helix formed by residues 12 - 34 (chain A) in PDB entry 5DIR
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 TRP 12 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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9A ARG* 3.2 32.6 + - + +
10A LEU 3.0 1.2 + - - -
11A PRO* 1.3 73.1 - - - +
13A LEU* 1.3 56.4 + - - +
14A TRP 3.0 5.8 - - - -
15A ILE* 3.0 50.1 + - + +
88A LEU* 4.1 12.1 - - + -
96A THR* 4.3 24.2 - - + -
99A ALA* 3.5 33.3 - - + +
100A ILE* 3.5 34.8 - - + -
103A ALA* 3.5 8.1 - - - +
204A OLC 3.2 69.5 - - + -
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Residues in contact with LEU 13 (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 LEU* 2.9 34.0 + - + +
12A TRP* 1.3 74.9 - - - +
14A TRP* 1.3 59.5 + - - +
15A ILE 3.1 1.3 - - - -
16A THR* 3.1 12.7 + - + +
17A VAL* 2.8 32.3 + - + +
85A VAL* 5.1 16.2 - - + -
88A LEU* 3.6 26.7 - - + -
103A ALA* 5.7 0.2 - - + -
106A LEU* 3.7 29.2 - - + -
205A OLC 3.8 24.7 - - + -
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Residues in contact with TRP 14 (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 PRO* 3.2 27.1 + - + +
12A TRP 3.0 0.8 - - - -
13A LEU* 1.3 78.0 - - - +
15A ILE* 1.3 59.7 + - - +
17A VAL* 3.8 26.0 - - + +
18A LEU* 2.9 29.9 + - - +
204A OLC 4.9 13.2 - - + -
205A OLC 3.3 87.1 + - + +
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Residues in contact with ILE 15 (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 TRP* 3.0 44.1 + - + +
14A TRP* 1.3 76.2 - - - +
16A THR* 1.3 59.6 + - - +
18A LEU* 3.2 6.8 + - + +
19A VAL* 2.9 30.9 + - + +
100A ILE* 4.3 13.2 - - + +
103A ALA* 3.9 15.3 - - + -
104A LEU* 4.3 17.3 - - + -
204A OLC 3.6 65.5 - - + -
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Residues in contact with THR 16 (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 TRP 3.7 0.2 + - - -
13A LEU* 3.1 19.5 + - + +
15A ILE* 1.3 80.4 - - - +
17A VAL* 1.3 57.6 + - + +
19A VAL* 3.4 2.6 + - - +
20A PHE* 2.9 27.2 + - - +
103A ALA* 2.8 34.1 + - - +
106A LEU* 3.6 27.2 - - + +
107A GLY* 3.5 22.8 - - - +
110A LEU* 4.1 13.7 - - + -
206A OLC 4.9 3.6 - - + -
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Residues in contact with VAL 17 (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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13A LEU* 2.8 25.2 + - + +
14A TRP* 3.8 31.9 - - + +
16A THR* 1.3 72.5 - - + +
18A LEU* 1.3 59.1 + - - +
20A PHE* 3.1 1.7 + - - +
21A VAL* 2.9 43.7 + - + +
205A OLC 4.4 39.0 - - + -
206A OLC 4.1 21.1 - - + -
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Residues in contact with LEU 18 (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 TRP 2.9 19.9 + - - +
15A ILE* 3.5 5.8 - - - +
17A VAL* 1.3 77.0 - - - +
19A VAL* 1.3 62.2 + - - +
21A VAL* 3.9 6.1 - - + +
22A LEU* 3.1 54.7 + - + +
204A OLC 3.9 42.6 - - + -
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Residues in contact with VAL 19 (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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15A ILE* 2.9 24.1 + - + +
16A THR* 3.6 4.7 - - - +
18A LEU* 1.3 74.5 - - - +
20A PHE* 1.3 66.8 + - - +
22A LEU* 3.9 1.4 - - - +
23A ASP* 2.9 23.5 + - + +
104A LEU* 3.9 26.7 - - + -
107A GLY* 3.6 21.8 - - - +
108A GLY* 3.8 1.3 - - - +
141A LEU 5.2 0.2 - - - +
142A ALA* 5.1 4.9 - - - -
145A ALA* 3.6 25.4 - - + -
204A OLC 3.7 34.9 - - + +
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Residues in contact with PHE 20 (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 THR 2.9 17.4 + - - +
17A VAL 3.1 4.5 + - - +
19A VAL* 1.3 77.1 - - - +
21A VAL* 1.3 60.4 + - + +
23A ASP* 3.2 6.3 + - - +
24A GLN* 2.9 55.3 + - + +
107A GLY* 4.2 9.6 + - - +
110A LEU* 3.5 21.8 - - + -
111A GLY* 3.6 19.5 - - - -
114A TYR* 3.8 25.6 - + + -
205A OLC 3.5 34.8 - - + -
206A OLC 3.7 46.7 - - + -
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Residues in contact with VAL 21 (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 VAL* 2.9 33.8 + - + +
18A LEU* 3.9 7.9 - - + +
20A PHE* 1.3 75.8 - - + +
22A LEU* 1.3 66.2 + - + +
24A GLN* 3.0 4.9 + - - +
25A VAL* 2.8 48.3 + - + +
205A OLC 4.3 26.7 - - + -
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Residues in contact with LEU 22 (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 LEU* 3.1 39.5 + - + +
19A VAL 4.0 2.9 - - - +
21A VAL* 1.3 84.4 - - + +
23A ASP* 1.3 52.1 + - - +
25A VAL* 4.0 7.9 - - + +
26A SER* 2.5 39.1 + - - -
141A LEU* 4.2 6.5 - - + -
202A OLC 4.1 36.1 - - + +
204A OLC 4.0 29.4 - - + -
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Residues in contact with ASP 23 (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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19A VAL* 2.9 20.4 + - + +
20A PHE* 3.3 6.5 - - - +
22A LEU* 1.3 78.2 - - - +
24A GLN* 1.3 61.0 + - - +
26A SER* 3.4 5.0 - - - -
27A LYS* 2.8 65.6 + - - +
107A GLY 5.6 0.2 - - - +
111A GLY* 3.6 17.8 - - - -
125A PHE* 5.2 0.3 - - - -
140A ASN* 4.1 0.2 - - - +
141A LEU* 3.8 13.0 + - + +
142A ALA* 2.9 37.2 + - + +
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Residues in contact with GLN 24 (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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20A PHE* 2.9 45.4 + - + +
21A VAL* 3.0 6.0 + - - +
23A ASP* 1.3 81.9 + - - +
25A VAL* 1.3 61.3 + - + +
27A LYS* 4.0 7.0 - - - +
28A ALA* 3.0 30.8 + - - +
111A GLY 3.0 26.9 + - - -
114A TYR* 3.5 29.2 - - + -
115A ASP* 3.7 13.0 + - - +
205A OLC 5.7 5.8 - - + -
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Residues in contact with VAL 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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21A VAL* 2.8 38.7 + - + +
22A LEU* 4.0 10.1 - - + +
24A GLN* 1.3 69.0 - - + +
26A SER* 1.3 67.0 + - - +
28A ALA* 3.4 5.7 + - - +
29A PHE* 3.0 24.7 + - + +
202A OLC 6.2 3.8 - - + -
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Residues in contact with SER 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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22A LEU 2.5 23.5 + - - -
23A ASP* 3.4 6.7 - - - -
25A VAL* 1.3 79.8 - - - +
27A LYS* 1.3 62.8 + - - +
29A PHE* 3.2 9.4 + - - +
30A PHE* 3.1 26.5 - - - -
125A PHE* 3.3 26.7 - - - -
141A LEU* 3.5 7.5 - - - +
202A OLC 3.3 28.7 - - - +
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Residues in contact with LYS 27 (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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23A ASP* 2.8 48.6 + - - +
24A GLN* 4.0 9.6 - - - +
25A VAL 3.4 0.2 - - - -
26A SER* 1.3 76.4 - - - +
28A ALA* 1.3 67.5 + - - +
30A PHE* 3.3 2.5 + - - +
31A GLN* 2.9 30.6 + - - +
111A GLY 3.6 2.2 + - - -
112A ASN* 2.9 22.6 + - - -
115A ASP* 2.6 36.4 + - - +
123A VAL* 3.5 25.8 - - + +
125A PHE* 3.7 19.5 - - + -
140A ASN* 3.1 21.0 - - - +
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Residues in contact with ALA 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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24A GLN 3.0 19.3 + - - +
25A VAL* 3.7 7.2 - - - +
27A LYS* 1.3 77.1 - - - +
29A PHE* 1.3 63.3 + - - +
31A GLN* 3.4 14.5 + - - +
32A ALA* 3.1 22.9 + - - +
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Residues in contact with PHE 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 VAL* 3.0 15.8 + - + +
26A SER* 3.4 10.3 - - - +
28A ALA* 1.3 76.7 - - - +
30A PHE* 1.3 84.0 + + + +
32A ALA* 2.9 10.2 + - + +
33A GLU* 2.9 54.9 + - + +
202A OLC 3.6 57.0 - - + -
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Residues in contact with PHE 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 SER 3.1 24.6 + - - +
27A LYS 4.1 2.5 - - - +
29A PHE* 1.3 96.3 - + - +
31A GLN* 1.3 64.5 + - - +
32A ALA 3.1 1.8 - - - -
33A GLU 4.2 1.3 - - - +
34A LEU* 3.1 53.5 + - + +
40A ILE* 5.4 0.9 - - + -
49A TRP* 3.5 46.4 - + + -
50A THR 4.3 4.7 - - - +
51A LEU* 3.7 10.0 - - + +
123A VAL* 5.7 0.2 - - + -
125A PHE* 3.5 42.2 - + + -
202A OLC 3.7 35.0 - - + -
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Residues in contact with GLN 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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27A LYS* 2.9 21.8 + - - +
28A ALA* 3.6 14.6 + - - +
29A PHE 3.2 0.2 - - - -
30A PHE* 1.3 77.4 - - - +
32A ALA* 1.3 60.1 + - - +
34A LEU 3.6 10.9 - - - +
51A LEU* 4.1 9.8 - - + +
53A TYR* 3.7 24.2 + - - +
119A LEU* 3.7 21.2 - - - +
121A HIS* 5.0 0.8 + - - -
123A VAL* 3.5 36.6 - - + +
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Residues in contact with ALA 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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28A ALA 3.1 11.0 + - - +
29A PHE* 2.9 12.8 + - + +
31A GLN* 1.3 80.0 - - - +
33A GLU* 1.3 65.6 + - - +
34A LEU 4.8 0.4 - - - +
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Residues in contact with GLU 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 PHE* 2.9 43.0 + - + +
32A ALA* 1.3 84.9 - - - +
34A LEU* 1.3 71.7 + - + +
38A GLN* 4.7 6.6 + - - +
40A ILE* 5.4 0.5 - - - +
202A OLC 3.2 33.8 + - - +
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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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29A PHE* 5.4 0.2 - - + -
30A PHE* 3.1 30.1 + - + +
31A GLN 3.6 10.6 - - - +
32A ALA 4.8 0.6 - - - +
33A GLU* 1.3 97.0 - - + +
35A SER* 1.3 65.8 + - - +
38A GLN* 3.6 23.1 - - + +
40A ILE* 3.5 35.0 - - + -
49A TRP 4.3 3.6 - - - +
50A THR* 3.4 41.7 - - - +
51A LEU* 3.2 19.5 - - + +
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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