Contacts of the helix formed by residues 15 - 36 (chain A) in PDB entry 1F16
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 SER 15 (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* 6.4 2.7 - - - +
11A GLY* 6.2 0.2 - - - -
12A GLY 3.4 20.4 + - - -
14A THR* 1.3 77.8 - - - +
16A SER* 1.3 53.7 + - - +
17A GLU* 2.4 33.9 + - - +
18A GLN* 2.9 29.7 + - - +
19A ILE* 3.4 7.2 + - - +
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Residues in contact with SER 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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9A ARG* 5.2 8.7 + - - -
14A THR 4.3 0.8 + - - -
15A SER* 1.3 70.1 - - - +
17A GLU* 1.3 57.8 + - - +
19A ILE* 4.2 5.8 - - - -
20A MET* 3.3 27.1 + - - +
149A LEU* 3.9 34.4 - - - +
153A GLN* 4.3 10.2 - - - +
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Residues in contact with GLU 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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15A SER* 2.4 28.4 + - - +
16A SER* 1.3 70.7 + - - +
18A GLN* 1.3 97.5 + - - +
19A ILE 3.2 0.2 - - - -
20A MET* 4.0 1.9 - - - +
21A LYS* 3.0 57.8 + - + +
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Residues in contact with GLN 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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13A PRO* 3.3 13.4 - - - +
14A THR* 2.9 40.1 + - - +
15A SER* 2.9 21.5 + - - +
17A GLU* 1.3 88.9 + - - +
19A ILE* 1.3 63.3 + - - +
21A LYS* 3.7 5.0 - - - +
22A THR* 2.6 35.2 + - - +
156A GLY 4.4 8.3 + - - -
157A GLY* 5.2 4.4 - - - -
158A TRP* 5.5 0.4 - - - -
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Residues in contact with ILE 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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14A THR* 5.1 2.5 - - - -
15A SER 3.4 17.2 + - - +
16A SER* 4.4 4.5 - - - +
17A GLU 3.2 0.4 - - - -
18A GLN* 1.3 88.4 - - + +
20A MET* 1.3 68.9 + - - +
21A LYS 3.0 0.5 + - - -
22A THR 3.1 0.2 + - - -
23A GLY* 2.8 21.0 + - - -
144A LEU* 4.9 3.8 - - + -
149A LEU* 4.2 19.1 - - + -
152A ILE* 3.8 51.6 - - + +
153A GLN* 3.6 32.8 - - + +
156A GLY 5.5 0.9 - - - +
157A GLY* 5.3 2.9 - - - -
158A TRP* 3.6 17.1 + - + +
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Residues in contact with MET 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 SER 3.3 19.0 + - - +
17A GLU* 4.0 3.6 - - - +
19A ILE* 1.3 81.0 - - - +
21A LYS* 1.3 63.6 + - + +
23A GLY* 3.3 1.9 + - - -
24A ALA* 3.0 24.4 + - - +
141A LEU* 3.5 33.2 - - + +
144A LEU* 4.3 11.2 - - + -
145A ARG* 3.6 53.8 - - + +
149A LEU* 4.3 13.7 - - - -
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Residues in contact with LYS 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 GLU* 3.0 56.0 + - + +
18A GLN* 3.7 4.0 - - - +
19A ILE 3.1 0.8 - - - -
20A MET* 1.3 81.2 - - + +
22A THR* 1.3 65.3 + - - +
23A GLY 3.1 0.2 + - - -
24A ALA* 3.1 4.4 + - - +
25A LEU* 2.8 40.0 + - + +
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Residues in contact with THR 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 GLN* 2.6 25.1 + - - +
19A ILE 3.9 1.3 - - - -
21A LYS* 1.3 77.3 - - - +
23A GLY* 1.3 58.6 + - - +
25A LEU* 4.3 6.7 - - - -
26A LEU* 2.8 58.7 + - + +
56A THR* 4.3 18.8 - - + +
59A LEU* 5.5 2.2 - - + -
158A TRP* 3.9 19.6 - - + -
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Residues in contact with GLY 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 ILE 2.8 14.3 + - - -
20A MET* 3.7 4.3 - - - -
22A THR* 1.3 79.5 - - - +
24A ALA* 1.3 61.3 + - - +
26A LEU* 4.1 3.1 - - - +
27A LEU* 3.4 21.7 + - - +
141A LEU* 4.5 5.9 - - - +
144A LEU* 4.4 13.8 - - - +
158A TRP* 3.9 22.5 - - - +
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Residues in contact with ALA 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 MET* 3.0 16.4 + - + +
21A LYS* 3.9 4.5 - - - +
23A GLY* 1.3 75.1 - - - +
25A LEU* 1.3 64.6 + - + +
27A LEU* 4.9 2.0 - - - +
28A GLN* 3.1 31.1 + - - +
49A PRO* 5.8 2.0 - - + -
137A MET* 5.4 1.9 - - - +
141A LEU* 3.8 30.2 - - + +
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Residues in contact with LEU 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 LYS* 2.8 44.9 + - + +
22A THR* 3.2 6.9 + - - +
24A ALA* 1.3 82.4 - - + +
26A LEU* 1.3 57.2 + - - +
28A GLN* 3.2 6.4 + - - +
29A GLY* 2.7 34.8 + - - -
49A PRO* 3.5 40.8 - - + -
50A VAL 4.9 10.5 - - - +
51A PRO* 6.2 0.4 - - + -
52A GLN 5.6 6.1 - - - +
53A ASP* 5.6 5.8 - - + +
56A THR* 4.4 19.7 - - + +
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Residues in contact with LEU 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 THR* 2.8 40.3 + - + +
23A GLY* 4.1 3.6 - - - +
25A LEU* 1.3 72.4 - - - +
27A LEU* 1.3 64.7 + - - +
29A GLY* 3.0 9.6 + - - -
30A PHE* 3.1 14.0 + - - +
56A THR* 3.5 29.4 - - + +
59A LEU* 3.6 45.8 - - + +
60A SER* 4.6 3.6 - - - +
63A LEU* 4.8 6.9 - - + +
114A PHE* 6.1 5.6 - - + -
158A TRP* 4.3 23.3 - - + -
161A LEU* 5.5 2.0 - - + -
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Residues in contact with LEU 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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23A GLY 3.4 14.1 + - - +
24A ALA* 4.9 1.6 - - - +
25A LEU 3.3 0.4 - - - -
26A LEU* 1.3 80.5 - - - +
28A GLN* 1.3 66.5 + - - +
29A GLY 2.8 1.6 + - - -
30A PHE* 3.3 16.0 + - + +
31A ILE* 3.3 34.1 + - + +
63A LEU* 5.4 3.4 - - + -
114A PHE* 4.1 45.3 - - + +
117A ALA* 5.3 3.8 - - + -
118A SER* 5.3 3.6 - - - +
121A VAL* 5.9 1.8 - - + -
137A MET* 4.6 11.4 - - - -
140A THR* 3.8 37.7 - - + +
141A LEU* 6.1 2.2 - - + -
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Residues in contact with GLN 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 ALA 3.1 22.4 + - - +
25A LEU* 3.2 4.8 + - - +
27A LEU* 1.3 79.1 - - - +
29A GLY* 1.3 61.2 + - - +
31A ILE* 3.9 11.7 - - - +
32A GLN* 3.3 23.5 + - + +
45A LEU* 3.7 22.7 - - + +
48A ASP* 2.6 41.4 + - - +
49A PRO* 3.3 33.1 + - - +
50A VAL* 5.1 1.2 - - - +
51A PRO* 5.6 3.7 - - + +
137A MET* 3.8 20.9 - - + +
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Residues in contact with GLY 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 LEU 2.7 14.5 + - - -
26A LEU* 3.4 4.3 - - - -
27A LEU 2.8 2.0 + - - -
28A GLN* 1.3 74.8 - - - +
30A PHE* 1.3 57.7 + - - -
31A ILE 2.7 10.7 + - - -
32A GLN* 3.2 1.9 + - - +
33A ASP* 3.1 32.2 + - - +
51A PRO* 4.9 19.5 - - - -
60A SER* 5.0 2.5 - - - -
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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 LEU 3.1 7.0 + - - +
27A LEU* 3.3 7.8 + - + +
29A GLY* 1.3 73.5 - - - +
31A ILE* 1.3 60.8 + - + +
33A ASP* 4.3 8.2 - - + +
34A ARG* 2.8 62.2 + - + +
60A SER* 4.7 8.6 + - - +
63A LEU* 3.2 62.4 - - + -
64A LYS* 4.1 13.7 - - + -
67A GLY* 3.8 20.2 - - - -
114A PHE 5.2 2.7 - - - -
115A TYR* 4.5 11.2 - + - -
118A SER* 3.7 32.8 - - - -
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Residues in contact with ILE 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 LEU* 3.3 35.4 + - + +
28A GLN* 3.9 4.7 - - + +
29A GLY 2.7 5.5 + - - -
30A PHE* 1.3 76.5 - - + +
32A GLN* 1.3 70.1 + - - +
33A ASP 3.0 1.1 - - - -
34A ARG* 2.7 17.4 + - - -
35A ALA* 2.7 15.4 + - + +
44A GLU* 6.2 0.4 - - - +
45A LEU* 5.7 9.0 - - + -
118A SER* 5.0 9.4 - - - -
121A VAL* 4.0 35.4 - - + -
122A LEU* 4.5 12.3 - - + +
125A LEU* 6.5 0.7 - - + -
133A ILE* 6.3 0.7 - - + -
137A MET* 3.6 30.5 - - - -
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Residues in contact with GLN 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 GLN* 3.3 16.8 + - + +
29A GLY* 3.2 4.6 + - - +
31A ILE* 1.3 80.5 - - - +
33A ASP* 1.3 76.0 + - - +
35A ALA* 3.2 18.7 + - - +
36A GLY 3.4 7.8 + - - +
37A ARG 3.0 29.8 + - - +
38A MET* 4.2 8.8 - - - +
45A LEU* 5.7 8.9 - - + +
51A PRO* 4.9 17.9 - - + +
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Residues in contact with ASP 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 GLY* 3.1 19.0 + - - +
30A PHE* 4.2 5.8 + - + +
31A ILE 3.0 0.8 - - - -
32A GLN* 1.3 88.7 + - - +
34A ARG* 1.3 62.0 + - + +
35A ALA 3.4 0.7 + - - -
36A GLY* 3.5 15.7 + - - +
51A PRO* 4.2 16.3 - - - +
60A SER* 3.6 19.4 + - - -
64A LYS* 3.9 31.7 + - - +
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Residues in contact with ARG 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 PHE* 2.8 60.5 + - + +
31A ILE* 2.7 11.6 + - - +
33A ASP* 1.3 74.4 - - + +
35A ALA* 1.3 59.6 + - - +
36A GLY 3.4 0.2 - - - -
64A LYS* 6.0 5.2 - - - +
67A GLY 4.4 14.8 + - - -
68A ASP* 5.0 9.1 + - - +
71A ASP* 3.2 32.3 + - - +
115A TYR* 5.5 3.6 - - - -
119A LYS* 6.4 0.6 - - - +
122A LEU* 4.2 37.1 - - + +
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Residues in contact with ALA 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 ILE* 2.7 20.9 + - + +
32A GLN* 3.2 15.2 + - - +
34A ARG* 1.3 75.3 - - - +
36A GLY* 1.3 58.4 + - - +
122A LEU* 4.5 8.1 - - + -
125A LEU* 4.2 24.6 - - + +
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Residues in contact with GLY 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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32A GLN* 3.4 10.7 + - - +
33A ASP* 3.5 12.3 + - - +
34A ARG 3.4 2.4 - - - -
35A ALA* 1.3 83.3 - - - +
37A ARG* 1.3 70.1 + - - +
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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