Contacts of the helix formed by residues 15 - 36 (chain A) in PDB entry 1USK
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 ILE 15 (chain A).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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10A ALA* 4.0 7.3 - - + +
12A SER 5.1 0.2 + - - -
13A GLY 3.3 0.6 - - - -
14A PRO* 1.3 89.1 - - + +
16A ALA* 1.3 63.8 + - - +
17A GLN 3.1 3.6 + - - -
18A TRP* 3.3 30.5 + - + +
19A GLY 3.8 2.1 + - - -
52A ALA 5.6 0.7 - - - +
53A CYS* 4.0 14.8 - - + -
77A LEU* 4.9 0.2 - - - +
78A CYS* 3.4 32.5 - - - -
202A TYR* 3.8 52.7 - - + -
203A TYR* 3.4 11.9 - - + -
204A PRO* 4.0 11.7 - - + -
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Residues in contact with ALA 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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10A ALA* 3.6 14.4 - - - +
11A MET 4.2 4.9 - - - +
12A SER* 4.0 22.2 + - - +
13A GLY 3.4 16.6 + - - +
14A PRO 3.6 0.6 - - - -
15A ILE* 1.3 75.4 - - - +
17A GLN* 1.3 58.7 + - - +
18A TRP 3.3 0.2 - - - -
19A GLY* 3.2 3.6 + - - -
20A ASP* 2.9 34.7 + - - +
203A TYR* 4.0 0.8 + - - -
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Residues in contact with GLN 17 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
15A ILE 3.1 0.8 - - - -
16A ALA* 1.3 75.5 - - - +
18A TRP* 1.3 64.7 + - - +
20A ASP* 3.3 27.8 + - - +
21A MET* 3.5 19.4 + - - +
203A TYR* 3.4 18.3 + - + +
230A ASN* 3.1 30.9 - - - +
231A ALA* 3.7 19.1 - - - +
232A SER* 4.0 10.2 + - - +
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Residues in contact with TRP 18 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
15A ILE* 3.3 24.1 + - + +
16A ALA 3.3 0.4 - - - -
17A GLN* 1.3 78.5 - - - +
19A GLY* 1.3 61.4 + - - +
21A MET* 3.1 52.7 + - + +
22A GLU* 3.3 10.7 + - - +
77A LEU* 3.8 15.9 - - + +
202A TYR* 4.5 1.9 - + - -
203A TYR* 3.6 20.5 - + - -
226A GLU 3.2 25.1 - - - -
227A GLY* 3.2 22.8 + - - -
229A GLY 3.4 23.6 - - - -
230A ASN* 3.4 21.8 - - + -
275A PRO* 4.2 11.7 - - + -
276A TYR* 3.8 18.9 - + - +
1347A LEU* 3.8 28.4 - - + +
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Residues in contact with GLY 19 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
10A ALA 3.3 25.4 - - - -
15A ILE 3.8 1.4 + - - -
16A ALA 3.2 5.2 + - - -
18A TRP* 1.3 80.6 - - - +
20A ASP* 1.3 61.9 + - - +
22A GLU* 3.1 5.9 + - - +
23A PHE* 3.1 31.1 + - - -
77A LEU* 3.4 18.6 - - - +
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Residues in contact with ASP 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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10A ALA 4.9 1.6 - - - +
11A MET* 5.5 3.8 - - - +
16A ALA* 2.9 23.5 + - - +
17A GLN* 3.5 27.6 - - - +
18A TRP 3.2 0.6 - - - -
19A GLY* 1.3 74.8 - - - +
21A MET* 1.3 61.4 - - - +
23A PHE* 3.7 3.9 + - - +
24A ASN* 3.1 37.7 + - - +
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Residues in contact with MET 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 GLN* 3.7 22.7 - - - +
18A TRP* 3.1 40.8 + - + +
20A ASP* 1.3 74.6 - - + +
22A GLU* 1.3 63.4 + - - +
24A ASN* 3.4 3.0 + - - +
25A GLY 3.0 19.1 + - - -
230A ASN* 4.9 1.1 - - - -
271A ASP 5.7 1.6 - - - +
274A GLY* 3.3 27.6 - - - -
275A PRO 3.4 1.8 - - - -
276A TYR* 3.1 37.2 - - + +
277A VAL* 3.4 32.0 - - + +
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Residues in contact with GLU 22 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
7A VAL* 3.8 9.9 - - + +
8A VAL 2.7 25.8 - - - +
9A GLY* 3.2 23.0 - - - -
18A TRP 3.3 8.0 + - - +
19A GLY* 3.1 8.2 + - - +
21A MET* 1.3 79.9 - - - +
23A PHE* 1.3 61.5 + - - +
25A GLY 3.4 0.2 + - - -
26A ALA* 3.1 24.3 + - - +
74A ILE 3.7 12.5 - - - +
77A LEU* 3.5 25.4 - - + +
99A PRO* 4.0 10.1 - - + +
276A TYR* 4.0 2.8 + - + -
280A THR* 3.2 41.9 - - + +
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Residues in contact with PHE 23 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
7A VAL* 3.5 33.9 - - + -
8A VAL 4.2 0.9 - - - -
9A GLY* 3.6 36.8 - - - -
10A ALA 4.4 2.0 - - - -
11A MET* 3.5 27.8 - - + -
19A GLY 3.1 28.9 + - - +
20A ASP* 4.4 3.8 - - - +
22A GLU* 1.3 77.3 - - + +
24A ASN* 1.3 64.7 + - - +
26A ALA* 4.0 3.1 - - + +
27A ARG* 3.1 54.3 + - - +
48A GLU* 3.6 32.9 - - + +
49A TYR 3.7 12.1 - - - -
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Residues in contact with ASN 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 ASP* 3.1 31.1 + - - +
21A MET* 3.7 7.2 - - - +
23A PHE* 1.3 78.4 - - - +
25A GLY* 1.3 60.2 + - - +
27A ARG* 3.7 13.4 + - - +
28A GLN* 3.3 24.1 + - - +
265A LEU* 4.3 16.7 - - + +
270A LYS* 2.9 52.0 + - - +
271A ASP 5.4 5.1 + - - +
277A VAL* 4.9 5.3 - - + +
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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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21A MET 3.0 13.6 + - - -
22A GLU 3.9 1.1 - - - -
24A ASN* 1.3 74.7 - - - +
26A ALA* 1.3 63.8 + - - +
28A GLN* 3.6 1.5 + - - -
29A ALA* 3.1 19.6 + - - +
265A LEU* 5.7 0.2 - - - -
277A VAL* 3.4 31.1 - - - +
281A TYR* 3.4 24.2 - - - -
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Residues in contact with ALA 26 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
7A VAL* 4.1 29.6 - - + -
22A GLU 3.1 17.7 + - - +
23A PHE* 4.0 3.6 - - + +
24A ASN 3.4 0.2 - - - -
25A GLY* 1.3 74.7 - - - +
27A ARG* 1.3 65.4 + - + +
29A ALA* 3.1 2.9 + - - +
30A ILE* 2.9 31.8 + - + +
48A GLU* 5.9 1.1 - - - +
74A ILE* 5.5 0.2 - - + -
280A THR* 3.9 13.3 - - + +
284A VAL* 4.2 17.3 - - + -
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Residues in contact with ARG 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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11A MET* 5.5 3.4 - - - -
23A PHE* 3.1 38.0 + - - +
24A ASN* 3.7 25.0 + - - +
26A ALA* 1.3 77.8 - - - +
28A GLN* 1.3 58.0 + - - +
30A ILE* 3.5 8.7 + - - +
31A LYS* 3.0 29.7 + - - +
48A GLU* 3.1 39.1 + - - +
270A LYS* 4.0 11.0 - - - +
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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 ASN 3.3 16.3 + - - +
25A GLY* 4.0 4.9 - - - +
26A ALA 3.2 1.0 - - - -
27A ARG* 1.3 78.2 - - - +
29A ALA* 1.3 57.5 + - - +
31A LYS* 3.4 22.6 + - - +
32A ASP* 2.9 66.8 + - - +
261A ILE* 4.3 14.6 - - + -
264A ALA* 3.8 30.2 - - + +
265A LEU* 4.5 12.8 - - + +
268A ASP* 4.2 14.6 - - - +
281A TYR* 3.8 10.3 - - + -
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Residues in contact with ALA 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 3.1 17.0 + - - +
26A ALA 3.1 5.0 + - - +
28A GLN* 1.3 74.6 - - - +
30A ILE* 1.3 58.9 + - - +
32A ASP* 3.3 0.7 + - - +
33A ILE* 3.0 40.7 + - + +
281A TYR* 3.4 35.6 - - + +
284A VAL* 3.8 23.8 - - + -
285A GLN 5.2 0.2 - - - +
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Residues in contact with ILE 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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5A VAL* 5.4 6.7 - - + -
7A VAL* 4.7 13.0 - - + -
26A ALA* 2.9 24.9 + - + +
27A ARG* 3.8 7.4 - - + +
29A ALA* 1.3 75.1 - - - +
31A LYS* 1.3 57.6 + - - +
33A ILE* 4.1 4.0 - - - +
34A ASN* 3.1 39.7 + - - +
44A LEU* 3.6 37.1 - - + +
45A VAL* 4.7 1.3 - - - -
46A GLY* 3.8 30.5 - - - +
284A VAL* 4.0 20.6 - - + -
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Residues in contact with LYS 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 ARG 3.0 17.8 + - - +
28A GLN* 3.6 24.9 - - - +
29A ALA 3.2 0.2 - - - -
30A ILE* 1.3 76.9 - - - +
32A ASP* 1.3 61.1 + - - +
34A ASN* 4.1 5.4 - - - +
35A ALA* 3.1 28.0 + - + +
268A ASP* 4.9 11.3 + - - +
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Residues in contact with ASP 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* 2.9 41.8 + - - +
29A ALA 3.9 2.7 - - - +
31A LYS* 1.3 75.3 - - - +
33A ILE* 1.3 67.5 + - + +
35A ALA* 3.4 7.8 + - - +
36A LYS* 3.3 28.7 + - - +
261A ILE* 4.0 9.5 - - - +
281A TYR* 2.4 35.7 + - - +
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Residues in contact with ILE 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 ALA* 3.0 25.6 + - + +
30A ILE 4.1 2.7 - - - +
32A ASP* 1.3 77.4 - - + +
34A ASN* 1.3 62.3 + - - +
36A LYS* 3.4 12.0 + - - +
37A GLY 3.6 0.7 + - - -
38A GLY* 3.0 27.3 + - - +
39A ILE* 4.2 17.7 - - + -
44A LEU* 3.7 21.3 - - + -
281A TYR* 6.0 0.9 - - + +
284A VAL* 3.8 30.1 - - + +
285A GLN* 4.5 11.7 - - + -
288A ALA* 3.9 18.8 - - + -
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Residues in contact with ASN 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 ILE* 3.1 25.5 + - - +
31A LYS* 4.1 5.5 - - - +
33A ILE* 1.3 74.7 - - - +
35A ALA* 1.3 64.1 + - - +
37A GLY* 3.2 12.0 + - - -
38A GLY* 3.7 11.7 + - - +
43A LYS* 3.7 20.7 - - + +
44A LEU* 2.9 51.0 + - - +
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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 LYS* 3.1 21.1 + - + +
32A ASP* 3.6 9.9 - - - +
33A ILE 3.3 0.4 - - - -
34A ASN* 1.3 76.2 - - - +
36A LYS* 1.3 60.7 + - + +
37A GLY 3.8 0.3 + - - -
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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
----------------------------------------------------------
32A ASP* 3.3 17.1 + - - +
33A ILE* 3.4 6.7 + - - +
34A ASN 3.2 0.6 - - - -
35A ALA* 1.3 78.5 - - + +
37A GLY* 1.3 54.9 + - - +
38A GLY 3.8 1.6 - - - -
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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