Contacts of the helix formed by residues 18 - 39 (chain A) in PDB entry 1II7
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 LYS 18 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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14A GLU* 3.5 7.7 - - - +
15A GLN 3.1 10.6 + - - +
16A PHE* 3.1 13.8 + - + +
17A HIS* 1.3 77.1 + - - +
19A PRO* 1.3 61.1 - - - +
20A GLN* 2.8 20.6 + - + +
21A ARG* 2.8 22.9 + - + +
22A GLU 3.5 5.9 + - - -
301A TYR* 3.1 27.4 - - + +
324A GLU* 4.1 9.6 + - - -
325A TYR* 3.6 36.8 - - - -
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Residues in contact with PRO 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 GLU* 4.1 19.1 - - + +
17A HIS 3.4 11.0 - - - +
18A LYS* 1.3 82.0 - - - +
20A GLN* 1.3 61.7 + - - +
22A GLU* 3.5 11.6 + - + +
23A GLU* 3.2 34.2 + - - +
90B ARG* 3.8 32.5 - - - +
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Residues in contact with GLN 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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18A LYS* 2.8 11.7 + - + +
19A PRO* 1.3 80.3 - - - +
21A ARG* 1.3 59.2 + - - +
23A GLU* 3.2 20.2 + - - +
24A GLU* 2.9 43.1 + - + +
271A ARG* 3.7 17.7 + - - +
301A TYR* 4.9 7.8 + - - +
324A GLU* 4.4 9.4 + - - +
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Residues in contact with ARG 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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13A TYR 4.1 0.2 - - - -
15A GLN* 2.7 54.9 + - + +
18A LYS* 2.8 11.5 + - + +
20A GLN* 1.3 74.4 - - - +
22A GLU* 1.3 54.7 + - - +
24A GLU* 2.8 40.5 + - - +
25A PHE* 2.7 46.9 + - + -
227A GLU* 2.8 39.8 + - - +
228A ARG 3.3 18.0 + - - +
270A VAL* 5.1 0.2 - - - +
271A ARG* 3.9 11.3 - - - +
273A PHE* 3.5 19.5 - - - -
301A TYR* 3.6 36.1 - - + +
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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
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12A GLY* 3.8 35.7 + - - +
13A TYR 3.1 18.9 + - - +
14A GLU* 3.5 27.8 - - - +
18A LYS 3.5 2.2 + - - -
19A PRO* 3.5 15.2 - - - +
20A GLN 3.3 0.2 - - - -
21A ARG* 1.3 77.6 - - - +
23A GLU* 1.3 64.9 + - + +
25A PHE* 3.3 4.3 + - - +
26A ALA* 3.2 21.8 + - - +
57A SER* 5.5 0.3 + - - -
60A THR* 3.9 9.0 + - - -
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Residues in contact with GLU 23 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
19A PRO* 3.2 25.2 + - - +
20A GLN* 3.4 22.1 - - + +
21A ARG 3.1 0.4 - - - -
22A GLU* 1.3 80.9 - - + +
24A GLU* 1.3 57.4 + - + +
26A ALA* 3.3 7.0 + - - +
27A GLU* 2.9 29.4 + - - +
63A LYS* 6.5 0.2 - - - +
90B ARG* 5.9 0.2 + - - -
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Residues in contact with GLU 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 GLN* 2.9 31.3 + - + +
21A ARG* 2.8 43.6 + - - +
23A GLU* 1.3 76.7 - - + +
25A PHE* 1.3 59.0 + - - +
27A GLU* 3.7 7.2 - - + +
28A ALA* 2.9 30.7 + - - +
227A GLU* 3.6 16.8 - - - +
271A ARG* 3.0 41.3 + - - +
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Residues in contact with PHE 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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8A ASP 5.5 0.7 - - - -
9A ILE* 3.5 25.7 - - - +
10A HIS* 4.1 23.1 - - + +
11A LEU* 4.4 5.2 - - - +
13A TYR* 3.6 29.4 - + + +
15A GLN* 3.7 39.7 - - + -
21A ARG* 2.7 39.1 + - + +
22A GLU* 3.3 6.3 + - - +
24A GLU* 1.3 73.2 - - - +
26A ALA* 1.3 64.2 + - - +
28A ALA* 3.3 3.3 + - - +
29A PHE* 3.1 20.8 + - - +
225A SER* 5.5 3.6 - - - -
226A LEU* 5.4 0.2 - - - +
227A GLU* 3.7 40.4 - - + -
228A ARG 4.1 2.7 - - - -
229A TRP* 4.3 10.3 - + - -
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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
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11A LEU* 3.9 17.7 - - + +
12A GLY 6.1 0.9 - - - +
22A GLU 3.2 11.7 + - - +
23A GLU* 3.6 9.6 - - - +
24A GLU 3.2 0.2 - - - -
25A PHE* 1.3 79.6 - - - +
27A GLU* 1.3 57.2 + - - +
29A PHE* 3.1 5.5 + - - +
30A LYS* 2.9 25.2 + - - +
63A LYS* 4.2 25.4 - - + -
67A LEU* 3.5 19.2 - - + +
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Residues in contact with GLU 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 GLU 2.9 17.9 + - - +
24A GLU* 3.3 9.6 + - + +
26A ALA* 1.3 72.9 - - - +
28A ALA* 1.3 61.7 + - - +
30A LYS* 3.1 26.4 + - - +
31A ASN* 2.8 57.0 + - - +
63A LYS* 5.0 7.0 + - - +
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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 GLU 2.9 17.5 + - - +
25A PHE 3.4 6.5 - - - +
26A ALA 3.2 0.2 - - - -
27A GLU* 1.3 77.7 - - - +
29A PHE* 1.3 62.2 + - - +
31A ASN* 3.2 12.4 + - - +
32A ALA* 2.9 23.9 + - - +
226A LEU* 3.8 27.1 - - + +
227A GLU* 3.9 18.4 - - + +
268A ILE* 4.1 7.7 - - + +
270A VAL* 5.0 4.5 - - + -
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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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6A LEU* 3.7 25.8 - - + -
9A ILE* 3.4 40.8 - - + -
11A LEU* 3.9 12.3 - - + -
25A PHE 3.1 5.1 + - - +
26A ALA 3.1 9.3 + - - +
28A ALA* 1.3 79.7 - - - +
30A LYS* 1.3 61.6 + - - +
32A ALA* 3.3 0.7 + - - +
33A LEU* 3.0 51.5 + - + +
46A ILE* 3.7 23.6 - - + -
50A LEU* 3.8 15.3 - - + -
67A LEU* 3.8 24.2 - - + -
68A LEU* 4.2 14.4 - - + -
226A LEU* 3.7 6.9 - - + +
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Residues in contact with LYS 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 ALA 2.9 9.5 + - - +
27A GLU* 3.1 30.9 + - - +
29A PHE* 1.3 77.2 - - - +
31A ASN* 1.3 65.7 + - - +
33A LEU* 3.4 2.7 + - - +
34A GLU* 3.0 57.9 + - - +
63A LYS* 4.9 5.1 - - - +
67A LEU* 3.6 25.9 - - + +
70A ILE* 3.9 16.8 - - + -
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Residues in contact with ASN 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 GLU* 2.8 48.1 + - - +
28A ALA* 3.2 10.4 + - - +
30A LYS* 1.3 74.7 - - - +
32A ALA* 1.3 62.6 + - - +
34A GLU* 3.2 14.0 + - - +
35A ILE* 3.0 28.1 + - + +
268A ILE* 4.0 25.3 - - + +
269A LYS 5.7 1.0 + - - -
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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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6A LEU* 4.1 13.9 - - + -
28A ALA 2.9 16.3 + - - +
29A PHE 3.7 4.5 - - - +
31A ASN* 1.3 76.3 - - - +
33A LEU* 1.3 56.6 + - - +
35A ILE* 3.1 5.4 + - - +
36A ALA* 2.9 25.3 + - - +
226A LEU* 3.9 15.5 - - + -
255A PHE* 3.6 29.7 - - + -
268A ILE* 3.5 14.1 - - + +
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Residues in contact with LEU 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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6A LEU* 4.5 8.3 - - + -
29A PHE* 3.0 64.9 + - + +
30A LYS 3.9 2.7 - - - +
32A ALA* 1.3 76.4 - - - +
34A GLU* 1.3 58.1 + - - +
36A ALA* 3.1 7.4 + - + +
37A VAL* 3.0 32.1 + - - +
44A ILE* 4.1 27.8 - - + +
46A ILE* 5.5 0.9 - - + -
67A LEU* 3.5 29.8 - - + +
68A LEU* 4.5 4.3 - - + +
70A ILE* 4.2 16.4 - - + -
71A PRO* 4.3 11.7 - - + -
78A VAL* 5.7 0.4 - - + -
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Residues in contact with GLU 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 LYS* 3.0 49.2 + - - +
31A ASN* 3.6 14.1 - - - +
33A LEU* 1.3 74.3 - - - +
35A ILE* 1.3 62.9 + - + +
37A VAL* 3.4 3.8 + - - +
38A GLN* 2.9 44.7 + - - +
70A ILE* 4.1 22.8 - - + +
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Residues in contact with ILE 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 ASN* 3.0 19.8 + - + +
32A ALA 3.1 7.2 + - - +
34A GLU* 1.3 74.3 - - + +
36A ALA* 1.3 61.6 + - - +
38A GLN* 3.2 17.7 + - - +
39A GLU* 2.9 55.2 + - + +
255A PHE* 3.9 14.4 - - + -
257A ILE* 4.5 1.1 - - + -
266A VAL* 4.0 21.5 - - + -
267A GLU 4.9 2.7 - - - +
268A ILE* 4.1 26.2 - - + -
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Residues in contact with ALA 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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4A ALA* 4.0 15.3 - - + -
6A LEU* 6.0 1.3 - - + -
32A ALA 2.9 12.4 + - - +
33A LEU* 3.1 11.6 + - + +
35A ILE* 1.3 77.7 - - - +
37A VAL* 1.3 61.4 + - - +
39A GLU* 3.2 7.3 + - - -
41A VAL* 3.2 48.2 + - + +
44A ILE* 4.0 17.0 - - + -
255A PHE* 5.0 1.8 - - + -
257A ILE* 4.8 3.4 - - - -
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Residues in contact with VAL 37 (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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33A LEU 3.0 16.4 + - - +
34A GLU* 3.8 6.3 - - - +
36A ALA* 1.3 79.6 - - + +
38A GLN* 1.3 59.7 + - + +
40A ASN* 2.9 21.1 + - - -
70A ILE* 3.9 28.0 - - + +
71A PRO* 4.2 7.6 - - + -
74A HIS* 3.4 33.7 - - + +
76A ILE* 3.9 23.5 - - + +
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Residues in contact with GLN 38 (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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34A GLU* 2.9 35.2 + - - +
35A ILE* 3.6 19.7 - - - +
37A VAL* 1.3 77.8 - - + +
39A GLU* 1.3 61.7 + - + +
40A ASN* 3.3 4.9 + - - +
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Residues in contact with GLU 39 (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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2A LYS* 2.7 39.4 + - - +
35A ILE* 2.9 36.6 + - + +
36A ALA 3.7 3.4 - - - +
37A VAL 3.1 0.6 - - - -
38A GLN* 1.3 77.8 - - + +
40A ASN* 1.3 66.6 - - - +
41A VAL* 3.3 1.8 - - + -
257A ILE* 3.2 30.1 - - + -
264A ARG* 3.3 30.4 + - - -
266A VAL* 5.8 0.7 - - - +
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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