Contacts of the helix formed by residues 11 - 31 (chain A) in PDB entry 1X3W
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 ASP 11 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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9A ASN 3.5 3.7 + - - +
10A ILE* 1.3 71.1 - - - +
12A PHE* 1.3 65.2 + - - +
13A ASP* 3.1 19.6 + - - +
14A SER* 3.0 33.6 + - - +
15A ILE* 3.0 21.8 + - - +
294B ILE* 6.0 0.3 - - - +
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Residues in contact with PHE 12 (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 ILE* 3.4 46.1 + - + -
11A ASP* 1.3 72.0 + - - +
13A ASP* 1.3 56.4 + - - +
14A SER 3.1 1.6 - - - -
15A ILE* 2.6 22.2 + - + +
16A ALA* 2.6 34.0 + - - +
277B ALA* 3.9 21.8 - - + +
280B LEU* 3.6 22.0 - - + -
281B GLU* 3.4 51.6 - - + -
284B SER* 4.1 13.5 - - - -
291B ARG* 4.8 4.5 - - - -
294B ILE* 4.2 9.2 - - + -
301B PHE* 5.6 0.2 - + - -
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Residues in contact with ASP 13 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
11A ASP* 3.1 9.3 + - - +
12A PHE* 1.3 77.1 - - - +
14A SER* 1.3 61.4 + - - +
16A ALA* 3.5 2.0 + - - +
17A LYS* 3.1 24.8 + - - +
277B ALA* 3.5 20.6 - - - +
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Residues in contact with SER 14 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
11A ASP* 3.0 30.2 + - - +
12A PHE 3.1 0.4 - - - -
13A ASP* 1.3 79.8 - - - +
15A ILE* 1.3 64.3 + - - +
17A LYS* 3.9 8.4 - - - +
18A MSE 3.0 30.4 + - - +
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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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11A ASP 3.0 18.4 - - - +
12A PHE* 2.6 41.8 + - + +
14A SER* 1.3 76.6 + - - +
16A ALA* 1.3 64.8 + - - +
18A MSE 3.6 24.5 + - + +
19A LEU* 3.1 19.1 + - - +
280B LEU* 3.9 19.7 - - + -
294B ILE* 5.3 7.4 - - + -
298B PRO* 3.6 39.5 - - + +
301B PHE* 4.9 11.0 - - + -
302B VAL* 3.8 10.1 - - + -
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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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12A PHE 2.6 14.7 + - - +
13A ASP* 3.5 9.0 - - - +
15A ILE* 1.3 70.1 - - - +
17A LYS* 1.3 67.8 + - - +
19A LEU* 2.7 16.3 + - - +
20A LEU* 3.0 17.9 + - + +
273B PRO 5.8 0.7 - - - +
276B LEU* 3.7 32.3 - - + -
277B ALA* 3.9 22.0 - - + +
280B LEU* 4.3 0.2 - - - -
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Residues in contact with LYS 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 ASP 3.1 14.0 + - - +
14A SER* 3.9 7.2 - - - +
16A ALA* 1.3 78.1 - - - +
18A MSE 1.3 65.1 + - - +
20A LEU* 3.5 12.3 + - - +
21A ILE* 3.1 46.4 + - + +
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Residues in contact with MSE 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 SER 3.0 20.1 + - - +
15A ILE* 3.7 24.0 - - + +
16A ALA 2.9 0.2 + - - -
17A LYS* 1.3 80.1 - - + +
19A LEU* 1.3 61.7 + - - +
21A ILE* 3.6 8.0 + - - +
22A LYS* 3.1 39.8 + - + +
298B PRO* 4.6 5.6 - - + -
299B GLU* 3.3 38.1 - - - +
302B VAL* 4.1 14.1 - - - -
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Residues in contact with LEU 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 3.1 12.5 + - - +
16A ALA 2.7 14.1 + - - +
18A MSE 1.3 66.6 - - - +
20A LEU* 1.3 68.6 + - - +
21A ILE 2.7 4.0 + - - -
22A LYS* 2.7 16.0 + - - +
23A TYR* 2.8 16.7 + - + +
265B LEU* 5.1 3.6 - - + -
269B VAL* 4.7 9.6 - - + -
276B LEU* 3.6 34.5 - - + -
280B LEU* 4.3 11.2 - - + -
302B VAL* 3.7 32.8 - - + -
305B LEU* 3.9 28.9 - - + -
306B LEU* 4.4 15.0 - - + -
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Residues in contact with LEU 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 ALA* 3.0 23.9 + - + +
17A LYS* 3.5 12.8 - - - +
19A LEU* 1.3 78.9 - - - +
21A ILE* 1.3 58.8 + - + +
23A TYR* 3.3 9.0 + - + +
24A LYS* 2.9 30.4 + - - +
310A TYR* 4.8 6.6 + - - +
269B VAL* 3.9 22.7 - - + +
273B PRO* 3.7 43.5 - - + +
276B LEU* 3.8 24.7 - - + -
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Residues in contact with ILE 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 LYS* 3.1 47.5 + - + +
18A MSE 3.7 9.0 - - - +
19A LEU 2.7 4.9 + - - -
20A LEU* 1.3 75.6 - - + +
22A LYS* 1.3 68.2 + - + +
23A TYR 2.8 5.8 + - - -
24A LYS* 3.1 8.6 + - + +
25A ASP* 2.7 38.1 + - - +
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Residues in contact with LYS 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 MSE 3.1 35.0 + - + +
19A LEU 2.7 10.9 + - - +
21A ILE* 1.3 75.8 - - + +
23A TYR* 1.3 56.8 + - - +
25A ASP* 3.6 10.1 - - - +
26A PHE* 3.3 14.9 + - - +
299B GLU* 4.4 17.6 + - + +
302B VAL* 4.2 22.4 - - + -
306B LEU* 3.3 14.4 - - + +
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Residues in contact with TYR 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 LEU* 2.8 16.3 + - + +
20A LEU* 3.3 12.8 - - + +
21A ILE 2.8 1.0 + - - -
22A LYS* 1.3 73.4 - - - +
24A LYS* 1.3 59.8 + - - +
25A ASP 2.8 13.6 + - - -
26A PHE* 2.9 3.5 + + - -
27A ILE* 2.8 55.1 + - + +
310A TYR* 3.8 29.6 - + - -
313A ALA 5.0 1.6 + - - -
314A CYS* 4.6 5.2 - - - -
317A GLU* 4.0 15.8 + - - +
266B ARG* 5.2 2.3 + - + -
269B VAL* 3.3 38.6 - - + -
270B SER* 3.8 18.7 - - - -
306B LEU* 3.6 26.0 - - + +
309B VAL* 4.7 16.2 - - + -
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Residues in contact with LYS 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 LEU 2.9 17.1 + - - +
21A ILE* 3.7 8.1 - - + +
23A TYR* 1.3 76.0 - - - +
25A ASP* 1.3 61.5 + - - +
27A ILE* 4.0 2.2 - - - +
28A LEU* 3.3 30.8 + - + +
306A ASP 4.9 10.0 + - - -
307A ASP* 5.3 7.5 + - - +
310A TYR* 3.5 54.4 - - + +
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Residues in contact with ASP 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 ILE* 2.7 38.9 + - - +
22A LYS* 3.6 10.7 + - - +
23A TYR 2.8 1.0 + - - -
24A LYS* 1.3 80.0 - - - +
26A PHE* 1.3 67.2 + - - +
28A LEU* 2.9 17.7 + - - +
29A SER* 2.9 16.2 + - - -
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Residues in contact with PHE 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 LYS 3.3 11.0 + - - +
23A TYR* 2.9 4.6 + + - +
25A ASP* 1.3 79.5 - - - +
27A ILE* 1.3 74.8 + - + +
29A SER* 3.0 18.0 + - - -
30A LYS* 3.1 27.3 + - + -
306B LEU* 3.5 48.9 - - + -
307B GLU* 4.6 2.2 - - - -
309B VAL* 3.6 24.2 - - + -
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Residues in contact with ILE 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 TYR* 2.8 61.1 + - + +
24A LYS 4.0 4.0 - - - +
26A PHE* 1.3 88.3 - - + +
28A LEU* 1.3 61.8 + - + +
29A SER 2.9 10.8 + - - -
30A LYS* 3.2 29.1 + - + +
31A PHE* 3.3 10.1 + - + +
309A ILE* 5.0 1.1 - - + +
310A TYR* 3.6 29.6 - - + -
313A ALA* 3.8 28.0 - - + +
314A CYS* 6.0 0.4 - - - -
309B VAL* 5.4 3.8 - - + -
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Residues in contact with LEU 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 LYS* 3.3 26.4 + - + +
25A ASP* 2.9 9.4 + - - +
27A ILE* 1.3 77.5 - - + +
29A SER* 1.3 57.7 + - - +
31A PHE* 4.9 1.8 - - - +
32A LYS* 3.2 30.5 + - - +
306A ASP* 3.4 40.6 - - + +
309A ILE* 3.4 33.9 - - + +
310A TYR* 3.9 16.6 - - + +
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Residues in contact with SER 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 ASP 2.9 15.8 + - - -
26A PHE* 3.2 13.2 - - - -
27A ILE 2.9 0.4 - - - -
28A LEU* 1.3 78.7 - - - +
30A LYS* 1.3 69.7 + - - +
31A PHE 3.2 0.9 - - - -
32A LYS* 3.2 23.4 + - - +
33A LYS* 3.9 14.2 - - - +
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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 PHE* 3.1 24.3 + - + +
27A ILE* 3.3 20.3 - - + +
29A SER* 1.3 79.2 - - - +
31A PHE* 1.3 86.9 + - + +
32A LYS 3.2 8.7 - - - +
33A LYS* 5.6 1.2 - - - -
294A GLN* 3.7 26.7 + - - -
298A LYS* 3.6 14.9 - - - -
313A ALA* 6.1 1.3 - - + -
317A GLU* 5.7 2.4 + - - +
309B VAL* 3.8 29.9 + - - +
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Residues in contact with PHE 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 ILE* 3.3 11.7 + - + +
28A LEU* 4.6 1.6 - - - -
29A SER 3.2 0.2 - - - -
30A LYS* 1.3 105.2 - - + +
32A LYS* 1.3 63.4 + - - +
294A GLN* 4.9 9.9 - - + -
297A THR* 4.8 9.0 - - - -
298A LYS* 4.4 35.5 - - + +
301A ARG* 3.6 28.8 - - + -
302A TYR* 4.8 9.9 - - - -
309A ILE* 3.4 51.6 - - + +
313A ALA* 3.5 27.1 - - + -
316A ASP* 4.1 13.9 - - - -
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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