Contacts of the helix formed by residues 12 - 26 (chain O) in PDB entry 4WNC
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 GLY 12 (chain O).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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10O GLY 3.1 8.7 + - - -
11O PHE* 1.3 74.9 - - - +
13O ARG* 1.3 67.8 + - - -
14O ILE 3.2 2.7 - - - -
15O GLY 3.9 1.9 - - - +
16O ARG* 2.8 37.0 + - - +
35O ASP* 4.4 0.2 + - - -
38O ILE* 5.6 0.2 - - - -
98O SER 5.2 3.6 + - - -
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Residues in contact with ARG 13 (chain O).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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12O GLY* 1.3 73.2 - - - +
14O ILE* 1.3 67.2 + - + +
16O ARG* 3.2 26.8 - - - +
17O LEU* 3.1 34.9 + - - +
50O ASP* 2.9 43.3 + - - +
51O SER 5.4 1.4 - - - +
52O THR* 3.7 10.3 + - - +
53O HIS* 3.7 4.4 - - - -
183O ALA* 5.1 17.0 - - + +
317O GLU* 2.8 48.8 + - + +
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Residues in contact with ILE 14 (chain O).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
12O GLY* 3.2 0.6 - - - -
13O ARG* 1.3 81.6 - - + +
15O GLY* 1.3 59.6 + - - +
18O VAL* 2.8 50.8 + - + +
98O SER* 4.3 11.4 + - - +
122O SER* 4.1 28.7 - - - +
316O ASN 4.4 4.0 - - - +
317O GLU* 4.0 24.0 - - + +
320O TYR* 4.2 23.1 - - + -
321O SER* 3.8 15.0 - - - +
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Residues in contact with GLY 15 (chain O).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
8O VAL* 3.7 10.5 - - - +
10O GLY 3.3 25.2 + - - -
11O PHE* 4.1 5.6 - - - -
12O GLY* 3.4 5.6 + - - -
14O ILE* 1.3 78.9 - - - +
16O ARG* 1.3 56.6 + - - +
18O VAL* 3.8 4.7 - - - +
19O THR* 2.8 32.0 + - - -
98O SER* 3.7 11.4 + - - -
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Residues in contact with ARG 16 (chain O).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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11O PHE* 2.8 71.4 + - + +
12O GLY* 2.8 37.4 + - - +
13O ARG* 3.2 37.1 - - - +
15O GLY* 1.3 72.2 - - - +
17O LEU* 1.3 63.0 + - + +
19O THR* 3.3 3.8 + - - -
20O ARG* 2.9 24.4 + - - +
38O ILE* 4.7 0.6 - - - +
46O MET* 3.4 58.7 + - - +
47O PHE* 3.5 15.6 - - + +
49O TYR 5.9 0.2 + - - -
50O ASP* 4.8 4.4 + - - +
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Residues in contact with LEU 17 (chain O).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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13O ARG* 3.1 27.6 + - - +
16O ARG* 1.3 76.9 - - + +
18O VAL* 1.3 60.5 + - - +
20O ARG* 3.6 28.7 - - - +
21O ALA* 2.9 29.1 + - - +
50O ASP* 4.4 10.1 - - - +
53O HIS* 3.7 23.3 - - + +
317O GLU* 3.6 45.5 - - + +
318O PHE* 4.2 13.3 - - + -
321O SER* 3.3 20.0 - - - +
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Residues in contact with VAL 18 (chain O).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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8O VAL* 4.8 4.5 - - + -
14O ILE* 2.8 41.5 + - + +
15O GLY* 3.8 5.4 - - - +
17O LEU* 1.3 71.4 - - - +
19O THR* 1.3 58.5 + - - +
21O ALA* 3.2 2.6 + - - +
22O ALA* 2.8 29.3 + - - +
30O ILE* 4.8 9.2 - - + -
96O VAL* 4.4 19.3 - - + -
321O SER* 3.9 25.4 - - - +
324O VAL* 4.0 22.2 - - + -
325O VAL* 3.8 14.5 - - + +
328O MET* 4.6 4.7 - - + -
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Residues in contact with THR 19 (chain O).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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8O VAL* 4.0 15.2 - - - +
11O PHE* 3.7 15.5 - - + -
15O GLY 2.8 18.9 + - - -
16O ARG 3.4 8.7 - - - -
18O VAL* 1.3 77.5 - - - +
20O ARG* 1.3 61.5 + - - +
22O ALA* 3.3 2.4 + - - +
23O PHE* 3.1 50.2 + - + -
30O ILE* 4.3 17.5 - - + +
33O ILE* 4.5 4.3 - - + +
47O PHE* 3.6 18.6 - - + -
69O ILE* 3.9 9.6 - - + -
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Residues in contact with ARG 20 (chain O).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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16O ARG* 2.9 15.4 + - - +
17O LEU* 3.6 26.5 - - + +
19O THR* 1.3 73.4 - - - +
21O ALA* 1.3 58.4 + - - +
23O PHE* 3.3 1.3 + - - +
24O ASN* 2.8 47.4 + - - +
47O PHE* 3.4 47.2 + - + -
48O GLN 3.9 1.6 + - - -
50O ASP* 3.5 19.3 + - - +
53O HIS* 3.6 20.1 + - - +
54O GLY 2.8 30.7 + - - -
55O LYS 4.0 7.1 + - - -
56O PHE* 3.4 30.6 - - + +
57O HIS* 5.3 0.4 - - - +
318O PHE* 5.0 9.9 - - + -
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Residues in contact with ALA 21 (chain O).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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17O LEU 2.9 21.2 + - - +
18O VAL 3.6 4.5 - - - +
20O ARG* 1.3 72.8 - - - +
22O ALA* 1.3 63.9 + - - +
24O ASN* 3.9 5.3 - - - +
25O SER* 2.9 30.2 + - - -
318O PHE* 6.3 2.2 - - + -
321O SER 4.1 7.0 - - - +
322O ASN* 3.7 34.0 - - - +
325O VAL* 3.9 14.6 - - + -
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Residues in contact with ALA 22 (chain O).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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18O VAL 2.8 16.5 + - - +
19O THR 3.5 5.4 - - - +
21O ALA* 1.3 76.7 - - - +
23O PHE* 1.3 57.0 + - + +
25O SER* 3.7 3.5 + - - -
26O GLY* 2.8 31.7 + - - -
27O LYS 3.9 0.2 + - - -
28O VAL* 3.6 36.0 - - + +
30O ILE* 3.6 22.0 - - + -
325O VAL* 3.9 8.2 - - + +
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Residues in contact with PHE 23 (chain O).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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19O THR* 3.1 47.4 + - + +
20O ARG 4.1 2.5 - - - +
22O ALA* 1.3 74.3 - - - +
24O ASN* 1.3 65.9 + - - +
26O GLY* 3.9 6.3 + - - -
29O ASP* 6.1 1.1 - - - -
30O ILE* 3.9 29.4 - - + -
47O PHE* 5.0 0.9 - + - -
56O PHE* 4.6 7.2 - - + -
69O ILE* 3.6 36.3 - - + -
70O ASN* 4.1 23.1 + - - +
72O ASN* 3.6 34.8 - - + -
74O ILE* 3.9 18.2 - - + -
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Residues in contact with ASN 24 (chain O).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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20O ARG* 2.8 40.1 + - - +
21O ALA* 3.9 5.2 - - - +
23O PHE* 1.3 80.7 - - - +
25O SER* 1.3 59.0 + - - +
56O PHE* 3.9 17.4 - - - -
57O HIS* 4.5 8.0 - - - +
70O ASN* 5.6 0.7 + - - -
318O PHE* 5.1 10.9 - - - -
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Residues in contact with SER 25 (chain O).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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21O ALA 2.9 20.8 + - - -
22O ALA 3.7 1.0 + - - -
24O ASN* 1.3 77.3 - - - +
26O GLY* 1.3 63.6 + - - +
27O LYS* 3.2 39.9 + - - +
322O ASN* 5.3 7.0 - - - -
325O VAL* 3.8 8.8 - - - +
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Residues in contact with GLY 26 (chain O).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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3O LYS 4.8 4.7 + - - -
22O ALA 2.8 21.6 + - - -
23O PHE* 3.9 5.6 + - - -
24O ASN 3.5 1.6 - - - -
25O SER* 1.3 73.9 - - - +
27O LYS* 1.3 60.4 + - - +
28O VAL 3.4 7.1 + - - +
29O ASP* 4.8 4.9 - - - +
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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