Contacts of the helix formed by residues 16 - 28 (chain s) in PDB entry 4PJO
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 GLN 16 (chain s).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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14s MET* 3.6 15.2 + - + +
15s VAL* 1.3 75.7 - - - +
17s PRO* 1.3 70.7 - - + +
18s ILE* 4.7 7.4 - - + +
19s ASN* 2.8 63.3 + - - +
20s LEU* 3.1 9.2 + - - +
34u PHE 4.5 9.3 - - - +
35u ASP* 6.0 1.3 - - - +
41u VAL* 3.9 2.2 - - - -
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Residues in contact with PRO 17 (chain s).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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16s GLN* 1.3 88.1 - - + +
18s ILE* 1.3 64.3 + - + +
20s LEU* 3.4 3.7 + - + +
21s ILE* 3.2 30.2 + - + +
54s MET* 6.0 0.7 - - + -
34u PHE* 3.8 18.4 - - - +
35u ASP* 4.2 10.8 - - + +
39u ASN* 3.5 44.9 - - + +
40u LEU 4.1 5.2 - - - +
41u VAL* 3.5 23.3 - - + -
61u VAL* 3.9 10.9 - - + +
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Residues in contact with ILE 18 (chain s).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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1274 U 5.8 2.5 - - - +
16s GLN* 3.0 9.0 + - + +
17s PRO* 1.3 78.7 - - + +
19s ASN* 1.3 67.3 + - - +
21s ILE* 3.2 15.5 + - + +
22s PHE* 3.0 19.8 + - + +
50s PHE* 4.1 25.6 - - + -
51s ASP 5.5 4.9 - - - +
52s GLU* 5.6 8.7 - - - +
54s MET* 5.9 6.5 - - + -
35u ASP* 4.2 22.9 - - - +
39u ASN* 5.5 3.6 - - - +
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Residues in contact with ASN 19 (chain s).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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14s MET 5.3 1.0 - - - +
15s VAL* 5.2 4.3 - - + -
16s GLN* 2.8 47.3 + - - +
18s ILE* 1.3 79.1 - - - +
20s LEU* 1.3 52.4 + - - +
22s PHE* 2.7 16.5 + - + +
23s ARG* 2.7 35.3 + - - +
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Residues in contact with LEU 20 (chain s).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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15s VAL* 4.2 14.1 - - + +
16s GLN 3.1 8.1 + - - +
17s PRO 3.8 6.7 - - - +
18s ILE 3.3 0.2 - - - -
19s ASN* 1.3 78.9 - - - +
21s ILE* 1.3 56.8 + - - +
23s ARG* 3.5 14.0 + - + +
24s TYR* 3.0 53.8 + - + +
41u VAL* 3.7 14.1 - - + -
59u MET* 3.6 28.9 - - + -
60u VAL 3.5 16.8 - - - +
61u VAL* 3.4 25.6 - - + -
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Residues in contact with ILE 21 (chain s).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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17s PRO* 3.2 18.5 + - + +
18s ILE* 3.5 15.5 - - + +
19s ASN 3.1 0.4 - - - -
20s LEU* 1.3 74.3 - - - +
22s PHE* 1.3 59.2 + - - +
24s TYR* 3.0 11.7 + - + +
25s LEU* 2.9 26.0 + - - +
47s ILE* 4.3 17.2 - - + +
50s PHE* 3.4 37.5 - - + -
54s MET* 4.3 24.7 - - + -
56s LEU* 4.9 3.1 - - + -
87s LEU* 4.0 22.9 - - + -
61u VAL* 4.0 20.2 - - + -
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Residues in contact with PHE 22 (chain s).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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18s ILE* 3.0 13.0 + - + +
19s ASN* 2.7 23.4 + - + +
21s ILE* 1.3 68.6 - - - +
23s ARG* 1.3 62.0 + - - +
25s LEU* 2.9 30.5 + - + +
26s GLN* 2.9 53.7 + - + +
50s PHE* 4.1 14.3 - + + -
4t PRO* 5.5 6.3 - - + -
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Residues in contact with ARG 23 (chain s).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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27S ASN* 2.9 40.8 + - - +
28S ARG* 3.7 13.9 + - + -
29S SER* 3.7 17.8 + - - +
30S ARG 5.6 0.9 - - - +
19s ASN 2.7 15.4 + - - +
20s LEU* 3.5 20.2 - - + +
22s PHE* 1.3 73.7 - - - +
24s TYR* 1.3 63.2 + - + +
26s GLN* 3.1 20.4 + - - -
27s ASN* 2.3 66.6 + - - +
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Residues in contact with TYR 24 (chain s).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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20s LEU* 3.0 48.2 + - + +
21s ILE* 3.0 16.8 + - + +
23s ARG* 1.3 77.2 - - + +
25s LEU* 1.3 62.2 + - - +
27s ASN* 4.5 2.9 - - - -
28s ARG* 3.2 2.1 + - - -
29s SER* 3.1 36.1 + - - +
31s ILE* 3.4 35.4 - - + -
47s ILE* 4.4 12.7 + - + +
87s LEU* 3.9 16.6 + - + -
88s GLN 5.0 1.2 + - - -
89s SER* 3.7 19.5 - - - -
59u MET* 3.3 10.2 + - + -
60u VAL* 3.3 29.3 - - - -
61u VAL* 3.8 12.1 + - + -
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Residues in contact with LEU 25 (chain s).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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21s ILE 2.9 11.4 + - - +
22s PHE* 2.9 35.2 + - + +
24s TYR* 1.3 74.6 - - - +
26s GLN* 1.3 65.1 + - + +
28s ARG* 2.9 23.6 + - - +
47s ILE* 3.2 34.6 - - + +
48s ILE* 3.3 24.2 - - - +
49s GLY* 4.5 3.1 - - - -
50s PHE* 4.4 11.9 - - + -
3t LEU 5.6 0.4 - - - +
4t PRO* 4.0 21.1 - - + -
6t ASN* 5.4 0.7 - - - +
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Residues in contact with GLN 26 (chain s).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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90S VAL* 5.2 14.9 - - + +
22s PHE* 2.9 54.5 + - + +
23s ARG* 3.6 30.2 + - - +
25s LEU* 1.3 79.9 - - + +
27s ASN* 1.3 65.6 + - - +
28s ARG* 3.0 17.3 + - - -
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Residues in contact with ASN 27 (chain s).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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28S ARG* 5.2 10.0 + - - +
23s ARG* 2.3 58.8 + - - +
24s TYR* 4.5 3.2 - - - +
26s GLN* 1.3 79.0 - - - +
28s ARG* 1.3 72.9 + - - +
29s SER* 3.8 18.1 - - - +
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Residues in contact with ARG 28 (chain s).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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24s TYR 3.2 1.7 + - - -
25s LEU 2.9 17.9 + - - +
26s GLN 2.9 13.8 + - - +
27s ASN* 1.3 83.9 + - - +
29s SER* 1.3 66.3 + - - +
30s ARG 3.6 0.9 + - - -
46s CYS* 3.4 27.7 - - + -
47s ILE 5.6 3.1 - - - +
2t SER 5.6 4.0 + - - -
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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