Contacts of the helix formed by residues 22 - 32 (chain C) in PDB entry 4BPU
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 PRO 22 (chain C).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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16C TYR* 4.5 1.6 - - - +
20C LEU 3.0 9.1 - - - +
21C PHE* 1.3 87.2 - - + +
23C TYR* 1.3 65.0 + - - +
24C SER 3.1 4.3 + - - -
25C GLN* 3.2 24.8 - - + +
26C TYR* 3.0 20.9 + - + +
321C PHE* 3.8 50.7 - - + -
388C LEU* 4.9 2.7 - - + -
392C VAL* 4.5 12.8 - - + -
395C PHE* 5.1 1.6 - - + -
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Residues in contact with TYR 23 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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17C TYR* 2.5 35.9 + - - +
18C ARG 4.9 4.7 - - - -
21C PHE* 2.7 47.9 + + + -
22C PRO* 1.3 71.2 - - - +
24C SER* 1.3 57.8 + - - +
26C TYR* 3.3 6.8 - - - +
27C TYR* 2.9 31.7 + - - +
63C GLN* 3.8 6.1 + - + +
66C LEU* 4.1 14.9 - - + +
67C GLU* 3.6 54.1 - - + +
70C MET* 3.6 45.5 - - + +
71C GLN* 3.9 10.7 - - - +
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Residues in contact with SER 24 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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22C PRO 3.1 0.6 - - - -
23C TYR* 1.3 80.2 - - - +
25C GLN* 1.3 69.3 + - - +
27C TYR* 3.3 2.8 + - - +
28C ARG* 2.9 38.4 + - - +
63C GLN* 3.6 20.8 + - - +
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Residues in contact with GLN 25 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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22C PRO* 3.2 21.1 - - + +
24C SER* 1.3 85.7 - - - +
26C TYR* 1.3 53.4 + - - +
28C ARG* 3.9 9.9 - - - +
29C TRP* 2.8 35.0 + - - +
392C VAL* 3.3 22.3 - - + +
395C PHE* 3.5 23.7 - - + -
396C GLU* 3.0 40.9 + - + -
399C LEU* 3.4 17.5 - - + +
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Residues in contact with TYR 26 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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21C PHE* 3.5 29.4 - + + -
22C PRO 3.0 14.1 + - - +
23C TYR* 3.3 13.2 - - - +
25C GLN* 1.3 77.2 - - - +
27C TYR* 1.3 58.6 + - - +
29C TRP* 3.2 19.4 + + - +
30C LEU* 2.9 53.5 + - + +
40C PHE* 5.3 0.4 - + - -
45C PHE* 3.3 22.7 - + - -
66C LEU* 3.8 25.8 - - + -
70C MET* 5.3 2.0 - - - -
78C ILE* 4.2 4.7 - - + +
80C ILE* 3.3 18.1 - - + +
319C SER* 2.8 29.7 + - - -
320C PRO* 4.1 6.3 - - + -
321C PHE* 5.2 5.2 - + - -
395C PHE* 4.1 8.9 - + - -
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Residues in contact with TYR 27 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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23C TYR 2.9 16.9 + - - +
24C SER 3.9 1.3 - - - +
26C TYR* 1.3 74.2 - - - +
28C ARG* 1.3 62.8 + - + +
30C LEU 4.4 0.7 - - - +
31C ASN* 2.8 71.6 + - + +
40C PHE* 3.5 47.8 - + + -
41C GLN* 3.9 12.6 + - - -
62C ASN* 4.0 7.8 - - + +
63C GLN* 3.6 50.3 - - + +
66C LEU* 5.6 2.2 - - + -
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Residues in contact with ARG 28 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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24C SER* 2.9 27.8 + - - +
25C GLN* 3.4 16.1 - - - +
27C TYR* 1.3 82.2 - - + +
29C TRP* 1.3 62.8 + - - +
31C ASN* 4.6 1.3 - - - +
32C TYR* 3.5 13.9 + - - -
33C GLY 4.4 3.1 + - - -
396C GLU* 4.2 24.5 + - - +
399C LEU* 3.8 30.9 - - + +
400C GLU* 4.5 13.7 + - - +
403C ASP* 3.7 21.2 + - - -
406C ARG* 4.9 5.7 + - - -
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Residues in contact with TRP 29 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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25C GLN 2.8 16.8 + - - +
26C TYR* 3.3 18.2 - + - +
28C ARG* 1.3 77.5 - - - +
30C LEU* 1.3 87.3 + - + +
32C TYR* 3.0 48.4 + + - -
80C ILE* 3.6 31.0 - - + -
105C GLU* 4.3 3.1 - - - -
156C LEU* 4.6 3.1 - - + -
168C TRP* 3.9 32.1 - + + -
170C CYS* 3.5 21.5 - - - -
320C PRO* 3.8 24.7 - - + -
395C PHE* 3.9 19.5 - + + -
398C PHE* 3.8 18.3 - + - -
399C LEU* 3.5 14.1 - - + +
402C LEU* 4.2 3.5 - - + +
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Residues in contact with LEU 30 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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26C TYR* 2.9 44.6 + - + +
29C TRP* 1.3 111.1 - - + +
31C ASN* 1.3 59.2 + - - +
32C TYR* 3.4 13.0 - - - -
39C TYR* 3.9 11.6 - - - +
40C PHE* 3.7 26.1 - - + +
43C ARG* 3.9 29.2 + - + +
45C PHE* 3.4 35.2 - - + -
80C ILE* 4.5 8.1 - - + -
105C GLU* 4.3 0.7 - - - +
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Residues in contact with ASN 31 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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27C TYR* 2.8 61.3 + - + +
28C ARG* 4.6 1.6 - - - +
30C LEU* 1.3 76.0 - - - +
32C TYR* 1.3 71.6 + - - +
33C GLY* 4.5 3.0 - - - +
34C GLY* 3.3 33.2 + - - +
35C VAL* 5.4 0.3 - - - +
36C ILE 5.0 1.9 + - - +
39C TYR* 4.6 11.0 + - - +
40C PHE* 3.8 18.0 + - + +
41C GLN* 4.8 4.3 + - - +
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Residues in contact with TYR 32 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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28C ARG 3.5 5.4 + - - -
29C TRP* 3.0 42.3 + - - -
30C LEU* 3.5 17.0 - - - -
31C ASN* 1.3 78.7 - - - +
33C GLY* 1.3 61.6 + - - +
34C GLY 3.2 1.4 + - - -
35C VAL* 3.4 22.3 - - + +
39C TYR* 3.7 17.0 - + + -
43C ARG* 3.8 11.0 - - - -
105C GLU* 2.8 29.0 + - - +
170C CYS* 3.2 19.9 - - - +
175C ARG* 3.2 40.1 + - - +
402C LEU* 4.0 19.1 - - + -
406C ARG* 3.6 30.3 - - - +
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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