Contacts of the helix formed by residues 28 - 40 (chain C) in PDB entry 4PCW
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 SER 28 (chain C).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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21C ASP* 3.5 17.6 + - - -
27C LEU* 1.3 75.7 - - - +
29C LYS* 1.3 60.2 + - - +
30C LYS* 3.5 8.5 + - - +
31C GLU* 2.7 36.7 + - - +
32C LEU* 2.8 27.6 + - - +
57C MET* 4.5 2.0 - - - -
66C LYS 4.9 7.0 - - - -
67C LYS* 5.4 2.0 - - - +
102C CA 4.3 0.8 - - - -
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Residues in contact with LYS 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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28C SER* 1.3 74.5 - - - +
30C LYS* 1.3 59.0 + - + +
32C LEU* 3.5 1.9 + - - +
33C LYS* 2.9 27.5 + - - +
53C VAL* 3.6 17.9 - - + +
54C ASP* 2.8 35.3 + - - +
57C MET* 3.9 42.7 - - + +
66C LYS 5.1 0.6 + - - -
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Residues in contact with LYS 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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20C LYS* 5.0 15.3 - - + -
28C SER* 3.2 8.6 + - - +
29C LYS* 1.3 79.1 - - + +
31C GLU* 1.3 63.7 + - - +
33C LYS* 3.5 30.4 - - + +
34C GLU* 3.2 25.6 + - - +
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Residues in contact with GLU 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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17C TYR* 3.2 26.8 - - - +
18C SER 3.1 1.2 - - - +
20C LYS* 2.9 44.7 + - + +
21C ASP* 3.0 18.2 + - - +
26C THR 3.2 4.0 - - - +
27C LEU* 3.3 10.2 - - + +
28C SER* 2.7 32.7 + - - +
30C LYS* 1.3 76.0 - - - +
32C LEU* 1.3 62.2 + - - +
34C GLU* 3.4 7.8 + - - +
35C LEU* 3.1 21.8 + - - +
102C CA 2.3 30.3 - - - -
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Residues in contact with LEU 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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27C LEU* 4.2 25.5 - - + +
28C SER 2.8 17.7 + - - +
29C LYS 3.7 4.5 - - - +
31C GLU* 1.3 75.3 - - - +
33C LYS* 1.3 64.0 + - - +
35C LEU* 3.1 9.7 + - + +
36C LEU* 3.0 42.7 + - + +
53C VAL* 4.4 7.2 - - + +
56C PHE* 4.2 9.2 - - + +
57C MET* 3.6 48.0 - - + +
60C LEU* 4.5 17.3 - - + -
68C ILE* 4.4 5.4 - - + -
76C MET* 5.3 3.8 - - + -
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Residues in contact with LYS 33 (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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29C LYS 2.9 18.5 + - - +
30C LYS* 3.5 34.1 - - + +
32C LEU* 1.3 76.4 - - - +
34C GLU* 1.3 62.4 + - + +
36C LEU* 3.2 6.5 + - - +
37C GLU* 2.9 32.1 + - + +
48C ASP* 6.3 0.6 - - - +
49C ASP 5.5 0.8 - - - +
50C PRO* 4.5 21.8 - - - +
53C VAL* 3.8 37.3 - - + +
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Residues in contact with GLU 34 (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* 3.8 16.8 - - + +
20C LYS* 2.7 42.0 + - - -
30C LYS* 3.2 9.7 + - - +
31C GLU* 3.7 8.2 - - - +
32C LEU 3.3 0.2 - - - -
33C LYS* 1.3 83.7 - - + +
35C LEU* 1.3 58.2 + - - +
37C GLU* 3.9 8.0 - - + +
38C LYS* 3.1 49.3 + - - +
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Residues in contact with LEU 35 (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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13C LEU* 5.8 1.8 - - + -
14C PHE* 5.1 4.5 - - - -
17C TYR* 3.6 45.7 - - + -
27C LEU* 4.1 17.9 - - + -
31C GLU 3.1 12.9 + - - +
32C LEU* 3.1 12.1 + - + +
34C GLU* 1.3 75.0 - - - +
36C LEU* 1.3 66.6 + - + +
39C GLU* 2.9 50.2 + - + +
40C PHE* 4.6 8.7 - - + -
73C PHE* 3.9 33.0 - - + -
76C MET* 4.7 3.1 - - + -
3D LEU* 4.6 7.4 - - + -
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Residues in contact with LEU 36 (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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32C LEU* 3.0 37.6 + - + +
33C LYS* 3.6 6.7 - - - +
35C LEU* 1.3 77.9 - - + +
37C GLU* 1.3 63.3 + - - +
40C PHE* 3.1 59.1 + - + +
44C LEU* 4.6 10.5 - - + +
52C MET* 4.8 6.7 - - + -
53C VAL* 4.6 16.2 - - + -
56C PHE* 3.9 46.2 - - + -
76C MET* 4.6 4.7 - - - -
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Residues in contact with GLU 37 (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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33C LYS* 2.9 20.7 + - + +
34C GLU* 3.9 8.5 - - + +
36C LEU* 1.3 78.5 - - - +
38C LYS* 1.3 64.2 + - + +
41C ARG* 3.1 48.0 + - - +
47C PRO* 4.1 15.8 - - - +
48C ASP* 4.4 19.4 + - - +
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Residues in contact with LYS 38 (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* 3.1 34.3 - - - +
34C GLU* 3.1 36.8 + - - +
37C GLU* 1.3 85.2 - - + +
39C GLU* 1.3 67.1 + - + +
40C PHE 3.5 0.2 + - - -
41C ARG* 3.5 42.5 + - - +
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Residues in contact with GLU 39 (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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13C LEU* 3.6 21.8 - - + +
17C TYR* 2.7 32.4 + - + +
35C LEU* 2.9 35.4 + - + +
38C LYS* 1.3 78.6 - - - +
40C PHE* 1.3 79.4 + - + +
41C ARG 3.5 1.0 + - - -
2D THR* 3.6 16.7 - - - +
3D LEU* 2.8 33.4 + - + +
4D LEU* 3.8 19.4 + - - +
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Residues in contact with PHE 40 (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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35C LEU* 4.6 4.3 - - + -
36C LEU* 3.1 49.8 + - + +
39C GLU* 1.3 88.1 - - + +
41C ARG* 1.3 63.3 + - - +
42C GLN 3.3 2.7 - - - +
43C ILE* 3.6 31.0 - - + -
44C LEU* 3.4 36.8 + - + +
56C PHE* 5.9 0.2 - + - -
76C MET* 4.2 20.6 - - + -
77C VAL* 6.5 0.2 - - - -
80C LEU* 3.8 26.5 - - + -
103C 2PE 4.6 14.4 - - - -
3D LEU* 3.6 34.5 - - + -
4D LEU* 4.7 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