Contacts of the helix formed by residues 21 - 34 (chain C) in PDB entry 5DDP
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 LYS 21 (chain C).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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30B G 3.4 36.4 + - - +
31B G 2.7 39.1 + - - +
19C LYS 3.3 1.9 + - - +
20C ILE* 1.3 73.2 - - - +
22C LYS* 1.3 66.5 + - - +
23C ASP* 3.3 2.2 - - + +
24C GLU* 3.2 27.1 + - + +
25C LEU* 2.8 21.7 + - - +
46C ARG* 4.1 3.1 - - - +
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Residues in contact with LYS 22 (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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28B A 4.2 4.4 + - - -
29B A 2.8 46.0 + - - +
30B G 2.9 19.3 + - - +
43B C 5.9 0.4 + - - -
44B C 5.4 2.4 + - - -
20C ILE 3.6 2.5 + - - -
21C LYS* 1.3 70.8 - - - +
23C ASP* 1.3 58.6 + - - +
25C LEU* 3.4 3.8 + - - +
26C LYS* 3.0 45.1 + - + +
44C VAL* 3.3 41.4 + - + +
45C SER* 4.9 4.1 - - - +
46C ARG* 3.8 19.8 - - + +
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Residues in contact with ASP 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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30B G 4.9 0.2 + - - -
21C LYS* 3.3 2.7 - - + +
22C LYS* 1.3 77.8 - - - +
24C GLU* 1.3 68.0 + - - +
26C LYS* 3.4 11.5 + - - +
27C LYS* 2.9 66.1 + - - +
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Residues in contact with GLU 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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20C ILE* 5.1 7.4 - - + +
21C LYS* 3.2 32.4 + - + +
23C ASP* 1.3 80.5 + - - +
25C LEU* 1.3 51.1 + - - +
27C LYS* 3.3 5.9 + - - +
28C SER* 2.7 43.1 + - - +
77C TYR* 2.6 39.1 + - + +
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Residues in contact with LEU 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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16C LEU* 4.3 16.2 - - + -
17C ASN 5.4 1.1 - - - +
20C ILE* 3.6 40.1 - - + +
21C LYS 2.8 20.6 + - - +
22C LYS* 3.6 3.8 - - - +
24C GLU* 1.3 71.3 - - - +
26C LYS* 1.3 61.1 + - - +
28C SER* 4.4 3.1 - - - +
29C LEU* 2.8 51.3 + - + +
44C VAL* 3.8 27.6 - - + -
46C ARG* 6.1 2.5 - - + -
52C GLY 6.2 0.9 - - - +
53C GLN 4.7 10.1 - - - +
76C PHE* 3.7 20.0 - - + -
77C TYR* 5.7 0.7 - - - -
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Residues in contact with LYS 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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22C LYS* 3.0 32.1 + - + +
23C ASP* 3.6 16.6 - - - +
25C LEU* 1.3 75.6 - - - +
27C LYS* 1.3 65.0 + - + +
29C LEU* 3.2 2.4 + - - +
30C HIS* 3.0 20.7 + - - +
41C ASP* 5.9 0.7 - - - -
42C ILE* 3.4 43.5 + - + +
43C LEU* 4.6 4.9 - - - +
44C VAL* 3.7 41.3 + - + +
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Residues in contact with LYS 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 ASP* 2.9 51.1 + - - +
24C GLU* 3.8 5.4 - - - +
26C LYS* 1.3 78.4 - - + +
28C SER* 1.3 61.9 + - - +
30C HIS* 3.4 7.8 + - - +
31C ALA* 3.1 22.5 + - - +
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Residues in contact with SER 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 GLU* 2.7 26.3 + - - +
25C LEU* 4.0 1.6 - - - -
27C LYS* 1.3 69.4 - - - +
29C LEU* 1.3 65.7 + - - +
31C ALA* 3.4 7.0 + - - +
32C ILE* 3.1 25.6 + - - +
76C PHE* 3.8 21.6 - - - -
77C TYR* 2.8 29.3 + - - -
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Residues in contact with LEU 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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13C ILE* 4.4 8.3 - - + -
16C LEU* 5.1 4.3 - - + -
25C LEU* 2.8 41.2 + - + +
26C LYS 3.6 3.6 - - - +
28C SER* 1.3 72.5 - - - +
30C HIS* 1.3 62.2 + - - +
32C ILE* 3.3 4.9 + - + +
33C PHE* 2.8 56.5 + - + +
42C ILE* 4.1 22.9 - - + -
44C VAL* 4.3 1.3 - - + -
54C ALA* 3.6 31.0 - - + -
56C VAL* 4.4 7.4 - - + -
76C PHE* 3.8 24.9 - - + -
81C MET* 4.9 3.1 - - - -
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Residues in contact with HIS 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 LYS 3.0 10.8 + - - +
27C LYS* 3.6 11.9 - - - +
28C SER 3.3 0.4 - - - -
29C LEU* 1.3 77.5 - - - +
31C ALA* 1.3 57.5 + - - +
34C SER* 2.8 58.0 + - - -
39C ILE* 3.9 33.2 + - + +
42C ILE* 3.5 21.0 - - + +
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Residues in contact with ALA 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 LYS 3.1 14.0 + - - +
28C SER* 3.7 8.3 - - - +
29C LEU 3.3 0.2 - - - -
30C HIS* 1.3 80.8 + - - +
32C ILE* 1.3 61.7 + - + +
33C PHE 3.6 0.2 + - - -
34C SER* 3.9 10.5 + - - -
35C ARG* 5.0 3.8 + - - +
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Residues in contact with ILE 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 SER 3.1 15.4 + - - +
29C LEU* 3.3 11.4 - - + +
31C ALA* 1.3 79.7 - - - +
33C PHE* 1.3 91.2 + - + +
35C ARG* 3.9 19.5 + - - +
36C PHE* 3.8 14.2 - - - -
71C MET* 3.5 33.5 - - + +
74C PHE* 4.6 15.5 - - + -
76C PHE* 4.5 16.2 - - + -
81C MET* 5.2 1.1 - - - -
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Residues in contact with PHE 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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11C ILE* 4.0 7.9 - - + -
13C ILE* 3.5 26.5 - - + -
29C LEU* 2.8 26.5 + - + +
32C ILE* 1.3 98.8 - - + +
34C SER* 1.3 63.0 + - - +
35C ARG 3.2 2.9 - - - -
36C PHE* 3.3 20.5 + + - -
39C ILE* 3.7 13.7 - - + -
56C VAL* 4.4 11.2 - - + -
58C PHE* 3.5 23.3 - + + -
67C ALA* 3.8 27.8 - - + -
71C MET* 3.4 29.4 - - + -
81C MET* 3.3 29.2 - - + -
83C ILE* 4.4 0.7 - - + -
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Residues in contact with SER 34 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
30C HIS* 2.8 47.6 + - - -
31C ALA* 3.9 8.5 + - - -
32C ILE 3.7 0.4 - - - -
33C PHE* 1.3 69.2 - - - +
35C ARG* 1.3 61.6 + - - +
36C PHE 3.0 7.4 + - - -
37C GLY* 3.2 18.9 + - - +
39C ILE* 3.7 10.3 - - - +
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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