Contacts of the helix formed by residues 20 - 32 (chain C) in PDB entry 5D4P
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 HIS 20 (chain C).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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16C LEU* 4.6 3.0 - - + +
17C GLU* 3.0 41.4 + - + +
19C ALA* 1.3 90.1 - - + +
21C LYS* 1.3 65.0 + - - +
22C GLU 3.3 2.7 - - - -
23C PHE* 3.5 11.5 + - + +
24C ALA* 3.2 22.0 + - - +
85C PHE* 3.6 34.1 - + + -
89C HIS* 3.2 43.8 - + + +
204C BCT 5.5 2.7 - - - -
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Residues in contact with LYS 21 (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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43A SER* 4.9 7.5 + - - -
16C LEU* 5.0 0.2 - - - -
17C GLU 4.0 0.4 + - - -
18C GLY 3.0 17.9 + - - +
19C ALA 3.4 0.6 - - - -
20C HIS* 1.3 78.0 - - - +
22C GLU* 1.3 58.5 + - - +
24C ALA* 3.2 6.2 + - - +
25C THR* 2.9 35.1 + - + +
38C ILE* 3.4 36.2 - - + +
64C ILE* 3.9 22.9 - - + -
66C ILE* 4.9 1.1 - - + -
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Residues in contact with GLU 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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19C ALA 5.0 1.6 + - - -
20C HIS 3.3 0.6 - - - -
21C LYS* 1.3 76.6 - - - +
23C PHE* 1.3 61.1 + - - +
25C THR* 3.5 7.6 + - - -
26C ASP* 2.8 43.2 + - - +
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Residues in contact with PHE 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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20C HIS* 3.5 16.4 + - + +
21C LYS 3.4 0.4 - - - -
22C GLU* 1.3 79.0 - - - +
24C ALA* 1.3 62.0 + - + +
26C ASP* 3.6 7.9 - - + +
27C LEU* 3.1 40.2 + - + +
30C ARG* 5.4 10.0 + - - -
81C GLY 4.6 10.1 - - - -
82C PHE* 4.8 2.5 - + - -
84C PRO* 6.5 0.4 - - + -
85C PHE* 3.4 49.8 - + + -
204C BCT 4.0 21.5 - - - +
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Residues in contact with ALA 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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16C LEU* 4.1 16.2 - - + -
20C HIS 3.2 10.2 + - - +
21C LYS 3.2 8.8 + - - +
23C PHE* 1.3 84.1 - - + +
25C THR* 1.3 61.6 + - - +
27C LEU* 3.2 4.6 + - - +
28C LEU* 3.0 31.9 + - + +
66C ILE* 3.6 24.0 - - + -
82C PHE* 4.0 17.0 - - + -
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Residues in contact with THR 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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21C LYS* 2.9 37.7 + - + +
22C GLU* 3.5 9.0 + - - -
24C ALA* 1.3 74.0 - - - +
26C ASP* 1.3 64.4 + - - +
28C LEU* 3.3 8.7 + - + +
29C ASP* 2.9 38.7 + - - +
36C TYR* 3.2 46.0 + - + +
38C ILE* 4.2 4.3 - - + -
66C ILE* 4.4 7.9 - - + -
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Residues in contact with ASP 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 GLU* 2.8 31.0 + - - +
23C PHE* 3.6 8.2 - - + +
25C THR* 1.3 79.6 + - - +
27C LEU* 1.3 57.4 + - - +
29C ASP* 3.3 10.2 + - - +
30C ARG* 2.8 42.7 + - - +
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Residues in contact with LEU 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 PHE* 3.1 19.8 + - + +
24C ALA 3.2 8.5 + - - +
26C ASP* 1.3 79.9 - - - +
28C LEU* 1.3 61.3 + - - +
30C ARG* 3.0 36.4 + - + +
31C ALA* 3.0 24.1 + - + +
77C PRO 5.7 0.2 - - - +
78C LEU* 4.2 12.3 - - + +
81C GLY* 3.5 35.9 - - - +
82C PHE* 3.5 38.6 - - + -
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Residues in contact with LEU 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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12C LEU* 5.2 0.4 - - + -
14C ILE* 4.3 9.4 - - + -
24C ALA 3.0 20.0 + - - +
25C THR* 3.7 11.2 - - - +
27C LEU* 1.3 76.3 - - - +
29C ASP* 1.3 62.5 + - - +
31C ALA* 3.3 2.4 + - - +
32C GLY 3.2 4.5 + - - -
33C VAL* 3.1 51.7 + - + +
36C TYR* 4.2 23.1 - - + -
66C ILE* 3.6 31.4 - - + -
68C ALA* 4.3 14.1 - - + -
78C LEU* 4.0 21.1 - - + -
82C PHE* 4.2 12.8 - - + -
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Residues in contact with ASP 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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45A LYS* 3.4 32.7 - - - +
25C THR* 2.9 24.3 + - - +
26C ASP* 3.6 8.9 - - - +
28C LEU* 1.3 76.6 - - - +
30C ARG* 1.3 62.6 + - - +
32C GLY* 3.1 14.0 + - - -
33C VAL 4.5 7.0 - - - +
36C TYR* 3.8 11.6 + - - -
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Residues in contact with ARG 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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23C PHE* 5.4 10.9 + - - -
26C ASP* 2.8 30.8 + - - +
27C LEU* 3.0 45.9 - - + +
29C ASP* 1.3 74.6 - - - +
31C ALA* 1.3 60.4 + - - +
32C GLY* 3.5 0.7 + - - -
81C GLY* 5.9 0.2 - - - -
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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 LEU* 3.0 13.4 + - + +
28C LEU 3.7 3.1 - - - +
29C ASP 3.2 0.2 - - - -
30C ARG* 1.3 76.0 - - - +
32C GLY* 1.3 59.9 + - - +
33C VAL* 3.6 2.0 - - + -
74C LEU* 3.7 20.9 - - + +
77C PRO* 5.8 5.2 - - + -
78C LEU* 3.4 41.3 - - + +
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Residues in contact with GLY 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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29C ASP 3.1 14.1 + - - -
30C ARG 3.3 1.4 + - - -
31C ALA* 1.3 79.6 - - - +
33C VAL* 1.3 65.3 + - - +
34C LYS* 3.4 12.8 + - - +
71C PRO* 6.0 0.2 - - - +
74C LEU* 3.9 8.6 - - - +
106C PHE 5.1 1.6 - - - +
107C ARG* 5.5 1.7 - - - -
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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