Contacts of the strand formed by residues 24 - 33 (chain C) in PDB entry 3KDO
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 ASP 24 (chain C).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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17C TYR* 2.4 30.0 + - - -
19C PRO* 3.3 8.7 - - + +
20C SER* 2.7 37.1 + - - +
22C LYS 3.9 0.2 - - - -
23C ARG* 1.3 82.2 - - - +
25C ILE* 1.3 62.3 + - - +
26C ILE* 4.1 2.8 - - + +
90C ALA* 4.1 18.7 - - + +
91C TYR 3.5 3.1 - - - +
92C PRO* 3.8 19.8 - - - +
127C TYR* 3.5 16.6 - - - -
129C PRO* 3.5 14.9 - - - +
23J ARG* 5.3 4.2 + - - -
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Residues in contact with ILE 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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23C ARG 3.9 0.4 + - - -
24C ASP* 1.3 71.7 - - - +
26C ILE* 1.3 62.8 + - - +
90C ALA* 3.3 3.8 - - - -
91C TYR* 2.7 53.3 + - + +
93C PHE* 4.1 12.3 - - - -
96C PHE* 3.5 35.2 - - + -
104C LEU* 3.9 8.3 - - + -
108C ILE* 5.5 3.1 - - + -
126C LEU* 4.2 15.0 - - + -
127C TYR 3.5 13.9 - - - +
128C PHE* 4.1 12.6 - - + -
129C PRO* 3.9 11.0 - - + -
132C LEU* 3.4 33.2 - - + -
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Residues in contact with ILE 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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19C PRO* 4.0 23.6 - - + -
20C SER 5.7 1.6 - - - +
21C LYS* 6.2 1.6 - - + -
24C ASP* 3.8 9.8 + - + +
25C ILE* 1.3 81.1 - - - +
27C ALA* 1.3 69.8 + - - +
28C VAL* 4.0 0.6 + - + -
75C TYR* 3.5 27.4 - - + +
88C ARG* 4.2 7.2 - - + -
89C ILE 3.3 9.6 - - - +
90C ALA* 4.7 2.5 - - + -
125C ASP 4.0 0.9 - - - +
126C LEU* 3.5 3.8 - - - +
127C TYR* 2.8 54.6 + - + +
352C LEU* 3.4 32.9 - - + +
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Residues in contact with ALA 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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25C ILE 4.2 0.4 + - - -
26C ILE* 1.3 73.2 - - - +
28C VAL* 1.3 61.7 + - - +
29C PHE* 3.4 27.5 + - + -
87C VAL 3.6 1.9 - - - +
88C ARG* 3.5 2.8 - - - -
89C ILE* 2.9 32.1 + - - -
91C TYR* 3.8 17.8 - - + -
108C ILE* 3.8 11.0 - - + -
123C LEU* 3.8 12.1 - - + -
125C ASP 3.7 4.3 - - - -
126C LEU* 4.1 4.7 - - + -
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Residues in contact with VAL 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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26C ILE* 4.5 0.7 - - + +
27C ALA* 1.3 75.0 - - - +
29C PHE* 1.3 58.3 + - - +
86C ILE* 3.6 28.3 - - + -
87C VAL 3.7 3.4 - - - +
88C ARG* 4.3 13.9 - - + +
123C LEU* 3.5 3.9 - - - +
124C GLU* 2.6 38.7 + - + +
125C ASP* 3.0 20.4 + - + +
349C VAL 4.4 0.9 - - - +
350C PHE 3.3 29.2 - - - +
352C LEU* 3.7 34.8 - - + -
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Residues in contact with PHE 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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27C ALA* 3.4 27.8 - - + -
28C VAL* 1.3 74.6 - - - +
30C ARG* 1.3 59.3 + - - +
31C VAL* 3.6 18.7 + - + -
46C VAL* 4.0 4.3 - - + -
85C TRP 3.5 0.9 - - - +
86C ILE* 3.3 4.4 - - - +
87C VAL* 2.8 40.8 + - + +
89C ILE* 3.7 30.3 - - + -
91C TYR* 3.9 7.2 - - - -
108C ILE* 3.4 21.1 - - + -
112C ILE* 3.6 26.2 - - + -
113C PHE* 5.2 2.0 - + - -
121C LEU* 3.7 21.5 - - + -
122C ARG 3.3 3.6 - - - -
123C LEU* 3.6 33.4 - - + -
124C GLU* 4.3 2.9 - - - -
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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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29C PHE* 1.3 69.2 - - - +
31C VAL* 1.3 60.3 + - - +
32C THR* 3.9 1.1 + - - +
80C MET* 3.8 18.4 - - - +
82C ASP* 2.6 30.1 + - - -
84C SER* 3.0 23.6 + - - +
85C TRP 3.3 5.8 - - - +
86C ILE* 4.1 12.6 - - + -
120C GLY 3.9 1.2 - - - +
121C LEU* 3.5 6.7 + - - -
122C ARG* 2.8 34.2 + - + +
124C GLU* 3.2 22.8 + - + +
292C PRO* 3.4 27.0 + - - +
293C TYR* 3.5 25.8 + - + +
350C PHE* 3.5 25.5 - - - -
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Residues in contact with VAL 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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29C PHE* 3.8 14.1 - - + -
30C ARG* 1.3 72.1 - - - +
32C THR* 1.3 65.4 + - - +
33C PRO* 3.6 4.2 - - - +
39C ILE* 3.7 15.7 - - + +
42C ALA* 3.8 33.0 - - + -
43C ALA* 5.4 2.2 - - - -
46C VAL* 4.7 7.4 - - + -
84C SER* 3.2 1.6 - - - -
85C TRP 2.6 39.2 + - - +
87C VAL* 3.9 20.4 - - + -
89C ILE* 6.3 0.4 - - + -
118C VAL* 4.0 16.2 - - + -
120C GLY 4.0 2.2 - - - -
121C LEU* 3.7 20.2 - - + -
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Residues in contact with THR 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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30C ARG* 4.8 1.4 + - - +
31C VAL* 1.3 74.4 - - - +
33C PRO* 1.3 57.4 - - - +
83C GLY* 3.7 16.2 - - - +
84C SER* 3.1 21.0 - - - -
118C VAL* 3.6 1.9 - - - -
119C LYS* 2.7 64.5 + - + -
120C GLY* 3.0 27.4 + - - +
293C TYR* 4.3 13.3 + - - +
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Residues in contact with PRO 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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31C VAL* 3.6 8.7 - - + +
32C THR* 1.3 96.9 - - - +
34C ALA* 1.3 64.3 + - - +
35C GLU* 3.9 0.3 + - - +
37C TYR* 3.3 29.6 - - + +
38C THR 4.2 0.7 - - - +
39C ILE* 4.3 19.7 - - + +
42C ALA* 3.8 20.2 - - + -
83C GLY 3.6 15.9 - - - +
85C TRP* 4.5 6.3 - - + +
117C ARG 3.7 6.5 - - - +
118C VAL* 4.4 0.2 - - - -
119C LYS* 3.9 7.4 + - - -
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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