Contacts of the strand formed by residues 38 - 45 (chain C) in PDB entry 2CKE
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 GLU 38 (chain C).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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29C LYS* 3.0 34.8 + - - -
30C CYS 3.4 8.5 - - - +
31C ARG* 4.3 29.7 + - + +
36C GLY 3.9 2.7 + - - +
37C LEU* 1.3 75.0 - - - +
39C TYR* 1.3 70.5 + - - +
95C LEU* 3.8 29.6 + - + +
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Residues in contact with TYR 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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285B VAL* 4.2 6.9 - - - +
288B GLU* 4.2 7.9 + - - -
13C TYR* 4.2 11.0 - + - -
29C LYS* 3.8 3.6 - - - -
30C CYS* 2.7 37.3 + - - +
32C GLU* 3.9 9.4 + - - -
35C THR* 5.2 0.3 + - - -
37C LEU* 3.3 48.3 - - + +
38C GLU* 1.3 75.6 - - - +
40C ALA* 1.3 60.6 + - - +
80C HIS* 3.3 58.3 + + + -
92C ILE* 3.5 19.1 - - + -
93C LEU 3.5 15.0 - - - +
94C GLU* 4.4 6.7 - - - -
95C LEU* 4.0 14.2 - - - +
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Residues in contact with ALA 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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19C LEU* 4.4 2.0 - - + -
27C VAL* 4.1 12.8 - - + -
28C LYS 3.4 7.6 - - - +
29C LYS* 4.7 0.2 - - - +
30C CYS* 4.1 1.6 - - - -
39C TYR* 1.3 74.4 - - - +
41C ALA* 1.3 60.4 + - - +
42C LYS 3.9 0.6 + - - -
91C LEU 3.5 1.9 - - - +
92C ILE* 3.4 1.2 - - - -
93C LEU* 2.6 45.5 + - + +
95C LEU* 4.2 7.5 - - + +
1302C IQU 3.6 36.6 - - + +
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Residues in contact with ALA 41 (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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15C ILE* 4.2 8.5 - - + -
26C ILE 3.5 0.5 - - - +
27C VAL* 4.4 1.6 - - - -
28C LYS 2.8 34.5 + - - +
30C CYS* 3.8 10.9 - - - -
40C ALA* 1.3 69.9 - - - +
42C LYS* 1.3 60.0 + - - +
43C PHE* 3.5 28.5 - - + -
90C VAL* 3.9 4.5 - - + -
91C LEU 3.5 4.9 - - - -
92C ILE* 3.5 23.6 - - + -
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Residues in contact with LYS 42 (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 ALA* 4.0 25.4 - - + -
26C ILE 3.9 3.4 - - - -
27C VAL* 4.3 20.6 - - + +
40C ALA 3.9 1.0 + - - -
41C ALA* 1.3 69.7 - - - +
43C PHE* 1.3 60.7 + - - +
44C ILE* 3.4 22.3 + - + +
64C GLU* 3.2 28.2 + - - +
89C VAL 3.4 1.4 - - - +
90C VAL* 4.3 0.9 - - - -
91C LEU* 2.7 42.5 + - + +
93C LEU* 4.1 23.3 - - + -
161C ASP* 3.9 30.5 + - - +
162C PHE 4.8 0.2 - - - +
163C GLY* 4.9 1.4 - - - +
1302C IQU 5.4 8.7 + - + -
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Residues in contact with PHE 43 (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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9C VAL* 4.2 12.8 - - + -
15C ILE* 4.1 25.1 - - + -
24C PHE 3.9 0.5 - - - +
25C ALA* 3.1 5.1 - - - -
26C ILE* 2.9 47.9 + - + +
28C LYS* 3.8 27.1 - - + -
41C ALA* 3.5 27.4 - - + -
42C LYS* 1.3 69.3 - - - +
44C ILE* 1.3 60.9 + - - +
45C LYS 4.0 0.6 + - - -
85C ASN* 5.8 2.2 - - - -
88C ASP* 4.0 21.3 - - - +
89C VAL 3.8 3.6 - - - -
90C VAL* 3.3 33.7 - - + +
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Residues in contact with ILE 44 (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 PHE 3.7 5.8 - - - +
25C ALA* 4.1 7.4 - - + -
42C LYS* 4.0 30.1 - - + +
43C PHE* 1.3 73.5 - - - +
45C LYS* 1.3 65.4 + - - +
46C LYS* 3.4 1.0 + - - +
56C VAL* 3.5 37.2 - - + -
61C ILE* 3.9 21.9 - - + +
64C GLU* 3.9 24.9 - - - +
88C ASP* 3.3 3.5 - - - -
89C VAL* 2.8 42.9 + - + +
91C LEU* 4.4 17.9 - - + -
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Residues in contact with LYS 45 (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 PHE* 3.0 21.7 + - + +
26C ILE* 6.4 1.1 - - + -
43C PHE 4.0 1.4 + - - -
44C ILE* 1.3 74.6 - - - +
46C LYS* 1.3 63.9 + - - +
48C GLN* 5.1 13.9 - - - +
54C ARG* 5.0 15.3 - - + +
55C GLY* 3.3 13.9 - - - +
56C VAL* 2.8 32.4 + - - +
87C THR* 4.3 22.5 - - - +
88C ASP* 3.4 19.9 + - - +
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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