Contacts of the strand formed by residues 65 - 72 (chain C) in PDB entry 5X11
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 LEU 65 (chain C).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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60C ILE* 3.4 5.3 - - - -
61C GLN* 3.1 43.9 + - + +
64C LYS* 1.3 75.5 - - - +
66C GLU* 1.3 70.2 + - - +
67C LYS* 4.6 1.2 - - + +
20M C 4.0 13.5 - - - +
21M A 3.9 40.8 - - - +
22M T 6.2 0.2 - - - -
9N G 3.5 25.1 - - + +
10N T 3.5 24.4 + - - +
11N A 4.0 15.5 - - - +
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Residues in contact with GLU 66 (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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58C THR* 3.7 26.1 - - + +
59C THR 3.4 5.6 - - - +
60C ILE* 5.6 3.8 - - + -
64C LYS 3.4 9.2 + - - +
65C LEU* 1.3 81.3 - - - +
67C LYS* 1.3 61.6 + - - +
68C LYS* 5.8 1.3 - - + -
21M A 4.1 1.7 - - - +
22M T 3.6 19.7 - - - +
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Residues in contact with LYS 67 (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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18C SER* 4.1 18.8 - - - -
21C ASP* 5.3 4.1 + - - -
57C ARG 3.7 0.3 - - - +
58C THR* 3.6 1.8 - - - +
59C THR* 2.7 64.6 + - + +
61C GLN* 3.7 25.6 + - + +
65C LEU* 4.6 3.8 - - + +
66C GLU* 1.3 77.6 - - - +
68C LYS* 1.3 63.5 + - - +
69C MET* 4.2 14.9 - - - +
21M A 2.6 49.4 + - - +
22M T 3.5 12.6 - - - +
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Residues in contact with LYS 68 (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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18C SER* 3.4 16.0 - - - -
46C LYS* 5.8 5.7 - - - +
56C PHE* 3.9 38.8 - - + -
57C ARG 3.8 4.9 - - - -
58C THR* 4.5 11.4 - - + +
66C GLU* 5.8 0.7 - - + -
67C LYS* 1.3 73.5 - - - +
69C MET* 1.3 61.5 + - - +
70C TYR* 3.4 44.3 + - + +
22M T 3.0 16.7 + - - +
23M G 2.6 35.8 + - - +
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Residues in contact with MET 69 (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 GLU* 3.3 60.8 - - + +
17C LEU* 3.8 4.9 - - - +
18C SER* 3.9 21.8 - - - +
21C ASP* 4.8 5.8 - - - +
56C PHE* 3.2 4.1 - - - -
57C ARG* 3.1 49.6 + - + +
59C THR* 4.0 21.1 - - + -
67C LYS* 4.2 18.8 - - - +
68C LYS* 1.3 70.7 - - - +
70C TYR* 1.3 62.7 + - - +
71C THR* 4.0 1.6 + - - -
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Residues in contact with TYR 70 (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* 3.3 26.2 - - + +
15C GLY 4.0 0.2 - - - +
16C GLU* 3.1 20.9 + - - -
17C LEU 2.9 23.2 + - - +
19C GLY 4.6 5.4 - - - -
42C TYR* 6.3 0.4 - + - -
45C LEU* 3.9 43.9 + - + +
46C LYS* 5.0 1.4 + - - -
49C THR* 3.8 5.5 + - - -
54C ILE* 3.4 30.7 - - + -
55C THR 3.2 7.4 - - - -
56C PHE* 3.6 31.7 - + + -
68C LYS* 3.4 47.9 + - + +
69C MET* 1.3 74.0 - - - +
71C THR* 1.3 61.3 + - - +
22M T 5.8 0.2 - - - -
23M G 4.6 5.0 + - - -
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Residues in contact with THR 71 (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* 4.6 4.3 - - - +
15C GLY* 5.3 4.0 - - - -
16C GLU* 4.2 18.6 + - - +
54C ILE* 3.1 20.4 - - - +
55C THR* 2.9 34.3 + - + -
69C MET 4.0 2.0 + - - -
70C TYR* 1.3 74.9 + - - +
72C LEU* 1.3 82.9 + - + +
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Residues in contact with LEU 72 (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 LEU* 3.5 45.1 - - + +
12C LEU* 4.0 13.3 + - + +
13C ARG* 3.6 26.5 - - + +
53C PHE 4.2 0.7 - - - +
54C ILE* 3.9 18.2 - - + -
55C THR* 5.2 1.5 - - - +
71C THR* 1.3 88.6 - - + +
73C THR* 1.3 65.8 + - - +
76C GLY 4.1 17.5 - - - +
77C LYS* 4.2 26.9 - - + -
80C LEU* 4.5 7.2 - - + -
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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