Contacts of the helix formed by residues 62 - 72 (chain C) in PDB entry 5LSW
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 THR 62 (chain C).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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26C ILE* 3.7 12.1 + - + +
29C LEU* 3.8 27.9 - - + +
30C SER* 5.3 3.2 + - - -
56C LEU* 3.5 35.0 - - + +
59C SER* 2.6 33.9 + - - -
60C PHE 3.1 2.9 + - - -
61C GLY* 1.3 74.9 - - - +
63C ILE* 1.3 69.6 + - + +
65C ALA* 3.0 17.0 + - - +
66C LEU* 3.1 16.9 + - + +
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Residues in contact with ILE 63 (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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56C LEU* 4.1 15.9 - - + +
57C TRP* 3.5 69.8 - - + +
59C SER 4.5 1.0 + - - +
61C GLY 3.5 0.2 - - - -
62C THR* 1.3 75.0 - - - +
64C ALA* 1.3 64.0 + - - +
66C LEU* 3.1 18.3 + - + +
67C LEU* 3.0 33.4 + - + +
97C LEU* 5.1 5.8 - - + -
100C VAL* 4.6 7.2 - - + -
115C ILE* 4.0 16.2 - - + -
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Residues in contact with ALA 64 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
61C GLY* 3.4 14.4 + - - +
62C THR 3.2 0.2 - - - -
63C ILE* 1.3 78.7 - - - +
65C ALA* 1.3 61.3 + - - +
67C LEU* 3.5 12.3 + - - +
68C GLN* 3.0 24.1 + - - +
301C SO4 4.5 13.8 + - - +
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Residues in contact with ALA 65 (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 LEU* 3.7 29.8 - - + +
30C SER* 4.8 3.1 - - - -
35C ARG* 3.7 17.2 + - - +
61C GLY 2.9 14.7 + - - +
62C THR* 3.0 12.1 + - - +
64C ALA* 1.3 77.1 - - - +
66C LEU* 1.3 62.2 + - + +
68C GLN* 3.3 10.1 + - - +
69C GLU* 3.1 25.4 + - - +
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Residues in contact with LEU 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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29C LEU* 4.4 10.3 - - + -
35C ARG* 5.9 1.1 - - - -
39C LEU* 3.5 31.2 - - + -
56C LEU* 5.0 4.7 - - + -
62C THR* 3.1 25.1 + - + +
63C ILE* 3.6 18.2 - - + +
65C ALA* 1.3 78.4 - - + +
67C LEU* 1.3 62.7 + - - +
69C GLU* 3.1 16.9 + - + +
70C ILE* 3.1 17.2 + - - +
93C ALA* 4.0 12.7 - - + +
96C LEU* 4.0 28.9 - - + +
97C LEU* 3.9 30.1 - - + -
100C VAL* 6.0 0.2 - - + -
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Residues in contact with LEU 67 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
63C ILE* 3.0 29.7 + - + +
64C ALA* 4.0 8.7 - - - +
66C LEU* 1.3 72.5 - - - +
68C GLN* 1.3 59.8 + - - +
70C ILE* 3.1 9.3 + - + +
71C VAL* 2.9 33.6 + - + +
97C LEU* 4.3 15.5 - - + -
113C ALA* 6.1 0.9 - - + +
115C ILE* 4.0 34.8 - - + -
118C PHE* 4.1 37.0 - - + -
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Residues in contact with GLN 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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35C ARG* 3.8 31.0 + - - +
64C ALA 3.0 13.7 + - - +
65C ALA* 3.4 12.0 - - - +
67C LEU* 1.3 77.8 - - - +
69C GLU* 1.3 57.1 + - - +
71C VAL* 3.8 5.0 - - - +
72C ASN* 2.9 54.4 + - - +
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Residues in contact with GLU 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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35C ARG* 2.9 27.7 + - - -
39C LEU* 4.0 14.7 - - + +
65C ALA 3.1 17.6 + - - +
66C LEU* 3.3 12.1 - - - +
68C GLN* 1.3 77.7 - - - +
70C ILE* 1.3 62.6 + - - +
72C ASN* 3.4 22.9 + - - +
73C ILE* 3.9 5.7 + - - +
89C ARG* 2.8 56.2 + - - +
90C VAL* 3.9 13.6 - - + +
93C ALA* 4.1 14.1 - - + -
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Residues in contact with ILE 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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66C LEU 3.1 10.3 + - - +
67C LEU* 3.1 12.2 + - + +
69C GLU* 1.3 76.7 - - - +
71C VAL* 1.3 64.8 + - + +
73C ILE* 3.2 24.4 - - - +
74C TYR* 3.8 9.7 - - + +
90C VAL* 3.9 13.2 - - + -
93C ALA* 5.1 4.5 - - + -
94C LEU* 3.6 22.9 - - + -
97C LEU* 3.4 32.3 - - + -
118C PHE* 3.6 35.9 - - + +
119C LEU* 3.9 10.3 - - + -
122C PHE* 3.7 13.0 - - + -
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Residues in contact with VAL 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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67C LEU 2.9 19.1 + - - +
68C GLN* 4.1 5.2 - - - +
70C ILE* 1.3 76.8 - - + +
72C ASN* 1.3 64.8 + - - +
74C TYR* 3.0 45.4 + - + +
75C PRO* 3.8 3.5 - - - +
118C PHE* 3.9 32.1 - - + -
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Residues in contact with ASN 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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35C ARG* 5.1 2.4 - - - +
68C GLN* 2.9 49.2 + - - +
69C GLU* 3.5 21.9 + - - +
70C ILE 3.1 0.6 - - - -
71C VAL* 1.3 79.1 - - - +
73C ILE* 1.3 60.7 + - + +
75C PRO* 3.5 16.6 - - - +
76C SER* 5.1 0.7 + - - -
86C GLN* 5.7 0.9 + - - -
89C ARG* 5.7 0.6 - - - +
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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