Contacts of the strand formed by residues 67 - 74 (chain C) in PDB entry 6X0A
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 TYR 67 (chain C).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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16C ILE* 4.2 31.6 - - + +
31C PHE* 4.2 25.4 - + + -
35C ILE* 6.2 0.2 - - + -
63C THR* 3.7 4.3 - - - -
64C ILE* 2.9 40.7 + - + +
65C GLY 4.3 1.0 - - - +
66C ASN* 1.3 86.8 - - - +
68C LEU* 1.3 65.0 + - - +
83C ILE* 4.6 9.9 - - + -
84C VAL* 3.6 7.4 - - - +
85C HIS* 3.5 42.9 - + + +
22F ASN* 4.1 17.3 + - - +
23F ASP* 4.0 28.2 + - + +
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Residues in contact with LEU 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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52C ARG* 3.8 31.6 - - - +
55C ILE* 4.8 7.0 - - + -
61C ALA* 4.1 22.4 - - + -
62C LEU 3.5 2.0 - - - +
63C THR* 3.6 31.9 - - + -
67C TYR* 1.3 76.5 - - - +
69C ILE* 1.3 61.4 + - - +
70C LEU* 3.6 10.3 + - + +
83C ILE* 3.4 6.6 - - - +
84C VAL* 2.9 33.9 + - + +
85C HIS 5.3 0.4 - - - +
86C GLY* 4.0 23.3 - - - -
87C ALA 4.7 3.6 - - - +
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Residues in contact with ILE 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 ILE* 4.0 13.9 - - + +
38C ARG* 4.1 15.9 - - + -
39C ILE* 3.4 38.8 - - + +
42C LEU* 5.0 2.9 - - + -
61C ALA* 3.4 3.1 - - - -
62C LEU* 2.7 46.1 + - + +
64C ILE* 3.8 25.1 - - + -
68C LEU* 1.3 73.0 - - - +
70C LEU* 1.3 63.2 + - - +
71C TYR* 3.4 6.8 + - + -
80C ILE* 4.2 21.8 - - + -
82C ARG 3.7 7.4 - - - +
83C ILE* 4.4 11.7 - - + -
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Residues in contact with LEU 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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55C ILE* 3.6 48.7 - - + -
59C ALA* 5.3 5.6 - - + -
60C ARG 3.2 12.1 - - - +
61C ALA* 3.9 12.1 - - + -
68C LEU* 3.6 12.8 + - + +
69C ILE* 1.3 72.0 - - - +
71C TYR* 1.3 58.1 + - - +
80C ILE* 3.9 2.6 - - - +
81C VAL* 2.9 29.9 + - + -
82C ARG* 2.9 41.1 + - + +
84C VAL* 4.9 12.1 - - + +
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Residues in contact with TYR 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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42C LEU* 3.4 33.5 - - + +
46C PRO* 2.7 29.9 + - + -
49C GLY* 3.0 33.4 + - - -
59C ALA* 3.8 2.8 - - - +
60C ARG* 2.8 69.6 + - + +
61C ALA 3.8 7.0 - - - -
62C LEU* 4.2 3.1 - - + -
69C ILE* 3.5 12.6 - - + +
70C LEU* 1.3 75.2 - - - +
72C ARG* 1.3 66.6 + - - +
73C LEU* 4.4 6.3 - - + -
78C ILE* 4.0 12.3 - - + -
79C GLU 3.3 14.1 - - - +
80C ILE* 3.8 16.6 - - + -
81C VAL* 4.2 3.6 - - - +
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Residues in contact with ARG 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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58C ASP* 3.2 51.2 + - + +
59C ALA* 5.4 1.1 - - - +
60C ARG* 5.4 1.1 - - - -
71C TYR* 1.3 77.1 - - - +
73C LEU* 1.3 79.8 + - - +
74C ALA* 5.0 3.2 - - - +
78C ILE* 3.9 7.8 - - - +
79C GLU* 2.6 76.6 + - + +
81C VAL* 4.6 11.4 - - + +
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Residues in contact with LEU 73 (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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1C MET* 5.3 5.2 - - + -
46C PRO* 3.8 33.9 - - + +
47C GLU* 4.3 14.8 - - + +
58C ASP* 4.9 1.9 + - - +
60C ARG* 3.8 32.7 - - - +
71C TYR* 4.4 4.9 - - + -
72C ARG* 1.3 92.2 + - - +
74C ALA* 1.3 60.9 + - - +
77C TRP 4.4 0.4 - - - -
78C ILE* 4.2 20.0 - - + -
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Residues in contact with ALA 74 (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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1C MET* 3.9 5.7 - - - +
72C ARG* 4.1 5.1 + - - +
73C LEU* 1.3 75.5 - - - +
75C GLU* 1.3 67.3 + - + +
76C GLY 3.0 4.2 + - - -
77C TRP* 3.1 54.9 + - + +
79C GLU* 3.4 13.9 - - - +
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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