Contacts of the strand formed by residues 77 - 85 (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 TRP 77 (chain C).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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1C MET* 3.0 12.5 - - - +
2C PRO* 3.5 23.8 - - + +
4C ILE* 3.9 22.2 - - + +
74C ALA* 3.1 39.5 + - + +
75C GLU* 3.3 27.7 - - + -
76C GLY* 1.3 82.2 - - - +
78C ILE* 1.3 58.5 + - - +
79C GLU* 2.9 41.3 + - + +
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Residues in contact with ILE 78 (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 19.7 - - + -
2C PRO 3.0 11.3 + - - +
3C ILE* 3.6 15.0 - - + +
4C ILE* 3.0 29.6 + - - +
42C LEU* 3.4 42.2 - - + +
43C ALA* 3.9 9.0 - - - +
46C PRO* 4.9 2.5 - - + -
71C TYR* 4.0 19.5 - - + -
72C ARG 3.9 11.2 - - - +
73C LEU* 4.2 14.6 - - + -
77C TRP* 1.3 77.4 - - - +
79C GLU* 1.3 64.0 + - - +
80C ILE* 4.4 14.4 - - + -
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Residues in contact with GLU 79 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
4C ILE* 3.5 13.2 - - + +
71C TYR* 3.3 5.2 - - - +
72C ARG* 2.6 81.6 + - + +
74C ALA* 3.4 13.2 - - + +
77C TRP* 2.9 39.2 + - + +
78C ILE* 1.3 71.0 - - - +
80C ILE* 1.3 64.2 + - - +
81C VAL* 3.4 8.7 + - + +
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Residues in contact with ILE 80 (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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3C ILE* 3.8 22.4 - - + -
4C ILE 2.7 14.0 + - - +
5C ARG* 4.0 10.8 - - + -
6C SER* 3.0 25.5 + - - -
9C ALA* 3.7 4.5 - - + +
13C LEU* 6.3 0.4 - - + -
39C ILE* 3.8 30.5 - - + -
42C LEU* 4.0 12.3 - - + -
69C ILE* 4.2 11.4 - - + -
70C LEU 4.1 5.6 - - - +
71C TYR* 3.8 20.0 - - + -
78C ILE* 4.4 5.8 - - + -
79C GLU* 1.3 69.9 - - - +
81C VAL* 1.3 61.3 + - - +
83C ILE* 3.8 28.0 - - + -
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Residues in contact with VAL 81 (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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6C SER* 2.7 30.3 + - - +
9C ALA* 3.3 2.4 - - - +
70C LEU* 2.9 22.6 + - + +
71C TYR* 4.6 2.7 - - - -
72C ARG* 4.6 18.6 - - + +
79C GLU* 3.9 19.5 - - + +
80C ILE* 1.3 73.4 - - - +
82C ARG* 1.3 78.1 + - + +
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Residues in contact with ARG 82 (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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8C ALA* 3.6 27.2 - - - +
9C ALA* 4.0 4.3 - - - +
12C ASP* 2.5 39.4 + - - +
69C ILE* 3.7 1.0 - - - +
70C LEU* 2.9 43.4 + - + +
80C ILE* 3.8 1.0 - - - +
81C VAL* 1.3 102.8 - - + +
83C ILE* 1.3 71.4 + - - +
84C VAL* 3.8 29.3 - - + +
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Residues in contact with ILE 83 (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 ALA* 3.7 31.2 - - + +
12C ASP* 2.8 33.4 + - + +
13C LEU* 3.9 23.8 - - + -
16C ILE* 3.5 30.3 - - + +
35C ILE* 4.9 9.2 - - + -
39C ILE* 5.0 2.0 - - + -
64C ILE* 5.7 0.4 - - + -
67C TYR* 4.6 12.5 - - + -
68C LEU 3.4 8.5 - - - +
69C ILE* 4.4 21.1 - - + -
80C ILE* 3.8 14.1 - - + -
82C ARG* 1.3 81.9 - - - +
84C VAL* 1.3 58.7 + - - +
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Residues in contact with VAL 84 (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 ASP* 4.9 0.2 - - - -
67C TYR* 3.6 5.5 - - - -
68C LEU* 2.9 32.4 + - + +
70C LEU* 4.9 11.6 - - + +
82C ARG* 3.8 43.2 - - + +
83C ILE* 1.3 78.4 - - - +
85C HIS* 1.3 85.2 + - + +
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Residues in contact with HIS 85 (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 ASN* 3.8 17.5 + - + +
67C TYR* 3.5 33.9 - + + +
68C LEU* 5.3 1.4 - - - +
84C VAL* 1.3 90.8 - - + +
86C GLY* 1.3 93.6 + - - +
87C ALA 5.3 0.4 - - - -
88C ARG* 3.6 39.4 + - + +
22F ASN 3.0 21.9 + - - -
23F ASP 3.0 22.9 + - - -
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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