Contacts of the helix formed by residues 67 - 81 (chain C) in PDB entry 6P7B
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 PRO 67 (chain C).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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64A PHE* 4.2 11.4 - - + -
10C ILE* 3.7 23.6 - - + -
65C LYS 4.9 0.2 - - - +
66C SER* 1.3 82.6 - - - +
68C ASN* 1.3 67.8 + - - +
69C SER 3.0 3.1 - - - -
70C LYS* 2.9 58.3 + - + +
71C ILE* 3.0 6.4 + - - +
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Residues in contact with ASN 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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8C ILE* 3.0 38.0 + - + +
9C GLY* 3.2 23.7 - - - -
10C ILE 3.8 5.4 + - - -
11C LYS* 4.0 6.3 - - - +
62C GLN* 3.7 31.7 + - + +
66C SER* 3.0 16.2 + - - +
67C PRO* 1.3 79.5 - - - +
69C SER* 1.3 56.0 + - - +
71C ILE* 3.3 6.2 + - - +
72C ILE* 2.9 32.9 + - - +
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Residues in contact with SER 69 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
64A PHE* 4.1 10.6 - - - -
62C GLN* 4.7 1.4 - - - +
63C GLY 4.6 6.7 - - - -
64C PHE* 4.8 6.2 - - - +
66C SER* 3.0 18.9 + - - -
68C ASN* 1.3 76.5 - - - +
70C LYS* 1.3 65.0 + - - +
72C ILE* 3.1 2.9 + - - +
73C TYR* 3.0 37.8 + - - -
16E T 3.8 38.1 - - - -
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Residues in contact with LYS 70 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
64A PHE* 4.7 8.1 - - + -
73A TYR* 3.4 61.8 + - + +
10C ILE* 4.1 13.3 - - - +
41C TRP* 3.5 41.0 - - + +
67C PRO* 2.9 43.2 + - + +
69C SER* 1.3 80.2 + - - +
71C ILE* 1.3 60.4 + - + +
73C TYR* 3.5 3.1 + - - +
74C PHE* 2.9 28.8 + - - +
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Residues in contact with ILE 71 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
8C ILE* 3.7 25.1 - - + -
9C GLY 4.6 1.3 - - - +
10C ILE* 4.2 21.8 - - + -
37C TRP* 3.7 34.8 - - + -
41C TRP* 4.1 16.2 - - + -
45C VAL* 4.1 13.7 - - + -
67C PRO 3.0 12.9 + - - +
68C ASN* 3.5 11.9 - - - +
69C SER 3.2 0.2 - - - -
70C LYS* 1.3 81.4 - - + +
72C ILE* 1.3 59.5 + - - +
74C PHE* 3.3 6.0 + - - +
75C ILE* 2.9 45.6 + - + +
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Residues in contact with ILE 72 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
8C ILE* 4.7 8.3 - - + -
59C LEU* 4.1 21.2 - - + +
60C GLU 3.6 24.5 - - - +
62C GLN* 4.1 7.9 - - + +
68C ASN 2.9 19.1 + - - +
69C SER* 3.1 8.2 + - - +
71C ILE* 1.3 75.5 - - - +
73C TYR* 1.3 60.4 + - + +
75C ILE* 3.1 5.2 + - - +
76C LYS* 3.0 32.6 + - + +
88C VAL* 4.0 29.8 - - + -
16E T 3.2 40.8 - - + +
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Residues in contact with TYR 73 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
41A TRP* 3.6 34.3 - + - -
42A GLU* 4.3 5.2 - - - -
70A LYS* 3.6 43.0 - - + +
73A TYR* 4.1 5.6 - - + -
74A PHE* 3.6 14.2 - - + +
69C SER* 3.0 34.4 + - - +
70C LYS* 4.0 4.5 - - - +
72C ILE* 1.3 72.8 - - - +
74C PHE* 1.3 66.1 + - - +
76C LYS* 3.3 22.8 + - + +
77C GLY 3.0 18.9 + - - -
16E T 2.2 71.8 + + + -
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Residues in contact with PHE 74 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
73A TYR* 3.6 12.9 + - + +
76A LYS* 4.0 11.0 - - + -
77A GLY* 3.5 30.3 - - - -
80A TYR* 4.1 21.3 - + + -
41C TRP* 3.8 25.6 - + + -
42C GLU* 3.8 38.8 - - + -
45C VAL* 3.6 21.8 - - + -
46C ALA 4.5 1.6 - - - -
70C LYS 2.9 18.4 + - - +
71C ILE 3.5 4.5 - - - +
73C TYR* 1.3 76.5 - - - +
75C ILE* 1.3 70.5 + - + +
77C GLY 3.4 0.5 + - - -
78C PHE* 2.8 43.3 + + + +
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Residues in contact with ILE 75 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
37C TRP* 6.2 0.7 - - + -
45C VAL* 3.3 34.8 - - + -
49C LEU* 3.4 18.6 - - + -
57C VAL* 4.4 4.7 - - + -
59C LEU* 4.0 26.0 - - + -
71C ILE* 2.9 29.3 + - + +
72C ILE 3.1 6.7 + - - +
74C PHE* 1.3 82.2 - - + +
76C LYS* 1.3 63.7 + - - +
78C PHE* 3.2 4.9 + - + +
79C PHE* 3.0 35.6 + - + +
86C VAL* 3.6 23.0 - - + +
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Residues in contact with LYS 76 (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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42A GLU* 3.5 25.8 + - - +
74A PHE* 4.1 11.2 - - + -
59C LEU* 6.0 0.4 - - + -
61C LYS* 5.7 1.2 - - - +
72C ILE* 3.0 19.2 + - + +
73C TYR* 3.6 31.0 - - + +
75C ILE* 1.3 76.8 - - + +
77C GLY* 1.3 57.1 + - - +
79C PHE 3.8 0.5 - - - -
80C TYR* 2.9 33.8 + - + +
86C VAL* 4.1 27.5 - - + +
88C VAL* 4.0 26.6 - - + +
15E T 4.9 10.7 - - - +
16E T 4.7 12.5 + - - +
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Residues in contact with GLY 77 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
74A PHE* 3.6 37.8 - - - -
77A GLY 3.4 6.5 - - - -
78A PHE* 3.1 19.3 - - - +
73C TYR 3.0 11.1 + - - -
74C PHE 3.8 1.8 - - - -
76C LYS* 1.3 76.1 - - - +
78C PHE* 1.3 63.8 + - - +
80C TYR* 3.3 13.0 + - - +
81C ASN* 4.4 0.9 + - - +
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Residues in contact with PHE 78 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
77A GLY* 3.2 20.3 + - - +
80A TYR* 4.0 25.6 - + + -
81A ASN* 3.9 18.7 + - - -
46C ALA* 3.8 28.5 - - + -
49C LEU* 4.9 5.2 - - + -
50C THR* 3.6 34.1 - - + -
74C PHE* 2.8 32.3 + + + +
75C ILE* 3.2 7.4 + - - +
77C GLY* 1.3 79.7 - - - +
79C PHE* 1.3 89.1 + + - +
80C TYR 3.5 0.2 + - - -
81C ASN* 3.6 16.6 - - - +
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Residues in contact with PHE 79 (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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49C LEU* 3.6 50.0 - - + -
50C THR* 4.8 5.6 - - + -
54C PRO* 4.3 8.7 - - + -
57C VAL* 3.7 19.3 - - + -
75C ILE* 3.0 17.6 + - + +
76C LYS 3.8 1.3 - - - -
78C PHE* 1.3 96.1 - + - +
80C TYR* 1.3 64.8 + - - +
81C ASN* 3.3 3.3 + - - -
82C SER 3.5 16.0 + - - +
84C THR* 3.1 47.4 + - + +
86C VAL* 3.6 29.4 - - + -
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Residues in contact with TYR 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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42A GLU* 3.9 27.4 - - + -
43A ARG* 3.2 35.4 - - + +
46A ALA* 3.9 17.5 - - + -
74A PHE* 3.8 16.2 - + - -
78A PHE* 3.9 20.2 - + + -
76C LYS* 2.9 16.9 + - + +
77C GLY* 3.5 12.8 - - - +
78C PHE 3.3 2.0 - - - -
79C PHE* 1.3 77.3 - - - +
81C ASN* 1.3 70.0 + - - +
82C SER* 3.2 1.9 + - - -
86C VAL* 6.1 0.9 - - - -
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Residues in contact with ASN 81 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
78A PHE* 3.5 40.3 + - - +
81A ASN* 2.7 35.1 + - - +
77C GLY 4.5 0.3 - - - +
78C PHE 3.6 9.4 - - - +
79C PHE 3.3 0.4 - - - -
80C TYR* 1.3 81.4 - - - +
82C SER* 1.3 68.7 + - - +
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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