Contacts of the helix formed by residues 63 - 73 (chain C) in PDB entry 2CVD
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 GLN 63 (chain C).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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90B ALA* 3.4 22.0 - - - +
93B ASP* 3.6 20.1 - - + +
94B THR* 3.2 25.5 + - - +
97B ASP* 3.1 20.8 + - - -
52C PRO 3.9 6.7 + - - -
62C HIS* 1.3 91.1 + - - +
64C SER* 1.3 66.2 + - - +
65C LEU* 3.3 2.2 + - - +
66C ALA* 3.1 15.9 + - + +
67C ILE* 3.0 22.9 + - - +
2003C GSH 3.1 36.4 + - - +
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Residues in contact with SER 64 (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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14C ARG* 3.2 33.7 + - - +
17C ILE* 4.4 4.0 - - - +
18C ILE* 4.0 12.4 - - - +
52C PRO* 3.7 19.5 - - - +
63C GLN* 1.3 71.2 - - - +
65C LEU* 1.3 70.1 + - - +
67C ILE* 3.4 2.6 + - - +
68C ALA* 2.9 27.5 + - - +
152C TYR* 5.1 1.2 + - - -
2003C GSH 2.6 31.6 + - - -
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Residues in contact with LEU 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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93B ASP* 4.2 15.7 - - - +
17C ILE* 4.4 7.0 - - + -
63C GLN* 3.3 2.0 + - - +
64C SER* 1.3 86.8 + - - +
66C ALA* 1.3 59.9 + - - +
68C ALA* 3.7 3.1 - - - +
69C ARG* 2.9 38.5 + - - +
92C VAL* 3.5 32.5 - - + -
93C ASP* 4.0 11.2 - - - +
96C ASP* 3.7 33.2 - - + +
148C TRP* 3.7 18.3 - - + -
152C TYR* 4.0 21.8 - - + +
2003C GSH 4.6 2.4 + - - +
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Residues in contact with ALA 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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86B CYS* 3.6 12.0 - - - +
89B ASP* 3.7 12.7 - - + +
90B ALA* 3.7 27.1 - - - +
93B ASP* 4.5 3.2 + - - +
62C HIS 3.8 5.2 - - - +
63C GLN* 3.1 21.1 + - + +
65C LEU* 1.3 76.3 - - - +
67C ILE* 1.3 57.4 + - - +
69C ARG* 3.3 16.5 + - - +
70C TYR* 3.0 27.5 + - - +
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Residues in contact with ILE 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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86B CYS* 4.1 6.5 - - - -
18C ILE* 3.7 27.1 - - + -
52C PRO 4.3 2.5 - - - +
53C ILE* 4.2 4.9 - - - -
54C LEU* 3.6 43.1 - - + +
61C LEU* 3.7 35.7 - - + +
62C HIS* 3.7 15.3 - - - +
63C GLN 3.0 21.1 + - - +
64C SER 3.6 6.3 - - - +
66C ALA* 1.3 74.9 - - - +
68C ALA* 1.3 65.8 + - - +
70C TYR* 3.1 4.2 + - - +
71C LEU* 2.9 25.7 + - + +
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Residues in contact with ALA 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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17C ILE* 4.1 11.9 - - + -
18C ILE* 4.4 4.2 - - + +
21C ILE* 3.6 21.9 - - + +
64C SER 2.9 18.2 + - - +
65C LEU* 3.7 2.5 - - - +
66C ALA 3.3 0.2 - - - -
67C ILE* 1.3 76.4 - - - +
69C ARG* 1.3 63.8 + - - +
71C LEU* 3.3 5.2 + - - +
72C THR* 3.1 28.8 + - - +
148C TRP* 3.6 27.1 - - + -
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Residues in contact with ARG 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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69B ARG* 3.4 36.5 - - - +
89B ASP* 3.0 39.3 + - - +
93B ASP* 5.4 4.4 + - - -
65C LEU* 2.9 26.1 + - - +
66C ALA* 3.6 6.1 - - - +
68C ALA* 1.3 77.2 - - - +
70C TYR* 1.3 62.9 + - - +
72C THR* 3.1 19.4 + - - +
73C LYS* 3.2 33.6 + - + +
89C ASP* 2.9 34.7 + - - +
92C VAL* 5.5 1.2 - - - +
93C ASP* 4.9 9.3 + - - -
148C TRP* 4.0 23.3 - - + +
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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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82B GLU* 3.6 36.3 - - + +
83B MET* 3.4 43.9 - - + +
86B CYS* 3.9 20.0 - - + +
2C PRO* 5.6 1.2 - - - +
4C TYR* 4.6 9.2 + - - -
54C LEU* 5.2 1.1 - - + -
56C VAL* 4.2 16.2 - - + +
61C LEU* 3.9 19.3 - - + -
66C ALA 3.0 14.0 + - - +
67C ILE 3.4 7.4 - - - +
69C ARG* 1.3 78.1 - - - +
71C LEU* 1.3 83.6 + - + +
72C THR 3.4 0.2 + - - -
73C LYS* 3.4 24.1 + - + +
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Residues in contact with LEU 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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4C TYR* 4.0 22.7 - - + +
18C ILE* 3.7 32.1 - - + +
21C ILE* 3.8 19.5 - - + -
22C PHE* 3.7 32.8 - - + -
25C LEU* 3.6 18.8 - - + +
27C ILE* 5.6 4.3 - - + +
54C LEU* 4.2 2.2 - - + -
67C ILE* 2.9 26.8 + - + +
68C ALA* 3.7 5.6 - - - +
70C TYR* 1.3 91.7 - - + +
72C THR* 1.3 61.0 + - - +
73C LYS 3.4 1.6 + - - +
75C THR* 3.7 5.4 - - - +
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Residues in contact with THR 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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21C ILE* 3.7 31.6 - - + -
25C LEU* 5.0 0.4 - - - -
68C ALA 3.1 13.5 + - - +
69C ARG* 3.1 12.7 + - - +
71C LEU* 1.3 75.5 - - - +
73C LYS* 1.3 66.1 + - - +
74C ASN 3.3 0.3 + - - -
75C THR* 2.7 29.9 + - - -
77C LEU* 3.9 21.1 - - + -
78C ALA* 3.4 14.5 - - - +
148C TRP* 3.5 28.7 + - + -
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Residues in contact with LYS 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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69B ARG* 6.2 1.2 - - - +
73B LYS* 6.1 4.5 - - - +
82B GLU* 4.4 22.6 + - + +
85B GLN* 2.6 49.0 + - - +
86B CYS* 5.9 0.2 - - - +
89B ASP* 5.0 4.6 + - - -
69C ARG* 3.2 37.2 + - + +
70C TYR* 3.4 16.3 + - - +
71C LEU 3.4 3.1 - - - +
72C THR* 1.3 77.7 - - - +
74C ASN* 1.3 80.7 + - - +
75C THR* 3.3 7.1 + - - +
78C ALA* 4.7 5.6 - - + -
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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