Contacts of the helix formed by residues 66 - 80 (chain B) in PDB entry 2CX6
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 PHE 66 (chain B).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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8B PHE* 3.8 37.2 - + + -
11B ILE* 4.2 6.7 - - + -
12B GLU 3.2 33.0 - - - -
13B SER* 3.7 22.0 - - - -
14B GLN* 3.5 25.8 - - + +
17B PHE* 4.9 0.4 - - + -
55B PHE* 5.7 1.1 - - + -
58B LEU* 4.5 3.1 - - + -
62B THR* 2.8 32.1 + - - +
63B ARG* 3.6 6.1 - - - +
64B ARG 3.2 0.2 - - - -
65B ARG* 1.3 96.6 - - + +
67B GLY* 1.3 64.2 + - - +
68B ALA 3.2 3.1 - - - -
69B LEU* 3.1 22.1 + - + +
70B ILE* 2.9 27.8 + - + +
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Residues in contact with GLY 67 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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63B ARG 3.3 8.8 + - - -
64B ARG* 3.2 13.4 + - - -
65B ARG 3.2 1.8 + - - -
66B PHE* 1.3 78.8 - - - +
68B ALA* 1.3 61.8 + - - +
70B ILE* 3.8 6.8 - - - +
71B LEU* 2.9 25.8 + - - +
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Residues in contact with ALA 68 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
14B GLN* 4.7 11.2 - - - +
35B LEU* 3.8 31.2 - - + +
65B ARG 4.9 1.4 + - - +
66B PHE 3.2 1.0 - - - -
67B GLY* 1.3 76.3 - - - +
69B LEU* 1.3 63.1 + - - +
71B LEU* 3.7 5.7 - - - +
72B LEU* 3.0 24.8 + - - +
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Residues in contact with LEU 69 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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8B PHE* 5.2 0.4 - - + -
14B GLN* 4.0 17.4 - - - +
17B PHE* 3.4 44.0 - - + -
18B TYR* 4.2 8.7 - - + +
35B LEU* 3.8 16.4 - - + -
38B LEU* 3.6 31.0 - - + -
55B PHE* 4.6 12.6 - - + -
66B PHE* 3.1 29.8 + - + +
68B ALA* 1.3 75.9 - - - +
70B ILE* 1.3 65.7 + - - +
72B LEU* 3.3 2.1 + - + +
73B PHE* 3.1 32.7 + - + -
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Residues in contact with ILE 70 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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55B PHE* 4.4 16.6 - - + -
58B LEU* 4.2 10.1 - - + -
63B ARG* 3.3 65.1 - - + +
66B PHE* 2.9 16.3 + - + +
67B GLY* 3.8 6.3 - - - +
69B LEU* 1.3 77.5 - - - +
71B LEU* 1.3 62.4 + - - +
73B PHE 3.5 0.2 + - - -
74B ASP* 2.9 41.2 + - - +
86B PHE* 3.8 18.2 - - + -
88B VAL* 4.7 7.6 - - + -
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Residues in contact with LEU 71 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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67B GLY 2.9 17.2 + - - +
68B ALA* 3.7 5.8 - - - +
70B ILE* 1.3 78.9 - - - +
72B LEU* 1.3 58.3 + - - +
74B ASP* 3.2 9.6 + - + +
75B GLU* 2.9 58.2 + - + +
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Residues in contact with LEU 72 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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35B LEU* 3.6 41.3 - - + +
38B LEU* 3.7 17.3 - - + -
39B TRP* 3.6 30.2 - - + +
42B LEU* 3.3 28.3 - - + -
68B ALA 3.0 17.5 + - - +
69B LEU* 3.8 4.0 - - - +
71B LEU* 1.3 77.2 - - - +
73B PHE* 1.3 67.6 + - + +
75B GLU* 3.5 10.0 + - - +
76B ALA* 3.0 23.6 + - - +
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Residues in contact with PHE 73 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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17B PHE* 3.7 32.1 - + - -
21B PHE* 3.9 15.3 - + - -
38B LEU* 3.8 23.1 - - + -
42B LEU* 3.6 29.6 - - + -
53B ILE* 3.9 29.2 - - + -
55B PHE* 4.0 14.1 - + - -
69B LEU* 3.1 28.2 + - + +
72B LEU* 1.3 78.5 - - + +
74B ASP* 1.3 66.1 + - - +
76B ALA* 3.2 3.4 + - - +
77B GLU* 3.0 23.4 + - - +
84B LEU* 4.3 8.8 - - + +
86B PHE* 3.6 29.7 - + + +
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Residues in contact with ASP 74 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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90A HIS* 5.1 11.2 - - - -
70B ILE* 2.9 39.1 + - - +
71B LEU* 3.7 10.9 - - + +
73B PHE* 1.3 75.6 - - - +
75B GLU* 1.3 64.7 + - + +
77B GLU* 3.2 11.4 + - - +
78B GLU* 3.2 20.3 + - - +
86B PHE* 3.3 22.7 - - - +
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Residues in contact with GLU 75 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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39B TRP* 4.3 12.4 - - + -
71B LEU* 2.9 47.0 + - + +
72B LEU* 3.8 9.1 - - - +
74B ASP* 1.3 79.5 - - + +
76B ALA* 1.3 55.2 + - - +
78B GLU* 3.2 8.5 + - - +
79B GLU* 3.0 35.2 + - + +
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Residues in contact with ALA 76 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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39B TRP* 3.8 18.3 - - + -
42B LEU* 3.9 21.1 - - + -
43B MSE 5.7 1.3 - - - -
72B LEU 3.0 17.3 + - - +
73B PHE* 3.2 6.0 + - - +
75B GLU* 1.3 72.9 - - - +
77B GLU* 1.3 61.1 + - - +
78B GLU 3.1 1.6 - - - -
79B GLU* 4.3 2.9 - - - +
80B LEU* 2.8 44.3 + - + +
84B LEU* 4.1 11.0 - - + -
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Residues in contact with GLU 77 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
90A HIS* 5.6 4.7 - - - -
73B PHE 3.0 13.1 + - - +
74B ASP* 3.2 14.6 + - - +
76B ALA* 1.3 78.6 - - - +
78B GLU* 1.3 61.7 + - - +
80B LEU* 3.8 0.4 - - - -
81B GLU* 3.5 2.3 + - - -
82B GLY* 3.3 26.0 + - - -
84B LEU* 3.0 25.7 - - + +
85B ARG* 3.2 29.3 + - - +
86B PHE* 3.3 33.0 + - - +
87B ASN* 5.7 0.7 - - - +
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Residues in contact with GLU 78 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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74B ASP 3.2 11.6 + - - +
75B GLU* 3.3 13.0 - - - +
77B GLU* 1.3 76.8 - - - +
79B GLU* 1.3 65.8 + - + +
81B GLU* 3.8 7.6 + - - +
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Residues in contact with GLU 79 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
39B TRP* 3.8 27.1 - - + -
43B MSE 4.1 21.4 - - + +
75B GLU* 3.0 22.8 + - + +
76B ALA* 3.4 3.6 + - - +
78B GLU* 1.3 77.2 - - + +
80B LEU* 1.3 62.0 + - - +
81B GLU* 3.1 14.9 + - - +
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Residues in contact with LEU 80 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
42B LEU* 3.5 23.6 - - + +
43B MSE 3.7 29.2 - - + +
45B ASP* 6.0 1.6 - - - +
49B LEU* 4.7 14.8 - - + -
76B ALA* 2.8 32.3 + - + +
77B GLU 3.8 0.7 - - - +
79B GLU* 1.3 77.2 - - + +
81B GLU* 1.3 76.0 + - - +
82B GLY 3.2 2.0 - - - -
83B HIS* 2.5 24.0 + - + +
84B LEU* 3.7 36.3 - - + +
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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