Contacts of the helix formed by residues 66 - 80 (chain A) 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 A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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8A PHE* 3.6 35.2 - + + -
11A ILE* 4.2 5.8 - - + -
12A GLU* 3.7 19.1 - - - -
13A SER* 3.4 32.8 - - - -
14A GLN* 3.6 27.1 - - + +
17A PHE* 5.2 0.2 - - + -
55A PHE* 5.8 0.2 - - + -
58A LEU* 4.3 6.1 - - + -
62A THR* 2.9 49.4 + - + +
63A ARG* 3.4 6.1 - - - +
64A ARG 3.2 0.2 - - - -
65A ARG* 1.3 90.9 - - + +
67A GLY* 1.3 63.7 + - - +
68A ALA 3.3 3.1 - - - -
69A LEU* 3.1 26.7 + - + +
70A ILE* 3.1 13.3 + - + +
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Residues in contact with GLY 67 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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63A ARG 3.1 11.5 + - - -
64A ARG* 3.2 12.5 + - - -
65A ARG 3.3 1.6 + - - -
66A PHE* 1.3 74.9 - - - +
68A ALA* 1.3 61.0 + - - +
70A ILE* 3.7 7.3 - - - +
71A LEU* 2.8 30.3 + - - +
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Residues in contact with ALA 68 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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14A GLN* 4.1 12.3 - - - +
35A LEU* 4.0 26.9 - - + +
65A ARG 5.0 1.0 + - - +
66A PHE 3.3 0.4 - - - -
67A GLY* 1.3 75.3 - - - +
69A LEU* 1.3 58.2 + - - +
71A LEU* 3.1 8.7 + - - +
72A LEU* 2.8 31.5 + - - +
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Residues in contact with LEU 69 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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8A PHE* 4.8 0.9 - - + -
14A GLN* 3.6 16.1 - - + +
17A PHE* 3.5 49.6 - - + -
18A TYR* 4.2 5.8 - - + -
35A LEU* 4.1 13.9 - - + -
38A LEU* 3.6 31.2 - - + -
55A PHE* 4.5 12.1 - - + -
66A PHE* 3.1 28.1 + - + +
68A ALA* 1.3 77.0 - - - +
70A ILE* 1.3 60.2 + - - +
72A LEU* 3.3 3.3 + - + +
73A PHE* 2.9 38.8 + - + -
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Residues in contact with ILE 70 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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55A PHE* 4.3 10.5 - - + -
58A LEU* 4.1 11.0 - - + -
63A ARG* 3.4 61.5 - - + +
66A PHE* 3.1 9.9 + - + +
67A GLY* 3.8 8.5 - - - +
69A LEU* 1.3 76.0 - - - +
71A LEU* 1.3 63.1 + - - +
73A PHE 3.6 0.2 + - - -
74A ASP* 2.9 42.1 + - - +
86A PHE* 3.8 27.3 - - + -
88A VAL* 4.3 8.1 - - + -
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Residues in contact with LEU 71 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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67A GLY 2.8 19.0 + - - +
68A ALA* 3.4 8.5 - - - +
70A ILE* 1.3 76.0 - - - +
72A LEU* 1.3 65.6 + - - +
74A ASP* 3.2 10.0 + - + +
75A GLU* 3.0 51.3 + - + +
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Residues in contact with LEU 72 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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35A LEU* 3.8 40.2 - - + +
38A LEU* 3.3 31.2 - - + -
39A TRP* 3.9 25.0 - - + +
42A LEU* 3.4 26.7 - - + -
68A ALA 2.8 15.5 + - - +
69A LEU* 3.5 7.9 - - - +
71A LEU* 1.3 76.2 - - - +
73A PHE* 1.3 58.0 + - + +
75A GLU* 3.2 14.4 + - - +
76A ALA* 2.9 26.3 + - - +
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Residues in contact with PHE 73 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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17A PHE* 3.7 23.3 - + - -
21A PHE* 4.0 16.6 - + - -
38A LEU* 4.0 18.8 - - + -
42A LEU* 3.9 31.2 - - + -
53A ILE* 4.1 26.9 - - + -
55A PHE* 3.6 29.2 - + - -
69A LEU* 2.9 29.0 + - + +
71A LEU 3.3 0.2 - - - -
72A LEU* 1.3 75.2 - - - +
74A ASP* 1.3 63.7 + - - +
76A ALA* 3.4 3.6 + - - +
77A GLU* 3.1 21.7 + - - +
84A LEU* 4.2 7.4 - - + +
86A PHE* 3.6 31.1 - + + +
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Residues in contact with ASP 74 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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70A ILE* 2.9 32.0 + - - +
71A LEU* 3.2 11.7 + - + +
73A PHE* 1.3 75.4 - - - +
75A GLU* 1.3 58.7 + - + +
77A GLU* 3.3 12.1 + - - +
78A GLU* 2.9 44.2 + - - +
86A PHE* 3.4 19.7 - - - +
90B HIS* 5.0 15.7 + - - -
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Residues in contact with GLU 75 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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39A TRP* 4.2 13.4 - - + -
71A LEU* 3.0 43.9 + - + +
72A LEU* 3.5 11.7 - - - +
74A ASP* 1.3 78.4 - - + +
76A ALA* 1.3 59.9 + - - +
78A GLU* 3.2 17.6 + - - +
79A GLU* 2.9 37.0 + - + +
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Residues in contact with ALA 76 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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39A TRP* 3.8 13.9 - - + -
42A LEU* 3.7 37.0 - - + -
43A MSE 5.6 1.1 - - - -
72A LEU 2.9 15.6 + - - +
73A PHE* 3.8 7.0 - - - +
74A ASP 3.3 0.2 - - - -
75A GLU* 1.3 75.8 - - - +
77A GLU* 1.3 58.7 + - - +
79A GLU* 3.2 2.9 + - - +
80A LEU* 2.7 42.6 + - + +
84A LEU* 4.3 6.5 - - + -
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Residues in contact with GLU 77 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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73A PHE 3.1 12.2 + - - +
74A ASP* 3.5 15.1 - - - +
76A ALA* 1.3 75.5 - - - +
78A GLU* 1.3 68.5 + - + +
79A GLU 3.2 0.5 + - - -
80A LEU 3.3 8.5 + - - +
82A GLY* 3.6 19.6 + - - -
84A LEU* 3.2 25.3 - - + +
85A ARG* 3.3 17.5 + - - +
86A PHE* 3.2 31.1 + - - +
89B ARG* 2.5 30.0 + - - -
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Residues in contact with GLU 78 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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74A ASP* 2.9 33.7 + - - +
75A GLU* 3.2 18.5 + - - +
77A GLU* 1.3 78.8 - - + +
79A GLU* 1.3 63.2 + - + +
81A GLU* 4.0 6.8 + - - +
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Residues in contact with GLU 79 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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39A TRP* 4.1 19.9 - - + -
43A MSE 3.8 26.3 - - + +
75A GLU* 2.9 23.6 + - + +
76A ALA* 3.8 5.4 - - - +
77A GLU 3.1 0.2 - - - -
78A GLU* 1.3 77.0 - - + +
80A LEU* 1.3 61.2 + - - +
81A GLU* 3.3 16.4 + - - +
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Residues in contact with LEU 80 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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42A LEU* 3.5 26.0 - - + +
43A MSE 4.4 17.5 - - + +
47A LEU* 6.4 0.2 - - + -
49A LEU* 4.5 19.5 - - + -
76A ALA* 2.7 31.0 + - + +
77A GLU 3.3 1.9 + - - +
79A GLU* 1.3 76.4 - - - +
81A GLU* 1.3 58.4 + - - +
82A GLY 3.1 2.5 - - - -
83A HIS* 2.5 41.7 + - + +
84A LEU* 3.8 36.6 - - + +
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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