Contacts of the helix formed by residues 68 - 84 (chain E) in PDB entry 3CQ6
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 ALA 68 (chain E).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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65E GLU* 3.1 10.2 + - - -
66E ARG 3.4 2.2 - - - +
67E ASP* 1.3 78.1 - - - +
69E VAL* 1.3 63.0 + - - +
70E GLU 3.4 2.5 - - - -
71E LEU* 3.5 11.6 + - + -
72E ARG* 3.1 28.0 + - + +
94E ALA* 5.3 1.3 - - + +
258E HIS* 6.2 1.8 - - + -
259E LEU* 4.4 16.8 - - + -
264E GLN* 3.5 38.4 - - + +
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Residues in contact with VAL 69 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
65E GLU* 2.8 22.0 + - - +
67E ASP* 3.1 19.0 + - + +
68E ALA* 1.3 73.4 - - - +
70E GLU* 1.3 60.9 + - + +
72E ARG* 3.3 13.8 + - - +
73E ASP* 2.9 35.5 + - - +
89E ARG* 4.0 31.8 - - - +
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Residues in contact with GLU 70 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
65E GLU* 4.7 0.6 + - - -
68E ALA 3.4 0.2 - - - -
69E VAL* 1.3 78.9 - - + +
71E LEU* 1.3 66.8 + - - +
73E ASP* 3.3 13.5 + - - +
74E GLU* 3.2 31.0 + - + +
264E GLN* 5.9 1.5 - - - +
268E ILE* 3.8 30.5 - - + +
272E ARG* 5.7 1.0 + - - -
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Residues in contact with LEU 71 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
68E ALA* 3.5 16.6 + - + +
69E VAL 3.4 0.2 - - - -
70E GLU* 1.3 79.2 - - - +
72E ARG* 1.3 52.1 - - - +
74E GLU* 3.1 3.5 + - - +
75E LEU* 2.8 44.7 + - + +
94E ALA* 3.7 26.9 - - + -
237E LEU* 3.7 20.9 - - + -
259E LEU* 4.2 9.2 - - + -
264E GLN* 4.5 16.5 - - + +
267E ALA* 3.8 16.6 - - + -
268E ILE* 3.8 22.0 - - + +
271E LEU* 3.6 24.5 - - + -
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Residues in contact with ARG 72 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
67E ASP* 2.9 41.2 + - - +
68E ALA* 3.1 18.4 + - + +
69E VAL* 3.6 15.5 - - - +
71E LEU* 1.3 74.7 - - - +
73E ASP* 1.3 63.2 + - - +
75E LEU* 4.0 7.4 - - + +
76E ALA* 2.9 25.3 + - - +
89E ARG* 3.0 41.1 + - + +
90E ASP* 4.2 10.1 + - - +
92E LEU* 2.8 31.4 + - + +
93E TRP* 4.2 22.7 - - - +
94E ALA* 4.4 15.9 - - + +
247E ILE* 4.3 12.9 - - - +
251E MET* 4.8 5.9 - - - +
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Residues in contact with ASP 73 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
69E VAL* 2.9 23.1 + - - +
70E GLU* 3.3 17.1 - - - +
72E ARG* 1.3 74.4 - - - +
74E GLU* 1.3 69.2 + - - +
76E ALA* 3.3 5.4 + - - +
77E ALA* 3.0 26.3 + - - +
89E ARG* 3.3 40.3 + - - +
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Residues in contact with GLU 74 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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70E GLU* 3.2 19.8 + - + +
71E LEU* 3.1 8.5 + - - +
73E ASP* 1.3 85.5 - - - +
75E LEU* 1.3 65.1 + - - +
76E ALA 3.2 0.2 - - - -
77E ALA* 3.3 12.0 + - - +
78E TYR* 2.9 24.1 + - - +
268E ILE* 4.8 18.4 - - + +
271E LEU* 3.9 25.1 - - + +
272E ARG* 6.1 0.9 - - - +
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Residues in contact with LEU 75 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
71E LEU* 2.8 36.1 + - + +
72E ARG* 4.0 7.4 - - + +
74E GLU* 1.3 70.1 - - - +
76E ALA* 1.3 62.3 + - - +
78E TYR* 3.2 5.6 + - + +
79E ILE* 3.0 28.2 + - - +
92E LEU* 3.0 21.3 - - + -
94E ALA* 3.9 28.7 - - + +
226E MET* 4.4 10.5 - - + -
237E LEU* 4.5 1.8 - - + -
239E TYR* 3.8 43.1 - - + -
271E LEU* 3.8 23.1 - - + +
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Residues in contact with ALA 76 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
72E ARG 2.9 19.1 + - - +
73E ASP* 3.5 5.4 - - - +
75E LEU* 1.3 77.4 - - - +
77E ALA* 1.3 56.4 + - - +
80E THR* 2.8 34.4 + - - -
87E VAL* 3.3 14.5 - - - +
88E THR* 3.4 34.5 - - - +
89E ARG 3.7 0.9 - - - +
92E LEU* 3.7 14.3 - - + +
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Residues in contact with ALA 77 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
73E ASP 3.0 14.5 + - - +
74E GLU* 3.7 18.2 - - - +
76E ALA* 1.3 74.2 - - - +
78E TYR* 1.3 65.2 + - - +
80E THR* 3.6 7.1 + - - -
81E LYS* 3.3 22.0 + - - +
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Residues in contact with TYR 78 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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74E GLU 2.9 16.9 + - - +
75E LEU* 3.2 3.8 + - - +
77E ALA* 1.3 77.1 - - - +
79E ILE* 1.3 70.3 + - + +
81E LYS* 3.3 8.7 + - + +
82E GLN* 2.8 58.8 + - + +
202E GLU* 2.6 36.4 + - - +
230E PHE* 3.5 23.1 - + - -
239E TYR* 3.4 26.7 - + - -
271E LEU* 3.9 18.2 - - + +
274E SER* 4.5 11.9 - - - -
278E LEU* 3.6 24.9 - - + +
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Residues in contact with ILE 79 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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75E LEU 3.0 19.3 + - - +
76E ALA* 4.0 3.1 - - - +
78E TYR* 1.3 82.0 - - + +
80E THR* 1.3 59.7 + - - +
82E GLN* 4.3 1.8 - - - -
83E THR* 2.6 57.8 + - + +
85E VAL 4.5 1.1 - - - +
87E VAL* 3.8 18.6 - - + -
92E LEU* 4.5 1.3 - - + -
210E THR* 4.3 8.5 - - + -
224E ARG* 4.1 20.2 - - - +
239E TYR* 3.3 39.0 - - + +
241E VAL* 4.0 22.2 - - + -
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Residues in contact with THR 80 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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76E ALA 2.8 22.2 + - - -
77E ALA* 3.7 8.0 - - - -
79E ILE* 1.3 75.5 - - - +
81E LYS* 1.3 57.6 + - - +
84E GLY* 2.9 33.3 + - - -
85E VAL 3.3 15.3 - - - +
86E ALA* 4.1 13.0 - - + -
87E VAL* 3.3 24.3 + - - +
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Residues in contact with LYS 81 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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77E ALA 3.3 12.9 + - - +
78E TYR* 3.3 8.1 + - + +
80E THR* 1.3 81.3 - - - +
82E GLN* 1.3 64.3 + - - +
84E GLY* 4.1 3.5 + - - -
274E SER* 4.9 7.7 + - - -
275E ALA* 4.3 22.6 - - - +
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Residues in contact with GLN 82 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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78E TYR* 2.8 64.3 + - + +
79E ILE* 4.1 2.0 - - - +
81E LYS* 1.3 76.4 - - - +
83E THR* 1.3 70.2 + - + +
201E ALA* 5.1 2.2 + - - +
202E GLU* 4.2 23.8 + - - +
224E ARG* 4.0 8.9 - - - +
278E LEU* 4.8 4.5 - - - +
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Residues in contact with THR 83 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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79E ILE* 2.6 43.0 + - + +
82E GLN* 1.3 89.4 - - + +
84E GLY* 1.3 56.3 + - - +
85E VAL* 3.2 20.0 + - - +
207E PRO* 6.0 0.7 - - - +
208E SER* 3.8 21.0 + - - +
210E THR* 3.2 25.8 + - + +
211E THR* 4.2 9.9 - - - +
224E ARG* 4.0 10.8 - - - +
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Residues in contact with GLY 84 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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80E THR* 2.9 16.2 + - - +
81E LYS 4.1 4.1 + - - -
82E GLN 3.7 1.2 - - - -
83E THR* 1.3 76.8 - - - +
85E VAL* 1.3 60.9 + - - +
86E ALA 3.9 2.3 + - - -
211E THR* 5.8 0.2 - - - -
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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