Contacts of the helix formed by residues 64 - 77 (chain E) in PDB entry 2CNW
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 LEU 64 (chain E).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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24E TRP* 3.5 9.6 - - + -
25E GLY* 5.4 5.2 - - - +
26E GLY 4.9 3.6 - - - +
28E LEU* 4.4 33.4 - - + +
31E VAL* 3.7 42.6 - - + -
32E LEU* 4.8 15.9 - - + -
56E VAL* 4.8 11.2 - - + -
61E ARG* 4.3 10.2 + - - +
62E LYS 3.1 15.6 + - - +
63E ASP* 1.3 74.7 - - - +
65E LYS* 1.3 62.8 + - - +
67E ALA* 3.9 9.9 - - - +
68E VAL* 3.2 28.1 + - - +
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Residues in contact with LYS 65 (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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24E TRP* 3.8 44.9 - - + +
63E ASP 2.6 13.3 + - - +
64E LEU* 1.3 77.9 - - - +
66E GLU* 1.3 93.8 + - + +
68E VAL* 3.8 2.8 - - - +
69E LYS* 3.3 52.5 + - + +
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Residues in contact with GLU 66 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
63E ASP* 3.7 21.6 - - + +
65E LYS* 1.3 109.6 + - + +
67E ALA* 1.3 59.5 + - - +
68E VAL 3.3 0.2 - - - -
69E LYS* 4.0 16.5 - - - +
70E GLU* 3.0 48.8 + - - +
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Residues in contact with ALA 67 (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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56E VAL* 5.0 11.8 - - + +
61E ARG* 3.7 38.1 + - + +
63E ASP* 3.3 22.4 - - + +
64E LEU* 3.9 10.3 - - - +
65E LYS 3.3 0.4 - - - -
66E GLU* 1.3 74.9 - - - +
68E VAL* 1.3 64.3 + - + +
70E GLU* 3.9 2.0 - - - +
71E LYS* 3.3 21.8 + - - +
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Residues in contact with VAL 68 (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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24E TRP* 4.6 3.1 - - + -
35E LEU* 3.7 45.1 - - + -
52E ILE* 4.8 5.8 - - + +
56E VAL* 3.7 24.7 - - + -
64E LEU 3.2 19.8 + - - +
65E LYS 3.8 2.2 - - - +
66E GLU 3.3 0.2 - - - -
67E ALA* 1.3 77.6 - - - +
69E LYS* 1.3 60.0 + - - +
71E LYS* 3.3 8.1 + - - +
72E LEU* 3.1 40.5 + - + +
302E LEU* 3.9 21.5 - - + -
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Residues in contact with LYS 69 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
24E TRP* 5.7 2.9 - - - +
65E LYS* 3.3 48.2 + - - +
66E GLU* 4.0 23.8 - - - +
68E VAL* 1.3 73.8 - - - +
70E GLU* 1.3 61.3 + - - +
72E LEU* 4.0 0.2 - - - +
73E VAL* 2.9 39.6 + - + +
298E VAL* 3.9 17.7 - - + -
299E GLU* 4.2 29.8 - - - +
302E LEU* 3.8 30.7 - - + -
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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
----------------------------------------------------------
61E ARG* 3.2 36.5 + - - +
63E ASP* 4.7 2.4 - - - +
66E GLU* 3.0 34.9 + - - +
67E ALA 3.9 4.5 - - - +
69E LYS* 1.3 75.8 - - - +
71E LYS* 1.3 64.9 + - - +
73E VAL* 4.3 3.7 - - - +
74E GLY* 3.3 18.7 + - - -
86E ARG* 5.4 5.7 + - - +
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Residues in contact with LYS 71 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
52E ILE* 4.1 35.1 - - + +
55E GLU* 2.8 50.7 + - - -
56E VAL* 4.6 7.4 - - + -
67E ALA 3.3 12.8 + - - +
68E VAL* 3.4 9.9 - - - +
69E LYS 3.2 0.4 - - - -
70E GLU* 1.3 82.0 - - - +
72E LEU* 1.3 66.2 + - + +
74E GLY* 4.3 0.2 - - - -
75E MET* 3.5 32.8 + - - +
271E ARG* 4.2 12.7 - - - +
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Residues in contact with LEU 72 (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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39E LEU* 4.7 16.2 - - + -
52E ILE* 3.7 31.4 - - + -
68E VAL* 3.1 31.0 + - + +
69E LYS 4.0 1.8 - - - +
71E LYS* 1.3 80.2 - - + +
73E VAL* 1.3 65.4 + - - +
75E MET* 3.2 22.6 + - + +
76E LEU* 3.0 28.7 + - + +
267E ILE* 4.5 17.7 - - + -
298E VAL* 3.7 30.3 - - + -
301E LEU* 4.8 11.7 - - + -
302E LEU* 5.0 1.6 - - + -
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Residues in contact with VAL 73 (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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69E LYS* 2.9 27.4 + - + +
70E GLU* 4.3 3.1 - - - +
72E LEU* 1.3 72.9 - - - +
74E GLY* 1.3 63.0 + - - +
76E LEU* 3.4 1.3 + - - -
77E GLU* 3.3 25.8 + - - +
86E ARG* 3.7 31.2 - - - +
294E PRO* 3.9 12.6 - - + +
295E GLU* 3.8 34.8 - - + -
298E VAL* 3.8 25.4 - - + -
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Residues in contact with GLY 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 3.3 13.8 + - - -
71E LYS 4.3 0.4 - - - -
72E LEU 3.3 0.6 - - - -
73E VAL* 1.3 76.8 - - - +
75E MET* 1.3 64.1 + - - +
77E GLU* 3.3 34.2 - - - +
79E ASP 3.7 12.0 - - - +
83E ALA* 5.0 8.3 - - - -
86E ARG* 4.9 4.0 - - - +
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Residues in contact with MET 75 (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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52E ILE* 5.3 1.8 - - + -
71E LYS* 3.5 27.1 + - - +
72E LEU* 3.2 34.4 + - + +
74E GLY* 1.3 76.9 - - - +
76E LEU* 1.3 74.8 + - - +
77E GLU 3.3 7.6 - - - +
267E ILE* 4.4 11.4 - - + +
270E VAL* 3.9 17.0 - - + +
271E ARG* 3.6 46.9 - - + +
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Residues in contact with LEU 76 (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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72E LEU 3.0 15.3 + - - +
73E VAL 3.9 4.0 - - - +
74E GLY 3.3 0.2 - - - -
75E MET* 1.3 85.2 - - - +
77E GLU* 1.3 63.8 - - - +
78E PRO* 3.9 1.2 - - - +
266E LEU* 4.8 1.3 - - + +
267E ILE* 3.6 30.3 - - + -
270E VAL* 4.2 20.4 - - + +
276E PRO* 5.4 3.3 - - - +
277E ILE* 4.0 28.6 + - + +
292E PHE* 4.0 25.7 - - + -
294E PRO* 4.4 5.4 - - + +
297E PHE* 3.7 29.8 - - + -
298E VAL* 3.9 20.4 - - + -
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Residues in contact with GLU 77 (chain E).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
73E VAL* 3.3 16.2 + - - +
74E GLY* 3.3 31.5 - - - +
75E MET 3.3 10.6 - - - +
76E LEU* 1.3 81.2 - - - +
78E PRO* 1.4 65.6 - - + +
79E ASP* 2.8 27.3 + - + +
82E ARG* 3.4 27.0 + - - +
83E ALA* 3.8 6.1 + - - +
86E ARG* 2.8 36.4 + - - -
292E PHE* 5.9 0.2 - - - -
294E PRO* 4.0 19.7 - - + +
295E GLU* 6.0 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