Contacts of the helix formed by residues 68 - 87 (chain E) in PDB entry 4CEV
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 68 (chain E).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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55E GLU* 5.8 0.4 + - - -
60E GLN* 4.6 1.4 + - - -
61E GLY* 6.4 1.1 - - - -
62E ASP* 5.9 4.9 - - + +
65E LEU* 3.4 26.2 + - + +
66E ARG 3.2 2.4 - - - -
67E ASN* 1.3 75.9 - - - +
69E LYS* 1.3 59.6 + - + +
72E ALA* 2.8 34.0 + - - +
138E ILE* 3.7 12.1 - - + -
151E HIS* 3.8 38.4 - - + +
153E ALA* 4.0 13.2 - - + -
154E LEU* 3.6 40.4 - - + -
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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
----------------------------------------------------------
55E GLU* 3.4 40.6 + - - +
59E GLU 5.5 2.0 + - - -
61E GLY 5.4 6.1 - - - +
67E ASN 3.3 1.0 - - - -
68E LEU* 1.3 81.3 - - + +
70E ALA* 1.3 58.0 + - - +
72E ALA* 3.8 3.7 - - - +
73E GLU* 3.0 32.6 + - - +
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Residues in contact with ALA 70 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
11E MET* 4.5 0.3 - - - +
13E LEU* 3.3 31.2 - - + +
51E ILE* 5.0 1.4 - - - +
52E GLY* 3.9 15.3 + - - +
53E LYS 4.4 2.5 - - - +
54E ALA* 3.9 19.7 - - + +
67E ASN 3.2 5.9 + - - +
69E LYS* 1.3 79.2 - - - +
71E VAL* 1.3 61.4 + - - +
73E GLU* 3.7 4.0 + - - +
74E ALA* 3.2 26.0 + - - +
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Residues in contact with VAL 71 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
11E MET* 3.7 10.2 - - + +
13E LEU* 3.6 39.5 - - + +
14E GLY* 4.3 2.0 - - - +
67E ASN 2.9 23.6 + - - +
70E ALA* 1.3 76.0 - - - +
72E ALA* 1.3 64.6 + - - +
75E ASN* 2.8 45.2 + - - +
100E SER* 3.7 14.4 - - - +
138E ILE* 3.9 33.4 - - + -
154E LEU* 4.4 3.8 - - + -
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Residues in contact with ALA 72 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
68E LEU 2.8 23.2 + - - +
69E LYS* 3.8 4.3 - - - +
71E VAL* 1.3 74.7 - - - +
73E GLU* 1.3 58.1 + - - +
75E ASN* 3.4 0.9 + - - -
76E GLU* 3.0 23.3 + - - +
153E ALA* 3.6 31.0 - - + +
154E LEU* 4.3 11.0 - - + +
157E ILE* 3.2 18.9 - - + +
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Residues in contact with GLU 73 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
69E LYS 3.0 17.3 + - - +
70E ALA* 4.2 4.3 - - - +
72E ALA* 1.3 74.3 - - - +
74E ALA* 1.3 67.9 + - - +
76E GLU* 3.0 29.0 + - - +
77E LYS* 3.0 44.8 + - - +
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Residues in contact with ALA 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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9E VAL* 5.5 1.8 - - + -
11E MET* 3.6 16.4 - - + -
49E ILE* 3.8 3.9 - - - +
50E PRO 4.5 2.2 - - - +
51E ILE* 3.5 36.6 - - + -
52E GLY 5.3 0.7 - - - +
70E ALA 3.2 19.3 + - - +
73E GLU* 1.3 76.6 - - - +
75E ASN* 1.3 56.5 + - - +
77E LYS* 3.1 16.3 + - - +
78E LEU* 2.8 27.7 + - - +
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Residues in contact with ASN 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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11E MET* 4.1 5.6 - - - +
71E VAL* 2.8 37.7 + - - +
72E ALA* 3.7 5.6 - - - +
73E GLU 3.2 0.6 - - - -
74E ALA* 1.3 75.3 - - - +
76E GLU* 1.3 60.5 + - - +
78E LEU* 3.7 7.2 - - - +
79E ALA* 2.9 29.6 + - - +
100E SER 3.0 22.1 + - - +
101E ILE* 3.2 17.0 - - - +
103E ILE* 3.9 10.0 - - + +
104E GLY* 2.8 32.4 + - - +
154E LEU* 5.2 1.0 - - + +
157E ILE* 3.6 13.0 - - + +
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Residues in contact with GLU 76 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
72E ALA 3.0 16.9 + - - +
73E GLU* 3.0 28.6 + - - +
75E ASN* 1.3 76.7 - - - +
77E LYS* 1.3 63.2 + - - +
79E ALA* 3.2 5.5 + - - +
80E ALA* 3.2 20.8 + - - +
156E GLN 4.4 1.7 - - - +
157E ILE* 3.4 34.0 - - + +
158E GLY* 3.4 13.9 + - - -
159E GLY 5.0 0.5 + - - -
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Residues in contact with LYS 77 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
49E ILE* 3.7 14.4 - - + +
50E PRO* 3.1 43.1 + - + +
52E GLY 5.0 5.7 - - - +
73E GLU* 3.0 43.3 + - - +
74E ALA* 3.1 11.2 + - - +
76E GLU* 1.3 77.4 - - - +
78E LEU* 1.3 60.8 + - - +
80E ALA* 3.2 7.6 + - - +
81E ALA* 3.0 23.6 + - - +
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Residues in contact with LEU 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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7E ILE* 3.9 16.4 - - + -
9E VAL* 3.7 27.6 - - + -
49E ILE* 4.1 12.1 - - + +
74E ALA 2.8 16.9 + - - +
75E ASN* 3.7 8.3 - - - +
76E GLU 3.2 0.2 - - - -
77E LYS* 1.3 72.7 - - - +
79E ALA* 1.3 66.6 + - - +
81E ALA* 3.4 0.3 + - - +
82E VAL* 2.9 46.0 + - + +
94E VAL* 4.2 4.7 - - + -
101E ILE* 3.1 41.3 - - + +
104E GLY* 3.8 2.2 - - - -
105E THR* 3.4 21.8 - - - +
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Residues in contact with ALA 79 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
75E ASN 2.9 18.1 + - - +
76E GLU* 3.4 7.0 - - - +
78E LEU* 1.3 77.7 - - - +
80E ALA* 1.3 56.8 + - - +
82E VAL 3.4 0.2 + - - -
83E ASP* 2.8 31.3 + - - +
104E GLY 3.3 19.5 - - - +
107E ALA* 3.8 20.2 - - + +
108E GLY* 3.4 8.0 - - - +
111E LYS* 6.0 1.1 - - - +
157E ILE* 4.1 6.3 - - + -
158E GLY* 4.9 8.1 - - - -
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Residues in contact with ALA 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 GLU 3.2 10.1 + - - +
77E LYS* 3.2 10.3 + - - +
79E ALA* 1.3 79.8 - - - +
81E ALA* 1.3 62.7 + - - +
83E ASP* 3.3 7.2 + - - +
84E GLN* 3.0 24.9 + - - +
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Residues in contact with ALA 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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7E ILE* 3.9 15.5 - - + -
46E LEU* 5.4 1.7 - - + +
49E ILE* 3.9 21.3 - - + -
77E LYS 3.0 15.7 + - - +
78E LEU 3.7 4.0 - - - +
80E ALA* 1.3 75.5 - - - +
82E VAL* 1.3 63.6 + - - +
84E GLN* 3.4 10.0 + - - +
85E VAL* 3.1 25.8 + - - +
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Residues in contact with VAL 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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7E ILE* 4.1 11.0 - - + -
78E LEU* 2.9 43.7 + - + +
79E ALA* 3.8 3.4 - - - +
81E ALA* 1.3 72.3 - - - +
83E ASP* 1.3 66.8 + - - +
85E VAL* 3.3 5.0 + - - +
86E VAL* 3.1 22.2 + - - +
92E PRO* 4.0 13.2 - - + -
94E VAL* 4.0 16.8 - - + -
105E THR* 3.8 13.7 - - + +
108E GLY* 4.0 5.8 - - - -
109E VAL* 3.5 32.5 - - + -
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Residues in contact with ASP 83 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
79E ALA 2.8 18.6 + - - +
80E ALA* 3.3 9.1 + - - +
82E VAL* 1.3 76.0 - - - +
84E GLN* 1.3 57.7 + - - +
86E VAL* 3.2 4.5 + - - +
87E GLN* 3.0 42.8 + - - +
108E GLY* 3.5 15.0 + - - +
111E LYS* 3.6 22.9 + - - +
112E HIS* 2.7 33.1 + - - -
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Residues in contact with GLN 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 ALA 3.0 15.6 + - - +
81E ALA* 3.7 9.3 + - - +
82E VAL 3.3 0.2 - - - -
83E ASP* 1.3 77.8 - - - +
85E VAL* 1.3 56.8 + - + +
87E GLN* 3.2 18.0 + - + +
88E ARG* 2.9 58.1 + - + +
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Residues in contact with VAL 85 (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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5E SER* 3.6 23.8 - - - +
7E ILE* 4.0 9.0 - - + -
46E LEU* 3.5 32.8 - - + -
81E ALA 3.1 15.4 + - - +
82E VAL 3.3 8.0 + - - +
84E GLN* 1.3 75.7 - - + +
86E VAL* 1.3 65.5 + - - +
88E ARG* 3.1 20.1 + - - +
90E ARG* 3.1 41.2 + - + +
92E PRO* 3.9 17.3 - - + -
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Residues in contact with VAL 86 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
82E VAL 3.1 15.4 + - - +
83E ASP 3.6 6.1 - - - +
85E VAL* 1.3 75.5 - - - +
87E GLN* 1.3 59.3 + - - +
89E GLY* 2.9 22.0 + - - -
90E ARG 3.8 7.6 - - - +
92E PRO* 4.2 23.6 - - + -
108E GLY 4.2 10.8 - - - +
109E VAL* 4.4 11.2 - - + -
112E HIS* 3.6 35.0 - - + +
113E TYR* 5.0 9.9 - - + +
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Residues in contact with GLN 87 (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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83E ASP* 3.0 40.7 + - - +
84E GLN* 3.2 21.4 + - + +
86E VAL* 1.3 77.3 - - - +
88E ARG* 1.3 58.4 + - + +
89E GLY* 3.1 4.6 + - - -
111E LYS* 5.6 0.8 - - - +
112E HIS* 3.8 15.6 - - + -
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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
------------------------------------------------------------
Atomic class I II III IV V VI VII VIII
------------------------------------------------------------
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