Contacts of the helix formed by residues 61 - 79 (chain E) in PDB entry 1C17
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 ASP 61 (chain E).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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20E ALA* 3.4 31.0 - - - +
23E GLY* 3.8 0.3 - - - -
24E ALA* 3.4 14.1 + - + -
57E MET 3.4 11.0 + - - +
58E GLY* 3.1 15.1 + - - +
60E VAL* 1.3 74.8 - - - +
62E ALA* 1.3 55.8 + - - +
64E PRO* 3.0 19.6 - - - +
65E MET* 4.1 4.2 + - - +
21F ALA* 5.0 7.7 - - - +
22F ILE* 5.9 0.2 - - - -
25F ALA* 3.5 22.6 + - + +
28F ILE* 6.0 1.4 - - - +
59F LEU* 5.4 7.9 - - + +
62F ALA* 5.3 7.4 - - - +
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Residues in contact with ALA 62 (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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61D ASP* 5.3 5.8 - - - +
21E ALA* 3.3 38.6 - - + +
24E ALA* 3.3 14.4 - - + +
58E GLY 4.0 0.9 + - - +
59E LEU* 5.0 5.8 - - + +
60E VAL* 3.3 0.4 - - - +
61E ASP* 1.3 75.0 - - - +
63E ILE* 1.3 64.5 + - + +
64E PRO* 2.8 6.5 - - - +
65E MET* 3.2 2.1 + - - +
66E ILE* 2.9 36.4 + - + +
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Residues in contact with ILE 63 (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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59E LEU* 3.7 17.7 + - + +
60E VAL* 3.9 19.2 - - + +
62E ALA* 1.3 76.5 - - - +
64E PRO* 1.3 64.5 - - + +
66E ILE* 3.8 15.1 - - + +
67E ALA* 3.1 26.5 + - + +
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Residues in contact with PRO 64 (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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60E VAL* 2.7 28.0 - - + +
61E ASP* 3.0 15.3 - - - +
62E ALA 2.8 7.6 - - - -
63E ILE* 1.3 92.0 - - + +
65E MET* 1.3 53.3 + - - +
66E ILE 3.0 1.8 - - - -
67E ALA* 3.0 7.3 + - + +
68E VAL* 2.7 44.7 + - + +
66F ILE* 6.1 4.9 - - + -
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Residues in contact with MET 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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16E MET* 2.7 68.4 - - + +
17E MET* 3.3 5.9 - - - +
20E ALA* 3.0 27.4 - - + -
21E ALA 4.7 0.4 - - - +
61E ASP 4.1 2.0 + - - +
62E ALA 3.2 7.1 + - - +
64E PRO* 1.3 78.6 - - - +
66E ILE* 1.3 52.4 + - - +
68E VAL* 3.2 23.1 + - + +
69E GLY* 2.5 32.9 + - - -
17F MET* 4.1 13.9 - - + -
18F GLY* 5.1 9.6 - - - -
21F ALA* 5.8 2.0 - - - -
66F ILE* 6.1 6.1 - - + -
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Residues in contact with ILE 66 (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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64D PRO* 6.1 5.2 - - + -
65D MET* 6.1 5.8 - - + -
68D VAL* 5.8 10.3 - - + -
17E MET* 3.5 31.5 - - + +
21E ALA* 4.7 7.9 - - + -
62E ALA* 2.9 36.2 + - + +
63E ILE* 3.8 15.0 - - + +
65E MET* 1.3 72.7 - - - +
67E ALA* 1.3 57.7 + - - +
68E VAL 3.0 1.3 - - - -
69E GLY* 2.9 0.9 + - - -
70E LEU* 2.5 51.1 + - + +
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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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63E ILE* 3.1 17.1 + - + +
64E PRO* 3.0 7.5 + - + +
66E ILE* 1.3 79.9 - - - +
68E VAL* 1.3 58.2 + - + +
70E LEU* 3.6 9.9 - - - +
71E GLY* 2.9 23.6 + - - -
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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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16E MET* 4.4 9.0 - - - -
64E PRO* 2.7 35.0 + - + +
65E MET* 3.3 27.1 - - + +
67E ALA* 1.3 74.4 - - + +
69E GLY* 1.3 59.7 + - - +
70E LEU 3.2 0.2 - - - -
71E GLY* 3.1 1.7 + - - -
72E LEU* 2.9 44.7 + - + +
17F MET* 4.7 8.1 - - + -
66F ILE* 5.8 9.0 - - + -
70F LEU* 6.4 2.7 - - + -
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Residues in contact with GLY 69 (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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13E ALA* 3.1 34.9 - - - +
16E MET* 3.8 8.3 - - - +
17E MET* 3.9 5.4 - - - -
65E MET 2.5 20.0 + - - -
66E ILE 3.4 2.2 - - - -
68E VAL* 1.3 73.3 - - - +
70E LEU* 1.3 56.9 + - - +
72E LEU* 4.1 0.3 - - - +
73E TYR* 2.9 30.7 + - - +
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Residues in contact with LEU 70 (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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68D VAL* 6.4 2.2 - - + -
72D LEU* 6.6 0.4 - - + -
17E MET* 4.3 3.5 - - - -
66E ILE* 2.5 32.1 + - + +
67E ALA* 3.6 9.9 - - - +
69E GLY* 1.3 71.0 - - - +
71E GLY* 1.3 51.9 + - - +
73E TYR* 3.4 9.8 - - + +
74E VAL* 2.6 61.0 + - + +
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Residues in contact with GLY 71 (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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67E ALA 2.9 16.1 + - - -
68E VAL* 3.1 3.9 + - - -
70E LEU* 1.3 71.8 - - - +
72E LEU* 1.3 55.4 + - - +
73E TYR 3.0 1.1 - - - -
74E VAL* 2.8 9.7 + - - +
75E MET* 2.7 42.7 + - - +
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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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9E LEU* 2.9 36.8 - - + +
12E ALA* 4.6 4.9 - - + -
16E MET* 3.0 39.7 - - + -
68E VAL* 2.9 24.9 + - + +
69E GLY 4.1 2.9 - - - +
71E GLY* 1.3 72.9 - - - +
73E TYR* 1.3 60.3 + - - +
75E MET* 3.2 21.2 - - - +
13F ALA* 6.2 0.4 - - + -
17F MET* 5.4 2.0 - - + -
70F LEU* 6.6 0.2 - - + -
73F TYR* 2.9 54.3 - - + +
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Residues in contact with TYR 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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9D LEU* 4.7 2.3 - - - +
72D LEU* 2.9 53.4 + - + +
75D MET* 3.3 27.9 - - + +
9E LEU* 3.5 8.7 - - - +
10E TYR* 2.9 55.2 + + - -
13E ALA* 4.4 13.9 - - + -
69E GLY 2.9 21.8 + - - +
70E LEU* 3.4 12.3 - - + +
72E LEU* 1.3 73.6 - - - +
74E VAL* 1.3 70.4 + - + +
75E MET 3.0 1.6 - - - -
76E PHE* 3.1 16.4 + + - +
77E ALA* 3.2 10.4 + - + +
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Residues in contact with VAL 74 (chain E).
Click here for Legend to table.
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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70E LEU* 2.6 52.8 + - + +
71E GLY* 3.4 7.0 - - - +
73E TYR* 1.3 76.2 - - + +
75E MET* 1.3 64.2 + - - +
77E ALA* 3.0 27.7 - - + +
78E VAL* 3.3 12.1 + - + +
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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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9E LEU* 4.6 3.4 - - + -
71E GLY 2.7 20.6 + - - +
72E LEU* 3.2 25.1 - - - +
74E VAL* 1.3 70.4 - - - +
76E PHE* 1.3 57.6 + - - +
78E VAL* 2.7 38.5 + - - +
79E ALA 3.5 2.6 + - - -
10F TYR* 4.8 5.2 - - - +
73F TYR* 3.3 36.1 - - + +
77F ALA* 6.3 2.7 - - + -
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Residues in contact with PHE 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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5D ASN* 3.5 21.1 - - - -
5E ASN* 5.8 1.1 - - - -
6E MET* 3.1 52.0 - - + -
9E LEU* 3.4 21.4 - - + +
10E TYR* 2.9 37.5 - + + -
72E LEU 3.3 2.2 + - - -
73E TYR* 3.1 11.5 + + - +
75E MET* 1.3 78.8 - - - +
77E ALA* 1.3 69.7 + - + +
79E ALA* 2.9 19.9 + - - +
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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
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75D MET* 6.3 2.7 - - + -
73E TYR* 3.2 7.8 + - + +
74E VAL* 3.0 27.3 + - + +
75E MET 3.0 0.4 - - - -
76E PHE* 1.3 88.4 - - + +
78E VAL* 1.3 60.1 + - + +
79E ALA* 4.3 3.1 - - - +
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Residues in contact with VAL 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 VAL* 3.5 15.7 - - + +
75E MET* 2.7 25.0 + - - +
77E ALA* 1.3 71.8 - - + +
79E ALA* 1.3 76.6 + - - +
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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
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75E MET 3.5 3.6 + - - -
76E PHE* 2.9 17.4 + - - +
77E ALA 4.3 3.1 - - - +
78E VAL* 1.3 94.8 - - - +
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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