Contacts of the helix formed by residues 65 - 83 (chain E) in PDB entry 2EG5
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 GLY 65 (chain E).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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18E TYR* 4.4 12.5 - - - -
19E ALA* 3.9 19.1 - - - -
22E SER* 5.7 0.2 - - - -
64E SER* 1.3 78.8 - - - +
66E PRO* 1.4 73.0 - - - +
67E ASN* 3.1 3.3 - - - +
68E THR* 2.9 25.2 - - - +
69E LEU* 4.4 2.8 + - - +
110E VAL* 5.0 0.3 - - - +
113E LEU* 4.6 11.3 - - - +
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Residues in contact with PRO 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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19E ALA* 3.3 31.0 - - + +
22E SER* 5.2 4.7 - - - +
65E GLY* 1.4 83.8 - - - +
67E ASN* 1.3 71.1 + - - +
68E THR 3.2 0.9 + - - -
69E LEU* 3.4 7.4 + - + +
70E LEU* 3.1 32.7 + - + +
113E LEU* 5.4 6.7 - - + -
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Residues in contact with ASN 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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18E TYR* 4.6 8.2 + - + -
22E SER* 3.0 38.0 + - - +
23E ALA 4.7 0.6 - - - +
25E ASN* 3.1 23.8 - - - +
26E GLN* 4.1 15.7 - - - +
29E LEU* 4.2 9.3 - - + +
62E CYS 6.0 0.2 - - - +
65E GLY* 3.1 2.6 - - - +
66E PRO* 1.3 81.3 - - + +
68E THR* 1.3 64.0 + - - +
70E LEU* 3.3 21.8 + - - +
71E THR* 3.2 26.0 + - - -
2501E SAH 3.9 14.4 - - - +
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Residues in contact with THR 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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59E ASP* 5.0 3.1 - - - +
62E CYS* 2.9 34.0 + - - +
64E SER* 3.3 25.8 - - - +
65E GLY 2.9 23.3 - - - +
67E ASN* 1.3 77.9 - - - +
69E LEU* 1.3 61.6 + - + +
71E THR* 3.4 7.3 + - - -
72E VAL* 3.3 21.3 + - - +
99E LEU* 3.9 22.3 - - - +
110E VAL* 3.9 14.3 - - + +
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Residues in contact with LEU 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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65E GLY 5.3 1.3 - - - +
66E PRO* 3.4 8.4 + - + +
68E THR* 1.3 78.6 - - + +
70E LEU* 1.3 62.4 + - - +
72E VAL* 3.9 19.3 - - + -
73E ARG* 3.0 26.0 + - - +
99E LEU* 4.5 4.0 - - + -
110E VAL* 4.1 24.9 - - + +
113E LEU* 3.8 38.1 - - + +
114E LEU* 3.9 20.6 - - + -
117E PHE* 3.4 39.6 - - + -
134E ILE* 4.9 1.6 - - + -
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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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26E GLN* 4.2 23.3 - - + +
29E LEU* 4.9 7.4 - - + -
66E PRO* 3.1 25.6 - - + +
67E ASN* 3.3 27.8 + - - +
68E THR 3.2 1.2 - - - -
69E LEU* 1.3 78.1 - - - +
71E THR* 1.3 60.3 + - - +
73E ARG* 3.4 23.6 + - - +
74E ASP* 2.9 35.9 + - - +
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Residues in contact with THR 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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29E LEU* 3.6 23.1 - - + +
36E LEU* 6.2 0.7 - - + -
59E ASP* 4.1 16.8 + - + +
67E ASN 3.2 12.6 + - - -
68E THR* 3.4 10.1 + - - -
70E LEU* 1.3 72.5 - - - +
72E VAL* 1.3 61.4 + - - +
74E ASP* 3.1 7.8 + - + +
75E ILE* 2.8 40.4 + - + +
155E HIS* 3.6 35.0 - - + +
2501E SAH 4.9 6.8 + - - -
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Residues in contact with VAL 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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59E ASP* 5.8 2.2 - - + +
68E THR 3.3 15.1 + - - +
69E LEU* 3.9 19.3 - - + +
71E THR* 1.3 77.4 - - + +
73E ARG* 1.3 58.5 + - - +
75E ILE* 3.0 10.3 + - + +
76E VAL* 2.8 37.2 + - + +
97E ILE* 3.4 31.0 - - + -
99E LEU* 3.8 28.5 - - + -
117E PHE* 3.9 17.3 - - + -
134E ILE* 3.9 13.9 - - + -
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Residues in contact with ARG 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 LEU 3.0 20.2 + - - +
70E LEU* 3.5 22.6 - - - +
71E THR 3.2 0.2 - - - -
72E VAL* 1.3 76.0 - - - +
74E ASP* 1.3 60.1 + - - +
76E VAL* 3.4 4.5 + - - +
77E GLN* 2.9 60.9 + - + +
117E PHE* 4.0 25.8 - - + -
120E LYS* 3.1 42.4 - - - +
121E LEU* 4.9 10.4 - - + +
124E GLU* 3.6 18.7 + - - -
125E ASN* 5.3 2.7 + - - -
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Residues in contact with ASP 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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29E LEU* 4.5 18.2 - - - +
33E LYS* 4.0 37.4 - - + +
36E LEU* 3.8 14.4 - - + -
70E LEU* 2.9 21.8 + - - +
71E THR* 3.1 7.8 + - - +
73E ARG* 1.3 76.7 - - - +
75E ILE* 1.3 59.8 + - - +
77E GLN* 3.9 10.6 - - - +
78E SER* 2.9 33.4 + - - -
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Residues in contact with ILE 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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36E LEU* 4.1 25.8 - - + -
40E VAL* 5.7 1.1 - - + -
57E VAL* 4.0 28.5 - - + -
59E ASP* 4.9 7.9 - - + -
71E THR* 2.8 42.2 + - + +
72E VAL* 3.6 7.0 - - + +
74E ASP* 1.3 72.5 - - - +
76E VAL* 1.3 63.6 + - + +
78E SER* 3.2 5.7 + - - -
79E ILE* 3.1 39.3 + - + +
95E ILE* 5.5 0.2 - - + -
97E ILE* 5.1 11.4 - - + -
153E PHE* 4.4 6.5 - - + -
155E HIS* 4.2 22.7 - - + -
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Residues in contact with VAL 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 VAL* 2.8 28.6 + - + +
73E ARG* 3.8 6.7 - - - +
75E ILE* 1.3 72.9 - - + +
77E GLN* 1.3 58.9 + - - +
79E ILE* 3.2 4.0 + - - +
80E ASP* 2.9 42.3 + - - +
95E ILE* 4.2 15.0 - - + -
97E ILE* 4.0 13.7 - - + -
121E LEU* 4.5 17.3 - - + -
125E ASN* 4.6 5.8 - - - +
127E ARG* 3.9 19.7 - - - +
132E CYS* 3.9 24.7 - - - -
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Residues in contact with GLN 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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33E LYS* 4.6 12.2 + - - -
73E ARG* 2.9 42.9 + - + +
74E ASP* 4.0 14.7 - - - +
76E VAL* 1.3 76.0 - - - +
78E SER* 1.3 58.8 + - - +
80E ASP* 4.0 3.4 - - - +
81E LYS* 2.8 47.8 + - - +
125E ASN* 3.1 37.9 + - - +
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Residues in contact with SER 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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33E LYS* 5.3 1.6 - - - +
36E LEU* 3.7 17.0 - - - +
37E GLU* 3.3 31.6 + - - +
40E VAL* 3.3 28.4 - - - +
74E ASP 2.9 22.2 + - - -
75E ILE* 3.2 6.3 + - - -
77E GLN* 1.3 76.7 - - - +
79E ILE* 1.3 59.8 + - - +
81E LYS* 3.7 11.6 - - - +
82E VAL* 3.6 12.3 - - - +
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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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40E VAL* 4.3 17.7 - - + -
44E LEU* 4.0 15.0 - - + +
55E ILE* 3.6 41.1 - - + -
57E VAL* 4.4 1.8 - - + -
75E ILE* 3.1 31.1 + - + +
76E VAL 3.2 5.8 + - - +
78E SER* 1.3 75.1 - - - +
80E ASP* 1.3 67.0 + - - +
82E VAL* 3.5 16.1 + - - +
83E GLY 4.1 2.4 + - - -
93E PRO* 4.4 14.9 - - + +
95E ILE* 3.9 35.7 - - + -
153E PHE* 6.2 0.4 - - + -
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Residues in contact with ASP 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 VAL* 2.9 23.8 + - - +
77E GLN* 4.0 4.9 - - - +
79E ILE* 1.3 76.7 - - - +
81E LYS* 1.3 65.9 + - - +
83E GLY* 3.1 21.5 + - - +
92E ARG* 3.0 34.8 + - - +
93E PRO* 5.5 0.7 - - - +
125E ASN* 4.4 9.2 + - - +
127E ARG* 2.7 48.0 + - - +
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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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33E LYS* 4.7 8.8 - - - +
37E GLU* 3.0 38.5 + - + +
77E GLN* 2.8 34.4 + - - +
78E SER* 3.7 7.2 - - - +
79E ILE 3.4 0.2 - - - -
80E ASP* 1.3 76.2 - - - +
82E VAL* 1.3 62.5 + - + +
83E GLY 3.4 6.6 + - - +
84E GLN* 4.1 8.3 - - - +
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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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37E GLU 5.3 0.7 - - - +
40E VAL* 4.6 0.2 - - + -
41E ARG* 3.9 35.4 - - + +
44E LEU* 3.8 32.1 - - + -
78E SER 3.6 16.4 - - - +
79E ILE 3.5 7.6 + - - +
80E ASP 3.2 0.8 - - - -
81E LYS* 1.3 77.7 - - + +
83E GLY* 1.3 52.3 + - - +
84E GLN* 2.8 20.6 + - - +
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Residues in contact with GLY 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 4.1 2.8 + - - -
80E ASP* 3.1 18.7 + - - +
81E LYS 3.9 2.8 - - - +
82E VAL* 1.3 74.0 - - - +
84E GLN* 1.3 58.9 + - - +
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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