Contacts of the helix formed by residues 89 - 103 (chain E) in PDB entry 1V8P
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 THR 89 (chain E).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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83E ALA* 3.9 0.4 - - - -
88E LEU* 1.3 77.2 - - - +
90E PHE* 1.3 64.1 + - - +
91E TYR* 3.5 9.2 + - - +
92E ASP* 2.9 37.2 + - - +
93E ALA* 2.9 21.7 + - - +
1001E CL 4.6 13.7 - - + -
41F ASN* 4.6 3.8 - - - -
44F TRP* 3.5 28.5 - - + -
48G ARG* 5.7 2.2 - - - +
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Residues in contact with PHE 90 (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 LEU* 3.7 24.7 - - + -
79E VAL* 3.4 29.1 - - + +
80E LEU* 3.7 31.9 - - + -
83E ALA* 4.0 7.9 - - - -
89E THR* 1.3 73.7 - - - +
91E TYR* 1.3 64.4 + + - +
93E ALA* 4.5 0.2 - - - -
94E SER* 3.1 32.4 + - - -
36F ILE* 4.4 2.7 - - + -
37F TYR* 3.6 38.8 - + + -
40F GLY* 3.6 27.8 - - - -
41F ASN* 3.6 22.0 - - + +
44F TRP* 3.7 16.3 - - + -
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Residues in contact with TYR 91 (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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34E LEU* 3.5 28.9 - - + +
38E GLU* 3.8 17.0 - - + +
89E THR* 3.1 8.0 - - - +
90E PHE* 1.3 78.2 - - - +
92E ASP* 1.3 64.7 + - - +
94E SER* 3.2 19.7 + - - -
95E TYR* 3.3 13.9 - - - -
34F LEU* 4.9 2.4 - - + +
37F TYR* 3.4 31.6 - + + -
38F GLU* 3.5 29.8 - - + +
41F ASN* 3.2 38.2 + - + +
91F TYR* 5.3 15.7 - + - -
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Residues in contact with ASP 92 (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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38E GLU* 5.2 3.6 - - - +
88E LEU* 4.3 10.2 - - + +
89E THR* 2.9 32.3 + - - +
91E TYR* 1.3 79.4 - - - +
93E ALA* 1.3 63.1 + - - +
95E TYR* 3.1 17.1 + - - +
96E ALA 3.2 8.1 + - - -
110E ASP* 3.7 16.2 - - - +
112E GLU* 5.6 0.2 - - - +
113E LEU* 3.5 40.4 - - + +
48G ARG* 4.2 9.9 + - - -
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Residues in contact with ALA 93 (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 VAL* 3.5 20.9 - - + +
82E VAL* 4.1 6.7 - - + -
83E ALA* 3.5 30.5 - - + +
88E LEU* 4.2 5.3 - - + +
89E THR 2.9 17.4 + - - +
90E PHE 3.8 0.2 - - - +
92E ASP* 1.3 76.9 - - - +
94E SER* 1.3 58.1 + - - +
96E ALA* 3.0 8.7 + - - -
97E TYR* 2.8 33.8 + - - +
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Residues in contact with SER 94 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
32E LEU* 3.6 9.9 - - - +
34E LEU* 4.6 1.1 - - - -
74E PRO* 4.1 1.5 - - - +
79E VAL* 3.3 21.9 - - - +
90E PHE* 3.1 18.6 + - - -
91E TYR 3.3 12.1 - - - -
92E ASP 3.1 0.6 - - - -
93E ALA* 1.3 77.2 - - - +
95E TYR* 1.3 56.5 + - - +
98E VAL* 3.2 31.5 + - - +
37F TYR* 3.4 37.8 - - - -
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Residues in contact with TYR 95 (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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6E LEU* 3.6 17.0 - - + +
7E VAL 3.8 3.4 - - - -
8E ASP* 3.3 38.8 - - + -
9E ALA 4.1 1.6 + - - -
32E LEU* 3.9 20.4 - - + -
34E LEU* 3.7 17.2 - - + +
35E THR* 2.7 35.1 + - - -
38E GLU* 2.7 31.5 + - - -
91E TYR 3.3 13.9 - - - -
92E ASP* 3.1 12.3 + - - +
93E ALA 3.1 0.4 - - - -
94E SER* 1.3 76.7 - - - +
96E ALA* 1.3 68.2 + - - +
99E ALA* 3.1 28.1 + - - +
106E LEU* 4.0 18.9 - - + +
113E LEU* 4.6 6.5 - - + -
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Residues in contact with ALA 96 (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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82E VAL* 4.1 11.2 - - + -
86E ARG* 4.2 8.7 - - - +
88E LEU* 4.1 15.0 - - + -
92E ASP 3.2 9.7 + - - +
93E ALA* 3.0 12.2 + - - +
95E TYR* 1.3 78.0 - - - +
97E TYR* 1.3 62.5 + - - +
99E ALA* 4.1 0.3 - - - +
100E GLU* 3.1 31.9 + - - +
106E LEU* 4.9 0.2 - - - -
113E LEU* 4.2 1.7 - - + +
117E THR* 3.7 27.6 - - - +
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Residues in contact with TYR 97 (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 PRO* 4.0 15.7 - - + -
75E PRO* 3.7 23.7 - - + +
78E GLU* 3.5 40.1 + - + +
79E VAL* 4.3 15.0 - - + -
81E ARG* 4.7 5.6 - - - -
82E VAL* 4.1 26.6 - - + +
93E ALA 2.8 19.7 + - - +
94E SER 4.4 0.2 - - - +
96E ALA* 1.3 73.8 - - - +
98E VAL* 1.3 69.2 + - + +
100E GLU* 4.1 3.3 - - - +
101E SER* 2.9 55.7 + - - -
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Residues in contact with VAL 98 (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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6E LEU* 3.8 13.5 - - + -
32E LEU* 3.9 11.2 - - + -
71E LEU* 3.8 30.1 - - + -
72E GLU 4.7 4.7 - - - +
74E PRO* 3.0 42.6 - - + -
94E SER 3.2 15.1 + - - +
97E TYR* 1.3 77.7 - - + +
99E ALA* 1.3 64.0 + - - +
101E SER* 3.4 5.8 + - - -
102E SER* 2.8 36.2 + - - +
104E LEU* 5.3 0.2 - - + -
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Residues in contact with ALA 99 (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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6E LEU* 3.8 17.2 - - + +
95E TYR 3.1 18.4 + - - +
96E ALA 4.1 1.1 - - - +
98E VAL* 1.3 76.2 - - - +
100E GLU* 1.3 65.9 + - - +
102E SER 3.4 0.5 + - - -
103E GLY 3.2 2.8 + - - -
104E LEU* 2.9 46.3 + - - +
106E LEU* 3.8 26.0 - - + -
117E THR* 4.7 3.1 - - + -
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Residues in contact with GLU 100 (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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86E ARG* 2.7 39.0 + - - -
96E ALA 3.1 18.3 + - - +
97E TYR* 4.1 2.2 - - - +
99E ALA* 1.3 73.8 - - - +
101E SER* 1.3 64.5 + - - +
102E SER 3.0 1.6 + - - -
103E GLY* 3.0 13.7 + - - -
104E LEU 5.1 1.1 - - - -
117E THR* 3.7 13.0 - - + -
118E LYS* 2.9 56.1 + - + +
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Residues in contact with SER 101 (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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97E TYR* 2.9 57.3 + - - -
98E VAL* 3.4 6.1 + - - -
100E GLU* 1.3 76.1 - - - +
102E SER* 1.3 61.9 + - - +
103E GLY 3.5 0.2 - - - -
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Residues in contact with SER 102 (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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71E LEU* 5.2 2.3 - - - +
98E VAL* 2.8 29.0 + - - +
100E GLU 3.0 0.8 - - - -
101E SER* 1.3 82.0 + - - +
103E GLY* 1.3 63.8 - - - +
104E LEU* 4.1 24.9 - - - +
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Residues in contact with GLY 103 (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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99E ALA 3.8 0.2 - - - -
100E GLU* 3.0 13.6 + - - -
101E SER 3.5 0.6 - - - -
102E SER* 1.3 79.3 - - - +
104E LEU* 1.3 65.1 + - - +
105E VAL* 5.8 0.3 - - - +
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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