Contacts of the helix formed by residues 87 - 103 (chain E) in PDB entry 2VUU
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 87 (chain E).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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61E LEU* 4.3 13.3 - - + +
86E GLY* 1.3 67.5 - - - -
88E GLU* 1.3 62.0 + - - +
89E ILE* 3.3 19.8 + - - +
90E ALA* 3.5 26.4 + - + +
91E ILE* 3.1 25.5 + - - +
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Residues in contact with GLU 88 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
81E THR* 3.0 27.2 + - - +
82E THR* 3.4 8.1 - - - +
83E SER* 2.6 41.0 + - - +
85E ALA* 6.1 0.2 - - + -
86E GLY 2.8 16.7 + - - +
87E ASP* 1.3 72.7 + - - +
89E ILE* 1.3 57.4 + - - +
91E ILE* 4.5 6.1 - - - -
92E GLY* 3.0 25.4 + - - -
110E TYR* 5.7 0.7 - - - +
127E MET* 4.5 11.2 - - - +
130E PRO* 4.8 18.1 - - + +
131E LYS* 3.6 27.6 + - + +
134E VAL* 3.6 6.3 - - + +
1353E NAP 4.1 5.4 + - - -
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Residues in contact with ILE 89 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
87E ASP* 3.1 12.0 + - - +
88E GLU* 1.3 78.3 - - - +
90E ALA* 1.3 60.2 + - - +
91E ILE 3.3 0.2 - - - -
93E LYS* 3.0 54.9 + - + +
130E PRO* 3.6 40.6 - - + +
133E THR* 4.0 24.0 - - + +
134E VAL* 3.8 7.3 - - + +
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Residues in contact with ALA 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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61E LEU* 4.9 9.0 - - + -
62E ASN* 5.1 7.6 - - - +
87E ASP* 3.3 28.5 + - + +
89E ILE* 1.3 77.3 - - - +
91E ILE* 1.3 60.9 + - - +
93E LYS* 3.5 4.1 + - - +
94E ASP* 3.0 39.8 + - - +
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Residues in contact with ILE 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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60E LEU* 3.7 20.9 - - + -
61E LEU* 3.6 48.7 - - + +
62E ASN 5.0 0.4 - - - +
67E MET* 3.7 4.3 - - + +
81E THR* 3.8 15.5 - - + -
85E ALA* 3.9 31.9 - - + +
86E GLY 4.2 1.8 - - - +
87E ASP 3.1 17.5 + - - +
88E GLU* 4.3 4.3 - - - +
90E ALA* 1.3 77.3 - - - +
92E GLY* 1.3 56.9 + - - +
94E ASP* 3.4 5.0 + - - -
95E LEU* 3.0 50.1 + - + +
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Residues in contact with GLY 92 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
79E ILE* 5.9 0.7 - - - -
81E THR* 5.0 4.5 - - - -
88E GLU 3.0 21.4 + - - -
89E ILE 3.8 0.9 - - - -
90E ALA 3.3 0.2 - - - -
91E ILE* 1.3 76.4 - - - +
93E LYS* 1.3 61.1 + - - +
95E LEU* 4.0 10.5 - - - +
96E ALA* 3.4 21.1 + - - +
108E TYR* 4.5 2.3 + - - -
110E TYR* 5.4 3.4 - - - -
134E VAL* 3.6 26.5 - - - +
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Residues in contact with LYS 93 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
89E ILE* 3.0 42.8 + - + +
90E ALA* 4.1 4.9 - - - +
92E GLY* 1.3 75.0 - - - +
94E ASP* 1.3 63.4 + - - +
96E ALA* 3.2 2.6 + - - +
97E ASP* 2.9 37.2 + - - +
133E THR* 5.2 9.3 - - - +
134E VAL* 5.2 3.4 - - + -
137E TYR* 3.7 54.5 - - + -
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Residues in contact with ASP 94 (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 LEU 5.3 0.2 - - - +
62E ASN* 4.6 20.6 + - - -
63E ASN 5.3 0.3 + - - -
64E VAL* 4.3 19.2 - - + +
67E MET* 3.4 22.7 - - + +
90E ALA* 3.0 27.1 + - - +
91E ILE* 3.7 3.4 - - - +
93E LYS* 1.3 79.0 - - - +
95E LEU* 1.3 57.8 + - - +
97E ASP* 3.2 14.4 + - - +
98E ALA* 2.8 29.1 + - - +
101E ARG* 5.1 1.0 + - - -
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Residues in contact with LEU 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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11E VAL* 4.2 17.0 - - + -
60E LEU* 4.5 10.1 - - + -
67E MET* 3.3 27.4 - - + -
70E LEU* 4.9 2.2 - - + -
71E PHE* 3.4 25.0 - - + -
79E ILE* 3.8 23.8 - - + -
81E THR* 4.0 9.0 - - + -
91E ILE* 3.0 38.8 + - + +
92E GLY* 4.0 4.7 - - - +
93E LYS 3.2 0.2 - - - -
94E ASP* 1.3 76.5 - - - +
96E ALA* 1.3 58.2 + - - +
98E ALA* 2.9 4.8 + - - +
99E ALA* 2.8 27.2 + - - +
108E TYR* 3.8 13.2 - - - +
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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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92E GLY 3.4 12.8 + - - +
93E LYS 3.2 8.6 + - - +
95E LEU* 1.3 79.2 - - - +
97E ASP* 1.3 60.8 + - - +
100E LYS* 3.1 17.5 + - - +
108E TYR* 3.6 9.3 + - - +
137E TYR* 4.0 7.0 - - + -
138E VAL* 4.0 24.7 - - + -
141E LEU* 3.4 26.3 - - + +
143E LEU* 3.6 11.4 - - + +
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Residues in contact with ASP 97 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
93E LYS* 2.9 30.3 + - - +
94E ASP* 3.3 18.0 - - - +
95E LEU 3.1 0.2 - - - -
96E ALA* 1.3 75.4 - - - +
98E ALA* 1.3 66.6 + - - +
100E LYS* 3.2 4.1 + - - +
101E ARG* 2.9 44.4 + - - +
137E TYR* 2.8 28.9 + - - -
141E LEU* 3.7 7.8 - - - +
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Residues in contact with ALA 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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67E MET* 3.7 21.1 - - + +
68E ASP* 4.4 3.6 - - - +
71E PHE* 3.1 31.7 - - + +
94E ASP 2.8 13.2 + - - +
95E LEU 3.2 2.9 - - - +
97E ASP* 1.3 76.1 - - - +
99E ALA* 1.3 63.9 + - - +
101E ARG* 3.1 23.5 + - - +
102E ALA* 2.9 21.7 + - - +
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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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71E PHE* 3.5 22.4 - - + -
95E LEU 2.8 13.6 + - - +
96E ALA 3.8 4.0 - - - +
98E ALA* 1.3 72.1 - - - +
100E LYS* 1.3 63.2 + - - +
102E ALA* 3.0 17.8 + - - +
103E GLY* 3.3 4.7 + - - -
105E ILE* 4.0 15.4 - - + +
108E TYR* 3.5 37.7 - - + -
143E LEU* 4.4 6.2 - - + +
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Residues in contact with LYS 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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96E ALA 3.1 12.8 + - - +
97E ASP* 3.2 10.1 + - - +
99E ALA* 1.3 79.1 - - - +
101E ARG* 1.3 57.9 + - + +
103E GLY* 3.0 21.7 + - - -
141E LEU* 3.3 50.6 + - + +
143E LEU* 3.9 15.8 - - + +
118F LEU* 3.3 37.0 + - - +
119F TYR* 6.3 0.4 - - - -
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Residues in contact with ARG 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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64E VAL* 4.7 17.0 - - - +
68E ASP* 2.9 33.0 + - - +
94E ASP 5.1 0.4 + - - -
97E ASP* 2.9 32.9 + - - +
98E ALA* 3.1 22.0 + - - +
100E LYS* 1.3 75.3 - - + +
102E ALA* 1.3 65.7 + - - +
103E GLY* 4.3 0.6 - - - -
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Residues in contact with ALA 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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68E ASP 5.9 0.2 - - - +
71E PHE* 3.7 39.7 - - + +
72E GLU* 5.5 1.1 - - - -
98E ALA 2.9 6.5 + - - +
99E ALA* 3.0 11.4 + - - +
101E ARG* 1.3 78.3 - - - +
103E GLY* 1.3 58.1 + - - +
104E THR* 3.1 25.7 + - - +
105E ILE* 4.9 2.2 - - + -
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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 3.3 3.6 + - - -
100E LYS* 3.0 17.7 + - - -
101E ARG 4.3 0.9 - - - -
102E ALA* 1.3 76.8 - - - +
104E THR* 1.3 60.6 + - - +
105E ILE 3.6 3.2 - - - +
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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