Contacts of the helix formed by residues 73 - 88 (chain E) in PDB entry 1VHA
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 73 (chain E).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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37E ASP* 3.7 6.6 - - - +
71E ASN 4.5 3.3 + - - +
72E ALA* 1.3 78.4 - - - +
74E SER* 1.3 62.9 + - - +
75E ARG* 2.9 31.3 + - - +
76E GLY* 3.1 15.4 + - - +
77E LEU* 3.4 14.2 + - - +
79E ARG* 6.2 0.2 - - - -
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Residues in contact with SER 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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37E ASP* 2.7 36.0 + - - -
39E ASP* 3.5 4.4 - - - +
42E LEU* 3.6 30.1 - - - +
43E HIS* 3.1 24.6 + - - -
46E THR* 4.8 0.7 + - - -
72E ALA 3.3 1.4 + - - -
73E ASP* 1.3 67.5 + - - +
75E ARG* 1.3 61.3 + - - +
76E GLY 2.9 2.4 + - - -
77E LEU* 3.2 11.5 + - - +
78E LEU* 2.8 30.7 + - - +
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Residues in contact with ARG 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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37E ASP* 5.0 0.2 + - - -
42E LEU* 3.5 22.4 - - + +
73E ASP* 2.9 12.6 + - - +
74E SER* 1.3 76.6 - - - +
76E GLY* 1.3 62.0 + - - +
78E LEU* 3.5 6.5 + - - +
79E ARG* 3.2 44.8 + - - +
116E LYS* 3.4 49.2 + - - +
119E GLU* 3.7 24.7 + - - -
120E ASP* 2.6 42.3 + - - +
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Residues in contact with GLY 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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62E PHE* 5.8 2.0 - - - -
73E ASP* 3.1 15.2 + - - -
74E SER 2.9 1.2 - - - -
75E ARG* 1.3 75.1 - - - +
77E LEU* 1.3 57.9 + - - +
78E LEU 3.0 1.1 - - - -
79E ARG* 2.7 40.2 + - - +
80E GLU* 3.0 13.1 + - - +
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Residues in contact with LEU 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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43E HIS* 4.4 10.3 - - - +
46E THR* 4.5 2.2 - - - +
58E ILE* 3.7 32.1 - - + +
61E LEU* 3.7 27.3 - - + +
62E PHE* 3.9 20.6 - - + -
71E ASN* 3.6 44.9 - - + +
73E ASP 3.4 11.1 + - - +
74E SER* 3.2 7.5 + - - +
76E GLY* 1.3 73.5 - - - +
78E LEU* 1.3 56.3 + - - +
80E GLU* 3.8 4.5 - - - +
81E ALA* 2.9 32.7 + - - +
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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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42E LEU* 3.9 30.7 - - + +
45E LEU* 4.3 21.1 - - + -
46E THR* 3.5 31.2 + - - +
49E ILE* 4.6 3.6 - - + -
74E SER 2.8 17.1 + - - +
75E ARG* 3.5 7.0 - - - +
76E GLY 2.9 0.2 + - - -
77E LEU* 1.3 79.1 - - - +
79E ARG* 1.3 59.5 + - - +
81E ALA* 3.7 3.4 - - + +
82E PHE* 3.2 20.4 + - - +
117E ILE* 4.9 6.5 - - + -
120E ASP* 4.2 23.3 - - + +
121E LEU* 4.1 21.7 - - + +
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Residues in contact with ARG 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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73E ASP* 5.6 0.2 + - - -
75E ARG* 3.2 48.8 + - - +
76E GLY* 2.7 28.0 + - - +
78E LEU* 1.3 69.3 - - - +
80E GLU* 1.3 58.3 + - - +
81E ALA 3.1 1.3 - - - -
82E PHE* 3.1 8.2 + - - +
83E ARG* 2.8 28.8 + - - +
119E GLU* 5.7 0.6 + - - -
120E ASP* 2.5 47.4 + - + +
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Residues in contact with GLU 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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61E LEU* 4.1 11.3 - - + +
62E PHE* 3.3 44.2 - - + -
76E GLY 3.0 10.5 + - - +
77E LEU* 3.8 7.0 - - - +
79E ARG* 1.3 75.9 - - - +
81E ALA* 1.3 62.9 + - - +
83E ARG* 2.8 45.9 + - - +
84E GLN* 2.6 42.9 + - - +
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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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46E THR* 3.9 22.0 - - + +
49E ILE* 5.2 4.3 - - + -
50E LEU* 3.7 27.8 - - + +
61E LEU* 4.5 7.2 - - + -
77E LEU 2.9 19.0 + - - +
78E LEU* 3.7 6.7 - - + +
80E GLU* 1.3 77.3 - - - +
82E PHE* 1.3 59.9 + - - +
83E ARG 3.3 0.2 + - - -
84E GLN* 3.4 5.0 + - - +
85E VAL* 3.0 29.5 + - + +
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Residues in contact with PHE 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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49E ILE* 5.1 4.7 - - + +
78E LEU 3.2 11.9 + - - +
79E ARG* 3.1 8.8 + - - +
81E ALA* 1.3 75.3 - - - +
83E ARG* 1.3 66.1 + - - +
85E VAL* 3.4 13.1 + - + +
86E GLN* 3.0 64.0 + - + +
90E TYR 4.8 0.9 - - - -
91E LYS* 4.5 5.6 - - + -
92E ILE* 3.9 26.7 - - + -
120E ASP 4.2 15.0 - - - +
121E LEU* 3.4 42.0 - - + -
122E GLN* 3.7 28.5 - - + -
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Residues in contact with ARG 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 ARG 2.8 12.2 + - - +
80E GLU* 2.8 50.0 + - - +
81E ALA 3.2 0.4 - - - -
82E PHE* 1.3 78.9 - - - +
84E GLN* 1.3 69.9 + - - +
86E GLN* 3.0 11.4 + - - +
87E GLU* 2.9 63.6 + - + +
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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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50E LEU* 5.3 1.7 - - + +
55E LEU* 3.7 28.2 - - + +
60E LYS 4.9 3.9 + - - +
61E LEU* 3.7 30.4 + - - +
80E GLU* 2.6 36.2 + - - +
81E ALA 3.8 5.8 - - - +
83E ARG* 1.3 83.5 - - - +
85E VAL* 1.3 65.5 + - - +
87E GLU* 3.2 32.1 + - - +
88E LYS* 3.2 18.2 + - - +
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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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49E ILE* 3.3 34.1 - - + +
50E LEU* 4.6 2.2 - - + -
53E ALA* 4.2 10.8 - - + -
55E LEU* 4.2 9.4 - - + -
81E ALA 3.0 17.6 + - - +
82E PHE* 3.6 14.8 - - + +
84E GLN* 1.3 76.2 - - - +
86E GLN* 1.3 61.1 + - - +
88E LYS* 3.2 12.5 + - - +
89E GLY 3.6 0.5 + - - -
90E TYR* 3.2 28.9 + - + +
155E LEU* 3.4 35.0 - - + -
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Residues in contact with GLN 86 (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 PHE* 3.0 56.9 + - + +
83E ARG* 3.0 11.9 + - - +
85E VAL* 1.3 73.7 - - - +
87E GLU* 1.3 57.1 + - - +
88E LYS 3.0 1.6 - - - -
89E GLY* 2.6 26.2 + - - -
90E TYR 2.6 30.8 + - - +
91E LYS* 4.0 3.4 - - - +
122E GLN* 4.0 10.6 + - - -
158E GLN* 3.3 24.0 + - - +
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Residues in contact with GLU 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 ARG* 2.9 48.1 + - + +
84E GLN* 3.2 24.0 + - - +
86E GLN* 1.3 76.7 - - + +
88E LYS* 1.3 59.8 + - + +
89E GLY* 3.1 4.0 + - - -
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Residues in contact with LYS 88 (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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53E ALA* 2.9 27.0 + - + +
54E ALA* 4.5 3.6 + - - +
55E LEU* 3.5 31.1 - - + +
84E GLN 3.2 10.8 + - - +
85E VAL* 3.6 8.3 - - - +
86E GLN 3.0 1.2 - - - -
87E GLU* 1.3 77.1 - - + +
89E GLY* 1.3 60.1 + - - +
90E TYR* 3.5 25.4 - - + -
157E ARG* 4.0 12.5 + - - -
126F GLU* 3.2 30.0 + - - +
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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