Contacts of the helix formed by residues 73 - 88 (chain C) 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 C).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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37C ASP* 4.2 4.2 - - - +
70C LYS* 3.2 17.8 + - - +
71C ASN 3.1 3.5 - - - -
72C ALA* 1.3 80.4 - - + +
74C SER* 1.3 66.8 + - - +
75C ARG* 3.4 15.9 + - - +
76C GLY* 3.2 14.3 + - - +
77C LEU* 3.4 7.6 + - - +
79C ARG* 4.5 0.3 + - - -
83F ARG* 6.6 0.2 - - - -
86F GLN* 3.5 28.5 - - + +
87F GLU* 2.2 35.1 - - - +
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Residues in contact with SER 74 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
37C ASP* 2.6 35.4 + - - -
39C ASP* 3.6 4.1 - - - +
42C LEU* 3.7 30.9 - - - +
43C HIS* 3.0 23.2 - - - -
46C THR* 4.7 1.2 + - - -
71C ASN 5.1 0.7 + - - -
72C ALA 4.2 0.2 - - - -
73C ASP* 1.3 73.2 + - - +
75C ARG* 1.3 60.7 + - - +
77C LEU* 3.3 12.0 + - - +
78C LEU* 2.8 28.1 + - - +
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Residues in contact with ARG 75 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
42C LEU* 3.6 20.2 - - + -
73C ASP* 3.3 11.3 + - - +
74C SER* 1.3 74.3 - - - +
76C GLY* 1.3 61.3 + - - +
78C LEU* 3.6 4.8 - - - +
79C ARG* 2.8 49.0 + - - +
116C LYS* 3.5 54.3 + - - +
119C GLU* 3.7 24.4 + - - -
120C ASP* 2.8 35.0 + - - +
87F GLU* 3.6 27.8 + - - +
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Residues in contact with GLY 76 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
62C PHE* 4.6 6.7 - - - -
70C LYS 5.3 2.0 - - - -
73C ASP* 3.2 14.6 + - - -
74C SER 3.2 0.6 - - - -
75C ARG* 1.3 80.8 - - - +
77C LEU* 1.3 57.6 + - - +
79C ARG* 3.2 18.5 + - - +
80C GLU* 3.0 29.6 + - - +
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Residues in contact with LEU 77 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
36C SER* 5.9 0.2 - - - -
43C HIS* 4.4 11.9 - - + -
46C THR* 4.4 2.0 - - - +
58C ILE* 3.8 28.7 - - + +
61C LEU* 3.3 29.5 - - + +
62C PHE* 3.4 31.4 - - + -
70C LYS 4.1 8.1 - - - +
71C ASN* 3.6 39.9 - - + +
73C ASP 3.6 10.3 - - - +
74C SER* 3.5 7.4 - - - +
75C ARG 3.2 0.2 - - - -
76C GLY* 1.3 77.0 - - - +
78C LEU* 1.3 56.4 + - - +
80C GLU* 3.4 3.0 + - - +
81C ALA* 2.9 24.1 + - - +
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Residues in contact with LEU 78 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
42C LEU* 4.3 17.9 - - + +
45C LEU* 3.8 36.8 - - + -
46C THR* 3.4 27.1 + - - +
49C ILE* 4.2 13.7 - - + -
74C SER 2.8 20.3 + - - +
75C ARG* 3.2 7.2 + - - +
77C LEU* 1.3 71.9 - - - +
79C ARG* 1.3 60.1 + - - +
81C ALA* 3.2 5.5 + - + +
82C PHE* 2.9 26.9 + - - +
117C ILE* 4.8 5.6 - - + -
120C ASP* 3.9 27.4 - - + +
121C LEU* 4.2 9.6 - - + -
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Residues in contact with ARG 79 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
73C ASP* 4.5 0.4 + - - -
75C ARG* 2.8 28.8 + - - +
76C GLY* 3.8 18.7 - - - +
78C LEU* 1.3 72.3 - - - +
80C GLU* 1.3 57.8 + - - +
82C PHE* 3.4 4.2 + - - +
83C ARG* 2.9 27.4 + - - +
120C ASP* 2.6 71.3 + - + +
87F GLU* 2.9 47.1 + - - +
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Residues in contact with GLU 80 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
61C LEU* 4.3 20.2 - - + +
62C PHE* 3.7 40.7 - - + -
76C GLY 3.0 17.7 + - - +
77C LEU* 3.5 5.8 - - - +
79C ARG* 1.3 77.0 - - - +
81C ALA* 1.3 62.9 + - - +
83C ARG* 3.0 56.6 + - - +
84C GLN* 3.0 29.3 + - - +
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Residues in contact with ALA 81 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
46C THR* 3.8 25.1 - - + +
49C ILE* 4.4 7.3 - - + +
50C LEU* 3.9 26.1 - - + +
61C LEU* 4.5 4.5 - - + +
77C LEU 2.9 14.3 + - - +
78C LEU* 3.2 13.4 + - + +
80C GLU* 1.3 77.3 - - - +
82C PHE* 1.3 60.9 + - - +
84C GLN* 3.3 4.7 + - - +
85C VAL* 3.1 23.7 + - - +
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Residues in contact with PHE 82 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
49C ILE* 4.8 3.5 - - + +
78C LEU* 2.9 15.5 + - - +
79C ARG 3.7 4.9 - - - +
80C GLU 3.2 0.2 - - - -
81C ALA* 1.3 72.3 - - - +
83C ARG* 1.3 63.2 + - - +
85C VAL* 2.8 16.1 - - + +
86C GLN* 2.8 63.1 + - - +
91C LYS* 4.4 5.4 - - + -
92C ILE* 3.2 41.7 - - + -
120C ASP 3.7 22.2 - - - +
121C LEU* 3.3 25.1 - - + -
122C GLN* 3.4 38.1 - - + -
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Residues in contact with ARG 83 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
79C ARG 2.9 13.9 + - - +
80C GLU* 3.0 44.4 + - - +
82C PHE* 1.3 79.6 - - - +
84C GLN* 1.3 68.6 + - - +
86C GLN* 3.1 10.2 - - + +
87C GLU* 2.9 60.8 + - + +
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Residues in contact with GLN 84 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
50C LEU* 4.8 3.1 - - + +
55C LEU* 3.8 29.6 - - + +
60C LYS 5.0 2.8 + - - -
61C LEU* 4.1 30.5 + - - +
80C GLU* 3.0 36.0 + - - +
81C ALA 3.8 5.8 - - - +
83C ARG* 1.3 80.4 - - - +
85C VAL* 1.3 64.7 + - - +
87C GLU* 3.2 31.7 + - - +
88C LYS* 3.5 13.2 + - - +
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Residues in contact with VAL 85 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
49C ILE* 4.1 13.5 - - + +
53C ALA* 4.0 9.2 - - + -
55C LEU* 4.1 8.7 - - + +
81C ALA 3.1 9.1 + - - +
82C PHE* 2.8 50.9 - - + +
84C GLN* 1.3 76.6 - - - +
86C GLN* 1.3 62.9 + - - +
88C LYS* 3.0 14.4 + - - +
89C GLY 3.4 0.2 + - - -
90C TYR* 3.2 33.5 + - + +
155C LEU* 3.1 39.3 - - + -
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Residues in contact with GLN 86 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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82C PHE* 2.8 37.8 + - + +
83C ARG* 3.1 12.1 - - + +
85C VAL* 1.3 78.9 - - - +
87C GLU* 1.3 54.3 + - + +
89C GLY* 3.0 19.2 + - - -
90C TYR 2.7 31.8 + - - -
91C LYS* 4.3 1.2 - - - +
122C GLN* 3.7 21.8 + - - -
158C GLN* 2.9 31.4 + - - +
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Residues in contact with GLU 87 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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83C ARG* 2.9 43.6 + - + +
84C GLN* 3.4 23.4 - - - +
85C VAL 3.1 0.6 - - - -
86C GLN* 1.3 78.9 - - - +
88C LYS* 1.3 58.7 + - + +
89C GLY 3.1 3.1 + - - -
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Residues in contact with LYS 88 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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126A GLU* 3.1 30.5 + - - +
3C ARG* 5.8 0.2 - - - +
53C ALA* 2.8 33.8 + - + +
54C ALA* 4.8 1.4 + - - +
55C LEU* 4.0 24.3 - - + +
84C GLN 3.5 10.7 + - - +
85C VAL 3.0 9.6 + - - +
87C GLU* 1.3 78.9 - - + +
89C GLY* 1.3 59.4 + - - +
90C TYR* 3.6 15.5 - - + -
157C ARG* 3.1 30.7 + - - -
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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