Contacts of the helix formed by residues 132 - 149 (chain C) in PDB entry 3VON
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 ASN 132 (chain C).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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128C GLN* 3.1 35.5 + - - +
131C THR* 1.3 80.3 + - - +
133C GLU* 1.3 57.4 + - - +
134C ALA* 3.5 3.5 + - - +
135C GLN* 3.3 28.0 + - + +
136C ALA 2.8 23.4 + - - -
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Residues in contact with GLU 133 (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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116C ASN 4.9 3.1 - - - +
129C TRP* 3.6 43.2 + - + +
131C THR 2.9 12.3 + - - +
132C ASN* 1.3 68.9 - - - +
134C ALA* 1.3 60.2 + - - +
136C ALA* 3.0 6.3 + - - +
137C ILE* 2.8 47.5 + - + +
6G ARG* 4.8 11.0 + - - -
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Residues in contact with ALA 134 (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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132C ASN* 3.5 1.7 + - - +
133C GLU* 1.3 78.0 - - - +
135C GLN* 1.3 60.8 + - - +
137C ILE* 3.6 11.8 + - - +
138C GLU* 3.2 26.3 + - - +
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Residues in contact with GLN 135 (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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128C GLN* 3.9 19.2 - - - +
132C ASN* 3.3 34.9 + - - +
134C ALA* 1.3 78.4 - - - +
136C ALA* 1.3 63.3 + - - +
138C GLU* 3.4 8.1 + - - +
139C THR* 2.8 36.1 + - - +
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Residues in contact with ALA 136 (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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76C TYR* 3.9 6.7 - - + -
128C GLN* 4.0 19.7 - - - +
129C TRP* 3.7 35.6 - - + -
132C ASN 2.8 14.5 + - - +
133C GLU 3.3 8.1 - - - +
135C GLN* 1.3 77.2 - - - +
137C ILE* 1.3 56.2 + - - +
139C THR* 3.0 10.5 + - - -
140C ALA* 3.0 27.9 + - - +
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Residues in contact with ILE 137 (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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46C PRO* 3.8 27.4 - - + -
129C TRP* 4.3 14.8 - - - +
133C GLU* 2.8 44.4 + - + +
134C ALA* 3.9 9.9 - - - +
136C ALA* 1.3 72.9 - - - +
138C GLU* 1.3 58.2 + - + +
140C ALA* 3.4 7.3 + - - +
141C ARG* 3.0 44.2 + - - +
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Residues in contact with GLU 138 (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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134C ALA 3.2 19.1 + - - +
135C GLN* 3.8 8.5 - - - +
136C ALA 3.3 0.2 - - - -
137C ILE* 1.3 74.8 - - + +
139C THR* 1.3 64.1 + - - +
141C ARG* 3.6 15.8 + - + +
142C ALA* 3.2 22.0 + - - +
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Residues in contact with THR 139 (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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76C TYR* 3.8 33.9 - - + -
128C GLN* 4.6 2.6 + - - -
135C GLN* 2.8 33.2 + - - +
136C ALA* 3.0 10.3 + - - -
138C GLU* 1.3 73.4 - - - +
140C ALA* 1.3 60.3 + - - +
142C ALA* 3.2 4.9 + - + +
143C TRP* 2.9 52.9 + - + +
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Residues in contact with ALA 140 (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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46C PRO* 3.7 19.5 - - + -
47C PHE* 3.8 9.0 - - + -
76C TYR* 3.7 30.9 - - + +
129C TRP* 3.9 7.9 - - + -
136C ALA 3.0 12.0 + - - +
137C ILE 3.7 7.6 - - - +
139C THR* 1.3 72.9 - - - +
141C ARG* 1.3 57.1 + - - +
143C TRP* 3.4 1.6 + - - +
144C THR* 2.7 38.7 + - - -
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Residues in contact with ARG 141 (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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44C ASP* 5.5 3.0 + - - +
45C SER 3.8 23.2 + - - -
46C PRO* 3.5 17.2 + - + +
48C GLU* 5.0 15.4 + - - +
137C ILE* 3.0 34.0 + - - +
138C GLU* 3.7 18.6 - - + +
139C THR 3.2 0.2 - - - -
140C ALA* 1.3 77.4 - - - +
142C ALA* 1.3 61.2 + - - +
144C THR* 3.4 5.1 + - - -
145C ARG* 3.2 24.7 + - - +
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Residues in contact with ALA 142 (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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138C GLU 3.2 11.0 + - - +
139C THR* 3.5 10.3 - - + +
141C ARG* 1.3 79.1 - - - +
143C TRP* 1.3 67.7 + - + +
145C ARG* 3.2 15.6 + - - +
146C LEU* 3.3 27.2 + - + +
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Residues in contact with TRP 143 (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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39B GLU* 5.7 2.2 - - - -
52C PHE* 6.1 0.4 - - - -
74C LYS* 3.6 47.9 - - + +
75C ILE* 3.9 10.8 - - - -
76C TYR* 3.6 54.7 - + + +
82C LYS* 6.1 5.2 - - + -
139C THR* 2.9 32.8 + - + +
140C ALA 4.0 3.4 - - - +
142C ALA* 1.3 79.0 - - + +
144C THR* 1.3 64.4 + - - +
145C ARG 3.2 0.2 - - - -
146C LEU* 4.1 6.1 - - + +
147C TYR* 3.2 49.6 + + + +
148C ALA* 3.9 0.3 + - - +
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Residues in contact with THR 144 (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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46C PRO 3.4 11.4 + - - +
47C PHE* 3.5 40.0 - - - +
48C GLU 4.0 5.8 - - - +
50C GLY* 3.7 20.6 - - - +
52C PHE* 4.0 4.4 - - + -
140C ALA 2.7 21.2 + - - -
141C ARG* 3.4 8.3 - - - +
143C TRP* 1.3 77.3 - - - +
145C ARG* 1.3 58.0 + - + +
148C ALA* 3.0 29.1 + - + -
149C MET* 3.3 15.1 + - + +
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Residues in contact with ARG 145 (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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141C ARG 3.2 12.7 + - - +
142C ALA* 3.2 14.4 + - - +
144C THR* 1.3 82.8 - - - +
146C LEU* 1.3 64.4 + - + +
147C TYR 3.6 0.2 + - - -
149C MET* 3.2 57.8 + - - +
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Residues in contact with LEU 146 (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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142C ALA* 3.3 26.6 + - + +
143C TRP* 4.8 7.9 - - + +
145C ARG* 1.3 80.1 - - + +
147C TYR* 1.3 100.9 + - + +
149C MET 5.1 0.2 - - - -
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Residues in contact with TYR 147 (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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73C THR* 3.6 12.9 - - + +
74C LYS* 3.5 63.5 - - + +
143C TRP* 3.2 47.4 + + + +
145C ARG 3.4 0.2 - - - -
146C LEU* 1.3 111.2 - - + +
148C ALA* 1.3 62.0 + - - +
149C MET 3.4 2.5 + - - -
150C ASN* 4.7 8.2 + - - +
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Residues in contact with ALA 148 (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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49C GLY 4.9 0.3 - - - +
50C GLY* 3.8 9.8 - - - -
51C THR* 3.1 40.2 + - - +
52C PHE* 3.6 38.4 - - + -
73C THR* 3.9 3.1 - - + -
143C TRP 3.9 0.6 + - - +
144C THR* 3.0 16.6 + - - +
147C TYR* 1.3 78.2 - - + +
149C MET* 1.3 59.6 + - - +
150C ASN 3.5 4.5 + - - -
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Residues in contact with MET 149 (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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48C GLU 5.2 1.3 - - - +
49C GLY* 3.8 31.6 - - - +
50C GLY* 4.1 4.3 - - - -
144C THR* 3.3 17.9 + - - +
145C ARG* 3.2 71.6 + - - +
147C TYR 3.4 1.8 - - - -
148C ALA* 1.3 79.9 - - - +
150C ASN* 1.3 71.5 + - - +
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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