Contacts of the helix formed by residues 130 - 144 (chain C) in PDB entry 3VZC
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 130 (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 5.3 0.2 - - - -
129C VAL* 1.3 78.8 - - - +
131C ASN* 1.3 97.3 + - + +
133C ASP* 3.2 23.0 + - - +
134C LEU* 3.2 8.5 + - - -
270C SER* 3.8 16.4 + - - -
271C GLU* 4.5 21.9 + - - +
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Residues in contact with ASN 131 (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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33C LEU* 6.5 0.9 - - - -
109C PRO* 4.9 2.9 - - - +
130C THR* 1.3 96.6 + - + +
132C GLU* 1.3 79.3 + - - +
134C LEU* 3.3 9.1 + - - +
135C LEU* 3.0 25.7 + - - +
190C MET* 5.5 9.7 - - - +
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Residues in contact with GLU 132 (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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33C LEU* 4.2 21.1 - - + +
37C HIS* 3.4 33.0 - - + +
131C ASN* 1.3 94.9 - - - +
133C ASP* 1.3 57.4 + - - +
135C LEU* 3.6 8.5 - - + +
136C THR* 2.8 42.0 + - - -
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Residues in contact with ASP 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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129C VAL* 3.8 25.0 - - + +
130C THR* 3.2 12.9 + - - +
132C GLU* 1.3 81.3 - - - +
134C LEU* 1.3 61.1 + - - +
136C THR* 3.5 5.6 + - - -
137C ASN* 3.1 30.9 + - - +
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Residues in contact with LEU 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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109C PRO* 3.8 24.9 - - + -
114C ASN* 4.6 6.7 - - + -
117C ALA* 4.8 0.2 - - + -
118C ALA* 4.3 15.3 - - + +
121C ASN* 3.6 39.3 - - + +
129C VAL* 3.7 16.1 - - + +
130C THR* 3.2 15.0 + - - -
131C ASN 3.5 9.9 - - - +
133C ASP* 1.3 75.6 - - - +
135C LEU* 1.3 67.0 - - - +
137C ASN* 3.3 2.8 + - - +
138C CYS* 3.0 30.1 + - - -
270C SER* 3.9 27.6 - - - -
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Residues in contact with LEU 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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33C LEU* 3.8 37.2 - - + +
37C HIS* 3.9 21.5 - - + -
38C VAL* 4.0 11.2 - - + -
78C MET* 3.9 19.3 - - + -
108C LEU* 4.0 10.1 - - + -
109C PRO* 3.1 44.8 - - + +
131C ASN 3.0 13.6 + - - +
132C GLU* 3.3 9.4 + - - +
134C LEU* 1.3 77.2 - - - +
136C THR* 1.3 57.5 + - - +
138C CYS* 3.5 1.0 + - - +
139C THR* 2.7 33.2 + - - +
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Residues in contact with THR 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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37C HIS* 3.4 23.9 - - - +
41C LEU* 4.3 17.9 - - + +
132C GLU 2.8 27.6 + - - -
133C ASP* 3.8 6.7 - - - -
134C LEU 3.3 0.2 - - - -
135C LEU* 1.3 73.3 - - - +
137C ASN* 1.3 61.4 + - - +
139C THR* 3.0 8.5 + - - -
140C LEU* 2.9 39.4 + - + +
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Residues in contact with ASN 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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121C ASN* 3.0 31.6 - - - +
126C TYR* 3.2 37.9 + - + +
129C VAL* 3.5 18.2 - - - +
133C ASP* 3.1 14.3 + - - +
134C LEU 3.3 4.2 + - - +
136C THR* 1.3 76.1 - - - +
138C CYS* 1.3 64.5 + - - +
140C LEU* 2.9 18.6 + - - +
141C LEU* 2.9 25.6 + - - +
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Residues in contact with CYS 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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106C CYS* 4.8 2.8 - - - -
107C SER 3.8 16.1 - - - +
108C LEU* 3.7 9.8 - - + +
109C PRO* 3.8 14.1 - - + -
117C ALA* 3.6 43.7 - - - -
120C LEU* 5.7 1.8 - - - -
121C ASN* 4.7 5.6 - - - -
134C LEU* 3.0 24.2 + - - +
135C LEU 4.0 0.4 - - - +
137C ASN* 1.3 78.3 - - - +
139C THR* 1.3 59.4 + - - +
141C LEU* 3.4 17.4 - - + +
142C LEU* 3.3 16.8 + - - +
362C VAL* 4.9 0.9 - - - +
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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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37C HIS 4.6 0.6 + - - -
38C VAL* 3.8 48.3 - - + +
41C LEU* 3.8 24.9 - - + -
42C LEU* 4.4 4.5 - - + -
108C LEU* 3.9 13.0 - - + +
135C LEU* 2.7 20.8 + - - +
136C THR* 3.3 9.6 - - - -
137C ASN 3.0 1.2 - - - -
138C CYS* 1.3 75.3 - - - +
140C LEU* 1.3 59.9 + - - +
141C LEU 3.2 0.2 - - - -
142C LEU* 3.1 6.5 + - + +
143C CYS* 2.9 29.0 + - - -
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Residues in contact with LEU 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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41C LEU* 4.4 20.0 - - + -
126C TYR* 4.2 8.1 - - + +
136C THR* 2.9 27.1 + - + +
137C ASN* 3.3 19.3 - - - +
139C THR* 1.3 73.0 - - - +
141C LEU* 1.3 55.1 + - - +
143C CYS* 3.0 12.1 + - + +
144C ARG* 2.8 71.9 + - - +
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Residues in contact with LEU 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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120C LEU* 4.0 31.0 - - + +
121C ASN* 4.6 4.7 - - - +
124C ALA* 3.9 22.2 - - + -
126C TYR* 4.5 6.7 - - + -
137C ASN 2.9 13.4 + - - +
138C CYS* 3.4 22.7 - - + +
139C THR 3.2 0.2 - - - -
140C LEU* 1.3 75.9 - - - +
142C LEU* 1.3 62.0 + - - +
144C ARG* 3.4 29.2 + - + +
145C ARG* 3.4 8.1 + - - -
146C LEU 4.3 4.9 + - - -
362C VAL* 4.3 15.0 - - + +
363C SER* 4.1 18.0 - - - +
364C GLY* 4.0 18.6 - - - +
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Residues in contact with LEU 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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11C LEU* 3.9 23.8 - - + -
17C VAL* 5.0 10.1 - - + -
42C LEU* 4.2 18.6 - - + -
47C ILE* 3.6 19.0 - - + +
74C ALA* 5.5 0.7 - - + -
76C VAL* 3.9 21.5 - - + -
106C CYS* 3.8 25.4 - - + -
108C LEU* 4.6 11.9 - - + -
138C CYS 3.3 9.1 + - - +
139C THR* 3.1 11.7 + - - +
141C LEU* 1.3 79.2 - - - +
143C CYS* 1.3 57.3 + - - +
145C ARG* 3.0 20.0 + - - +
362C VAL* 4.0 18.3 - - + +
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Residues in contact with CYS 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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13C ARG* 5.2 2.8 + - - -
41C LEU* 3.7 43.1 - - - -
42C LEU* 4.2 13.0 - - - -
45C ALA* 3.9 15.0 - - + +
47C ILE* 3.9 7.6 - - - -
139C THR 2.9 19.1 + - - +
140C LEU* 3.0 15.9 + - + +
142C LEU* 1.3 76.3 - - - +
144C ARG* 1.3 61.9 + - + +
145C ARG* 3.5 18.2 + - - +
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Residues in contact with ARG 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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126C TYR* 2.7 30.1 + - - -
140C LEU* 2.8 51.4 + - - +
141C LEU* 3.7 20.0 - - + +
142C LEU 3.2 0.4 - - - -
143C CYS* 1.3 75.5 - - + +
145C ARG* 1.3 67.7 + - - +
146C LEU* 3.3 23.4 + - + +
363C SER 5.8 1.3 - - - +
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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