Contacts of the helix formed by residues 130 - 145 (chain F) 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 F).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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129F VAL* 1.3 76.2 - - - +
131F ASN* 1.3 96.7 + - + +
132F GLU* 5.1 0.2 - - - +
133F ASP* 3.3 12.2 + - - +
134F LEU* 3.1 16.9 + - - +
270F SER* 3.6 21.0 + - - -
271F GLU* 4.7 19.5 - - - +
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Residues in contact with ASN 131 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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109F PRO* 5.2 1.3 - - - +
110F ALA 6.1 0.4 - - - -
130F THR* 1.3 109.0 + - + +
132F GLU* 1.3 76.6 + - + +
134F LEU* 2.9 7.9 + - - +
135F LEU* 2.7 36.4 + - - +
190F MET* 5.9 4.4 - - - +
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Residues in contact with GLU 132 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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33F LEU* 4.0 13.3 - - - +
37F HIS* 3.3 39.5 + - + +
130F THR 5.1 0.2 - - - +
131F ASN* 1.3 101.6 + - + +
133F ASP* 1.3 55.2 + - - +
135F LEU* 3.2 7.9 + - - +
136F THR* 2.6 43.0 + - - +
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Residues in contact with ASP 133 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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129F VAL* 3.8 27.4 - - + +
130F THR 3.3 10.4 + - - +
131F ASN 3.2 0.6 - - - -
132F GLU* 1.3 80.6 - - - +
134F LEU* 1.3 63.0 + - - +
136F THR* 3.2 10.3 + - - -
137F ASN* 3.0 26.0 + - - +
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Residues in contact with LEU 134 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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109F PRO* 3.7 25.8 - - + -
114F ASN* 5.0 2.7 - - + +
117F ALA 4.2 3.6 - - - +
118F ALA* 4.5 11.9 - - + +
121F ASN* 3.7 36.1 - - + +
129F VAL* 3.7 23.1 - - - +
130F THR* 3.1 18.5 + - - +
131F ASN 2.9 13.8 + - - +
133F ASP* 1.3 73.8 - - - +
135F LEU* 1.3 64.5 + - - +
137F ASN* 2.9 14.1 + - - +
138F CYS* 3.1 24.3 + - - -
270F SER* 3.9 23.8 - - - -
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Residues in contact with LEU 135 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
33F LEU* 3.7 25.6 - - + +
37F HIS* 3.5 39.5 - - + +
38F VAL* 3.5 22.0 - - + -
78F MET* 3.8 12.8 - - + -
108F LEU* 4.3 5.8 - - + -
109F PRO* 3.6 39.2 - - + +
131F ASN 2.7 16.5 + - - +
132F GLU* 3.5 9.0 - - - +
134F LEU* 1.3 71.6 - - - +
136F THR* 1.3 55.7 + - - +
138F CYS* 3.6 1.6 + - - +
139F THR* 2.5 36.0 + - - +
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Residues in contact with THR 136 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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37F HIS* 4.7 15.5 - - - +
41F LEU* 4.4 15.2 - - + +
132F GLU 2.6 28.3 + - - -
133F ASP* 3.3 12.2 + - - -
135F LEU* 1.3 73.2 - - - +
137F ASN* 1.3 60.7 + - - +
139F THR* 3.3 7.6 + - - -
140F LEU* 3.0 41.2 + - + +
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Residues in contact with ASN 137 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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121F ASN* 3.0 33.9 - - - +
126F TYR* 3.3 38.1 - - + +
129F VAL* 3.6 20.6 - - - +
133F ASP* 3.0 12.9 + - - +
134F LEU 2.9 5.6 + - - +
136F THR* 1.3 80.5 - - - +
138F CYS* 1.3 58.9 + - - +
140F LEU* 3.0 17.4 + - - +
141F LEU* 2.8 32.1 + - - +
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Residues in contact with CYS 138 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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106F CYS* 4.7 0.3 - - - -
107F SER 3.7 21.1 - - - +
108F LEU* 3.7 14.9 - - + +
109F PRO* 3.9 20.4 - - + -
117F ALA* 3.6 25.4 - - - -
120F LEU* 5.7 1.8 - - - -
121F ASN* 4.7 5.4 - - - -
134F LEU* 3.1 22.9 + - - +
135F LEU 4.1 0.7 - - - +
137F ASN* 1.3 73.9 - - - +
139F THR* 1.3 55.9 + - - +
141F LEU* 3.2 19.5 - - + +
142F LEU* 3.0 22.5 + - - +
362F VAL* 4.6 2.8 - - - +
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Residues in contact with THR 139 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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37F HIS 5.3 0.4 - - - -
38F VAL* 3.7 42.8 - - + +
41F LEU* 3.7 32.5 - - + -
42F LEU* 4.1 7.4 - - + -
108F LEU* 3.9 8.8 - - + +
135F LEU* 2.5 26.5 + - - +
136F THR* 3.5 6.2 - - - -
137F ASN 3.1 0.8 - - - -
138F CYS* 1.3 73.2 - - - +
140F LEU* 1.3 56.6 + - - +
141F LEU 3.2 0.2 - - - -
142F LEU* 3.3 5.0 + - + +
143F CYS* 2.8 39.2 + - - -
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Residues in contact with LEU 140 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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41F LEU* 4.6 20.2 - - + +
126F TYR* 3.9 15.5 - - + +
136F THR* 3.0 29.8 + - + +
137F ASN* 3.0 18.6 + - - +
139F THR* 1.3 73.8 - - - +
141F LEU* 1.3 54.3 + - - +
143F CYS* 2.9 10.5 + - + +
144F ARG* 2.7 68.7 + - - +
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Residues in contact with LEU 141 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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120F LEU* 3.7 33.9 - - + +
121F ASN* 4.7 4.3 - - - +
124F ALA* 4.1 14.1 - - + -
126F TYR* 4.4 10.3 - - + -
137F ASN 2.8 17.8 + - - +
138F CYS* 3.2 19.7 - - + +
139F THR 3.2 0.2 - - - -
140F LEU* 1.3 75.4 - - - +
142F LEU* 1.3 63.5 + - - +
144F ARG* 2.9 29.1 + - + +
145F ARG* 3.1 9.4 + - - -
146F LEU 4.2 4.3 + - - +
362F VAL* 4.1 15.3 - - + +
363F SER* 4.2 10.1 - - - +
364F GLY* 3.8 27.4 - - - +
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Residues in contact with LEU 142 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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11F LEU* 4.0 21.3 - - + -
15F CYS* 5.7 0.2 - - - -
17F VAL* 4.7 14.6 - - + -
42F LEU* 4.0 22.9 - - + -
47F ILE* 3.6 24.4 - - + +
74F ALA* 5.5 1.1 - - + -
76F VAL* 4.4 16.4 - - + -
106F CYS* 4.0 24.5 - - + -
108F LEU* 4.6 13.5 - - + -
138F CYS 3.0 10.3 + - - +
139F THR* 3.6 6.7 - - - +
141F LEU* 1.3 78.0 - - - +
143F CYS* 1.3 58.0 + - - +
145F ARG* 3.0 20.9 + - - +
362F VAL* 3.7 15.3 - - + +
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Residues in contact with CYS 143 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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13F ARG* 5.0 3.5 + - - -
41F LEU* 3.7 33.0 - - - -
42F LEU* 4.1 11.2 - - - -
45F ALA* 3.5 26.7 - - + +
47F ILE* 3.9 6.3 - - - -
139F THR 2.8 26.7 + - - +
140F LEU* 2.9 14.8 + - + +
142F LEU* 1.3 73.4 - - - +
144F ARG* 1.3 61.6 + - - +
145F ARG* 3.8 17.2 + - - +
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Residues in contact with ARG 144 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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126F TYR* 2.7 33.3 + - - -
140F LEU* 2.7 50.7 + - - +
141F LEU* 3.4 19.2 - - + +
143F CYS* 1.3 72.8 - - - +
145F ARG* 1.3 72.2 + - - +
146F LEU* 3.4 23.4 + - + +
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Residues in contact with ARG 145 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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10F VAL* 3.3 6.6 - - + +
11F LEU* 2.8 60.6 + - + +
12F PRO 2.4 31.5 + - - -
13F ARG* 3.2 40.5 - - - +
15F CYS* 3.5 18.6 - - - +
45F ALA 2.8 30.3 + - - -
46F GLU 3.4 15.8 + - - -
47F ILE* 3.7 8.0 - - + +
141F LEU 3.1 3.6 + - - -
142F LEU* 3.0 21.9 + - - +
143F CYS 3.8 8.9 + - - +
144F ARG* 1.3 81.6 - - - +
146F LEU* 1.3 60.5 + - + +
147F LEU* 4.3 0.9 - - - -
362F VAL* 5.6 0.4 - - - -
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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