Contacts of the helix formed by residues 130 - 145 (chain B) 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 B).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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128B GLN 5.6 1.1 - - - +
129B VAL* 1.3 77.7 - - - +
131B ASN* 1.3 96.9 + - - +
132B GLU 3.2 1.0 + - - -
133B ASP* 3.2 19.1 + - - +
134B LEU* 3.9 5.4 - - - -
270B SER* 4.1 15.3 + - - -
271B GLU* 4.5 22.5 - - - +
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Residues in contact with ASN 131 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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33B LEU* 6.5 0.7 - - - -
109B PRO* 5.0 2.1 - - - +
130B THR* 1.3 95.7 + - + +
132B GLU* 1.3 84.0 + - + +
134B LEU* 3.1 10.2 + - - +
135B LEU* 3.0 22.3 + - - +
190B MET* 5.8 5.9 - - - +
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Residues in contact with GLU 132 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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33B LEU* 3.5 31.7 - - - +
37B HIS* 3.9 26.8 - - - +
130B THR 3.2 0.2 + - - -
131B ASN* 1.3 93.7 - - + +
133B ASP* 1.3 62.4 + - - +
135B LEU* 3.4 9.0 + - - +
136B THR* 2.9 33.0 + - - -
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Residues in contact with ASP 133 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
129B VAL* 3.8 25.3 - - + +
130B THR 3.2 10.9 + - - +
132B GLU* 1.3 80.6 - - - +
134B LEU* 1.3 59.3 + - - +
136B THR* 3.6 6.3 + - - -
137B ASN* 3.0 35.5 + - - +
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Residues in contact with LEU 134 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
109B PRO* 3.9 24.7 - - + -
114B ASN* 4.4 5.8 - - + +
117B ALA 4.1 6.5 - - - +
118B ALA* 4.2 14.4 - - - +
121B ASN* 3.6 37.9 - - + +
129B VAL* 3.7 24.8 - - + +
130B THR* 3.5 8.3 + - - -
131B ASN 3.1 10.7 + - - +
133B ASP* 1.3 77.8 - - - +
135B LEU* 1.3 58.8 + - - +
137B ASN* 3.9 0.8 - - - +
138B CYS* 2.9 37.5 + - - -
270B SER* 4.0 26.7 - - - +
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Residues in contact with LEU 135 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
33B LEU* 4.0 20.6 - - + +
37B HIS* 3.6 28.5 - - + -
38B VAL* 3.8 17.5 - - + -
78B MET* 3.8 28.3 - - + -
108B LEU* 3.9 17.3 - - + -
109B PRO* 3.3 31.1 - - + +
131B ASN 3.0 12.5 + - - +
132B GLU* 3.7 10.3 - - - +
133B ASP 3.3 0.2 - - - -
134B LEU* 1.3 76.7 - - - +
136B THR* 1.3 52.4 + - - +
138B CYS* 3.6 1.7 - - - +
139B THR* 2.7 41.0 + - - +
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Residues in contact with THR 136 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
37B HIS* 3.7 22.0 + - - +
41B LEU* 4.3 13.9 - - + +
132B GLU 2.9 19.7 + - - -
133B ASP* 3.6 8.4 - - - -
135B LEU* 1.3 76.3 - - - +
137B ASN* 1.3 68.9 + - - +
139B THR* 3.1 9.6 + - - -
140B LEU* 2.8 38.1 + - + +
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Residues in contact with ASN 137 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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121B ASN* 3.0 33.1 - - - +
126B TYR* 3.8 34.6 - - + +
129B VAL* 3.2 26.7 - - - +
133B ASP* 3.0 16.8 + - - +
134B LEU 3.9 2.7 - - - +
136B THR* 1.3 78.5 - - - +
138B CYS* 1.3 62.0 + - - +
140B LEU* 3.0 26.4 + - - +
141B LEU* 3.0 18.2 + - - +
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Residues in contact with CYS 138 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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106B CYS* 5.1 0.2 - - - -
107B SER 3.8 9.0 - - - +
108B LEU* 3.6 22.4 - - + +
109B PRO* 3.9 4.7 - - + -
117B ALA* 3.7 41.1 - - - -
120B LEU* 5.6 2.2 - - - -
121B ASN* 4.6 6.7 - - - -
134B LEU* 2.9 28.3 + - - +
135B LEU 3.7 1.8 - - - +
137B ASN* 1.3 75.1 - - - +
139B THR* 1.3 63.4 + - - +
141B LEU* 3.2 23.0 + - + +
142B LEU* 3.2 9.5 + - - +
362B VAL* 4.8 1.9 - - - +
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Residues in contact with THR 139 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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37B HIS 4.3 0.3 + - - -
38B VAL* 3.5 43.1 - - + +
41B LEU* 3.8 35.7 - - + -
42B LEU* 4.5 5.4 - - + -
108B LEU* 3.6 11.8 - - + +
135B LEU* 2.7 29.3 + - - +
136B THR* 3.4 6.2 - - - -
138B CYS* 1.3 72.4 - - - +
140B LEU* 1.3 57.5 + - - +
142B LEU* 2.9 20.2 + - + +
143B CYS* 2.9 16.9 + - - -
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Residues in contact with LEU 140 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
41B LEU* 4.4 23.1 - - + -
126B TYR* 4.3 9.4 - - + +
136B THR* 2.8 32.0 + - + +
137B ASN* 3.0 19.9 + - - +
139B THR* 1.3 71.8 - - - +
141B LEU* 1.3 66.3 + - - +
143B CYS* 3.3 10.1 + - + +
144B ARG* 3.1 57.1 + - + +
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Residues in contact with LEU 141 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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120B LEU* 3.7 35.2 - - + +
121B ASN* 4.4 4.7 - - - +
124B ALA* 3.8 22.7 - - + -
126B TYR* 4.2 11.4 - - + -
137B ASN 3.0 13.8 + - - +
138B CYS* 3.2 17.5 + - - +
140B LEU* 1.3 75.9 - - - +
142B LEU* 1.3 63.6 + - - +
144B ARG* 3.2 26.6 + - + +
145B ARG* 3.3 8.3 + - - -
146B LEU 4.5 3.1 + - - +
362B VAL* 3.7 18.1 - - + +
363B SER* 4.3 19.2 - - - +
364B GLY* 4.3 12.1 - - - +
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Residues in contact with LEU 142 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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11B LEU* 3.9 15.5 - - + -
17B VAL* 4.8 9.0 - - + -
42B LEU* 3.9 22.7 - - + -
47B ILE* 3.8 14.8 - - + +
74B ALA* 5.3 1.1 - - + -
76B VAL* 3.9 27.4 - - + -
106B CYS* 3.9 17.7 - - + -
108B LEU* 4.6 11.0 - - + -
138B CYS 3.2 5.0 + - - +
139B THR* 2.9 11.6 + - + +
141B LEU* 1.3 77.7 - - - +
143B CYS* 1.3 59.0 + - - +
145B ARG* 3.0 25.5 + - - +
362B VAL* 3.5 33.1 - - + +
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Residues in contact with CYS 143 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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13B ARG* 4.7 4.5 + - - -
41B LEU* 3.5 45.1 - - - -
42B LEU* 4.1 9.6 - - - -
45B ALA* 3.6 22.3 - - + +
47B ILE* 4.1 7.4 - - - -
139B THR* 2.9 20.5 + - - +
140B LEU* 3.3 14.8 + - + +
142B LEU* 1.3 75.8 - - - +
144B ARG* 1.3 60.6 + - + +
145B ARG* 3.4 11.8 + - - +
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Residues in contact with ARG 144 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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10B VAL* 5.6 0.2 - - - +
126B TYR* 2.9 29.7 + - - -
140B LEU* 3.1 43.6 + - + +
141B LEU* 3.8 18.3 - - - +
142B LEU 3.1 0.8 - - - -
143B CYS* 1.3 76.7 - - + +
145B ARG* 1.3 64.9 + - - +
146B LEU* 3.1 28.0 + - + +
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Residues in contact with ARG 145 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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10B VAL* 3.1 8.0 - - + -
11B LEU* 2.7 67.6 + - + +
12B PRO 2.9 14.9 + - - -
13B ARG* 3.1 41.9 - - - +
15B CYS* 3.6 16.0 - - - +
45B ALA* 2.7 30.9 + - - +
46B GLU 3.0 18.2 + - - -
47B ILE* 3.2 15.3 - - + +
141B LEU 3.3 4.5 + - - -
142B LEU 3.0 20.3 + - - +
143B CYS 3.9 8.8 + - - +
144B ARG* 1.3 79.4 - - - +
146B LEU* 1.3 61.9 + - - +
147B LEU* 4.6 1.3 - - - -
362B VAL* 5.4 0.9 - - - -
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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
------------------------------------------------------------
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