Contacts of the helix formed by residues 130 - 145 (chain A) 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 A).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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128A GLN 5.2 0.4 - - - -
129A VAL* 1.3 78.1 + - - +
131A ASN* 1.3 91.1 + - + +
132A GLU 3.1 3.3 + - - -
133A ASP* 3.1 16.6 + - - +
134A LEU* 3.2 7.5 + - - -
270A SER* 3.2 22.7 + - - -
271A GLU* 4.1 23.7 + - - +
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Residues in contact with ASN 131 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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109A PRO* 5.0 2.8 - - - +
110A ALA 5.6 3.0 + - - -
111A GLY 5.6 4.0 + - - -
130A THR* 1.3 92.9 + - + +
132A GLU* 1.3 73.5 + - + +
134A LEU* 3.2 9.1 + - - +
135A LEU* 3.0 26.2 + - - +
190A MET* 5.5 10.1 - - - +
270A SER* 5.4 0.8 + - - -
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Residues in contact with GLU 132 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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33A LEU* 3.6 25.2 - - + +
37A HIS* 3.9 29.7 + - + +
130A THR 3.1 0.2 + - - -
131A ASN* 1.3 82.5 + - + +
133A ASP* 1.3 62.8 + - - +
135A LEU* 3.4 10.6 + - - +
136A THR* 3.0 33.2 + - - -
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Residues in contact with ASP 133 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
129A VAL* 3.7 27.0 - - + +
130A THR 3.1 11.1 + - - +
132A GLU* 1.3 77.2 - - - +
134A LEU* 1.3 59.0 + - - +
136A THR* 3.4 7.2 + - - -
137A ASN* 3.0 33.0 + - - +
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Residues in contact with LEU 134 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
109A PRO* 3.7 25.6 - - + -
114A ASN* 4.5 7.0 - - + +
117A ALA 4.3 2.7 - - - +
118A ALA* 4.3 16.2 - - + +
121A ASN* 3.7 38.6 - - + +
129A VAL* 3.6 16.0 - - + +
130A THR* 3.2 12.7 + - - -
131A ASN 3.2 12.0 + - - +
133A ASP* 1.3 76.2 - - - +
135A LEU* 1.3 66.1 + - - +
137A ASN* 3.2 2.9 + - - +
138A CYS* 3.0 33.3 + - - -
270A SER* 4.1 25.4 - - - -
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Residues in contact with LEU 135 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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33A LEU* 3.8 33.2 - - + +
37A HIS* 3.8 26.7 - - + -
38A VAL* 3.7 21.8 - - + -
78A MET* 3.9 15.9 - - + -
108A LEU* 4.0 8.7 - - + -
109A PRO* 3.5 39.8 - - + +
131A ASN 3.0 11.1 + - - +
132A GLU* 3.4 10.3 + - - +
134A LEU* 1.3 75.3 - - - +
136A THR* 1.3 57.0 + - - +
138A CYS* 3.6 0.9 + - - +
139A THR* 2.7 34.0 + - - +
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Residues in contact with THR 136 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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37A HIS* 3.6 25.4 + - - +
41A LEU* 4.3 13.4 - - + +
132A GLU 3.0 17.7 + - - -
133A ASP* 3.6 9.6 + - - -
134A LEU 3.2 0.2 - - - -
135A LEU* 1.3 75.9 - - - +
137A ASN* 1.3 61.3 + - - +
139A THR* 3.4 7.2 + - - -
140A LEU* 3.0 41.6 + - + +
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Residues in contact with ASN 137 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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121A ASN* 3.2 26.8 - - - +
126A TYR* 3.9 31.1 - - + +
129A VAL* 3.1 34.6 - - - +
133A ASP* 3.0 14.3 + - - +
134A LEU 3.2 4.2 + - - +
136A THR* 1.3 79.2 - - - +
138A CYS* 1.3 57.6 + - - +
140A LEU* 3.2 17.6 + - - +
141A LEU* 3.0 31.1 + - - +
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Residues in contact with CYS 138 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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106A CYS* 4.7 0.7 - - - -
107A SER 3.8 16.6 - - - +
108A LEU* 3.7 9.8 - - + +
109A PRO* 3.8 20.9 - - + -
117A ALA* 3.7 31.4 - - - -
120A LEU* 5.6 2.2 - - - -
121A ASN* 4.6 6.7 - - - -
134A LEU* 3.0 28.0 + - - +
135A LEU 4.1 0.2 - - - +
137A ASN* 1.3 73.6 - - - +
139A THR* 1.3 60.6 + - - +
141A LEU* 3.4 15.1 + - + +
142A LEU* 3.0 22.7 + - - +
362A VAL* 4.7 2.4 - - - +
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Residues in contact with THR 139 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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37A HIS 4.7 0.7 + - - -
38A VAL* 3.5 42.7 - - + +
41A LEU* 3.7 32.3 - - + -
42A LEU* 4.5 5.2 - - + -
108A LEU* 3.7 12.0 - - + +
135A LEU 2.7 23.4 + - - -
136A THR* 3.6 6.7 - - - -
138A CYS* 1.3 76.9 - - - +
140A LEU* 1.3 51.8 + - - +
142A LEU* 3.1 5.5 + - + +
143A CYS* 2.8 35.3 + - - -
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Residues in contact with LEU 140 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
41A LEU* 4.2 15.5 - - + -
126A TYR* 4.2 7.9 - - + +
136A THR* 3.0 32.5 + - + +
137A ASN* 3.2 21.7 + - - +
139A THR* 1.3 72.7 - - - +
141A LEU* 1.3 60.5 + - - +
143A CYS* 3.3 11.7 + - + +
144A ARG* 2.9 64.2 + - - +
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Residues in contact with LEU 141 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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120A LEU* 3.9 33.2 - - + +
121A ASN* 4.4 5.2 - - - +
124A ALA* 3.8 17.7 - - + -
126A TYR* 4.1 15.7 - - + +
137A ASN 3.0 19.7 + - - +
138A CYS* 3.4 16.6 - - - +
139A THR 3.2 0.2 - - - -
140A LEU* 1.3 73.2 - - - +
142A LEU* 1.3 64.9 + - - +
144A ARG* 3.1 22.3 + - + +
145A ARG* 3.1 9.2 + - - -
146A LEU 4.5 2.6 + - - +
362A VAL* 3.8 17.4 - - + +
363A SER* 4.4 8.8 + - - -
364A GLY* 3.6 27.6 - - - +
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Residues in contact with LEU 142 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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11A LEU* 3.8 24.2 - - + -
17A VAL* 4.6 9.2 - - + -
42A LEU* 3.9 22.4 - - + -
47A ILE* 3.8 16.6 - - + +
74A ALA* 5.4 0.4 - - + -
76A VAL* 3.9 32.5 - - + -
106A CYS* 3.9 16.8 - - + -
108A LEU* 4.8 8.7 - - + -
138A CYS 3.0 14.3 + - - +
139A THR* 3.4 9.2 - - + +
141A LEU* 1.3 73.9 - - - +
143A CYS* 1.3 64.6 + - - +
145A ARG* 3.1 19.4 + - - +
362A VAL* 3.6 17.6 - - + +
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Residues in contact with CYS 143 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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13A ARG* 4.7 4.7 + - - -
41A LEU* 3.5 43.3 - - - -
42A LEU* 4.4 8.3 - - - -
45A ALA* 3.7 16.0 - - + +
47A ILE* 4.1 7.0 - - - -
139A THR* 2.8 24.1 + - - +
140A LEU* 3.6 16.8 - - + +
141A LEU 3.3 0.2 - - - -
142A LEU* 1.3 72.4 - - - +
144A ARG* 1.3 61.2 + - + +
145A ARG* 3.5 19.6 + - - +
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Residues in contact with ARG 144 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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126A TYR* 3.5 17.0 + - - -
140A LEU* 2.9 58.6 + - - +
141A LEU* 3.1 14.5 + - + +
143A CYS* 1.3 74.0 - - + +
145A ARG* 1.3 65.6 + - - +
146A LEU* 3.2 26.7 + - + +
364A GLY* 6.4 2.5 - - - -
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Residues in contact with ARG 145 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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10A VAL* 3.3 6.4 - - + -
11A LEU* 2.9 60.3 + - + +
12A PRO 2.8 17.1 + - - -
13A ARG* 3.5 35.1 - - - +
14A PRO* 3.6 0.6 - - - +
15A CYS* 3.4 18.2 - - - +
45A ALA 2.6 31.5 + - - -
46A GLU 3.2 17.4 + - - -
47A ILE* 3.3 16.9 - - + +
141A LEU 3.1 5.3 + - - -
142A LEU* 3.1 17.0 + - - +
143A CYS 3.6 17.8 + - - +
144A ARG* 1.3 76.0 - - - +
146A LEU* 1.3 65.0 + - - +
147A LEU* 3.8 5.2 - - - +
362A VAL* 5.3 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
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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