Contacts of the helix formed by residues 138 - 149 (chain A) in PDB entry 2A66
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 CYS 138 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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121A THR 4.9 0.4 - - - -
122A CYS* 3.9 2.2 - - - -
128A CYS* 4.3 8.7 - - + -
130A ILE* 4.2 4.8 - - + +
134A GLN 3.9 3.6 + - - -
135A ARG 4.0 4.4 + - - +
136A LYS 3.5 0.2 - - - -
137A ARG* 1.3 82.0 - - + +
139A PRO* 1.3 67.5 - - - +
140A TYR* 3.2 13.1 + - - -
141A CYS* 3.4 12.9 - - + +
142A ARG* 3.0 20.4 + - - +
402A ZN 2.6 34.8 - - - -
801A ACT 3.0 27.4 - - + +
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Residues in contact with PRO 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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109A PHE* 3.4 25.7 - - + -
120A TYR* 3.6 33.2 - - + -
121A THR 6.0 1.8 - - - +
135A ARG 4.6 2.0 - - - +
136A LYS 4.3 8.1 - - - +
137A ARG 3.8 6.5 - - - +
138A CYS* 1.3 86.8 - - - +
140A TYR* 1.3 58.2 + - - +
142A ARG* 4.0 3.6 - - + -
143A PHE* 2.8 33.3 + - - +
801A ACT 5.6 1.6 - - - +
301C C 5.9 0.7 - - - -
302C T 4.3 9.6 - - - +
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Residues in contact with TYR 140 (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 TYR* 3.2 40.5 - + + +
121A THR* 3.8 4.0 - - - -
122A CYS* 3.4 35.2 - - + +
126A GLN* 2.8 50.6 + - + +
138A CYS* 3.1 6.4 - - - -
139A PRO* 1.3 83.4 - - - +
141A CYS* 1.3 63.6 + - - +
143A PHE* 3.3 0.7 + - - +
144A GLN* 2.9 72.2 + - + +
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Residues in contact with CYS 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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126A GLN* 3.4 11.0 - - - -
127A ASN* 3.3 15.0 - - - -
128A CYS* 3.1 39.3 - - + +
130A ILE* 3.9 6.4 - - + +
138A CYS* 3.3 6.4 + - - +
140A TYR* 1.3 80.5 - - - +
142A ARG* 1.3 66.5 + - - +
144A GLN* 3.7 8.4 - - - +
145A LYS* 3.0 24.1 + - - +
402A ZN 2.5 32.3 - - - -
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Residues in contact with ARG 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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88A VAL* 4.2 12.9 - - + +
105A SER* 3.1 40.8 + - - -
106A CYS* 3.5 18.0 - - - +
109A PHE* 3.6 40.4 - - + +
130A ILE* 3.6 13.4 - - + +
135A ARG* 3.4 44.9 + - + +
136A LYS* 4.5 3.8 - - - +
138A CYS 3.0 17.2 + - - +
139A PRO* 3.2 5.1 + - + +
141A CYS* 1.3 76.2 - - - +
143A PHE* 1.3 59.0 + - - +
145A LYS* 3.2 5.0 + - - +
146A CYS* 2.9 27.5 + - - -
302C T 4.6 6.3 + - - -
303C G 2.9 25.5 + - - -
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Residues in contact with PHE 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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109A PHE* 3.6 15.2 - + + -
110A PHE* 3.7 32.8 - + - -
113A THR* 3.4 36.6 - - + -
114A VAL* 4.1 12.1 - - + -
118A LYS 5.3 3.6 - - - -
120A TYR* 4.2 10.3 - + + -
139A PRO 2.8 16.8 + - - +
140A TYR 3.7 3.1 - - - +
142A ARG* 1.3 76.2 - - - +
144A GLN* 1.3 75.4 + - - +
146A CYS* 3.2 4.2 + - + +
147A LEU* 3.1 47.0 + - + +
153A LEU* 4.4 7.9 - - + -
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Residues in contact with GLN 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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120A TYR* 6.1 0.2 - - - -
126A GLN 5.5 2.2 - - - +
140A TYR* 2.9 82.1 + - + +
141A CYS* 3.7 9.6 - - - +
142A ARG 3.3 0.4 - - - -
143A PHE* 1.3 88.1 - - - +
145A LYS* 1.3 58.7 + - - +
147A LEU* 3.3 12.9 + - - +
148A SER* 2.8 30.0 + - - -
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Residues in contact with LYS 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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87A PRO 3.4 16.6 + - - -
88A VAL* 2.7 38.0 + - + +
89A CYS* 5.0 0.2 - - - +
130A ILE* 3.5 34.0 + - + +
141A CYS 3.0 17.8 + - - +
142A ARG 3.5 5.2 - - - +
144A GLN* 1.3 74.9 - - - +
146A CYS* 1.3 65.2 + - - +
148A SER* 3.1 7.9 + - - -
149A VAL* 2.8 39.3 + - + +
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Residues in contact with CYS 146 (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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88A VAL* 4.0 15.9 - - - +
106A CYS* 4.8 6.5 - - - -
109A PHE* 4.1 23.1 - - - -
110A PHE* 3.9 18.8 - - + -
142A ARG* 2.9 19.1 + - - -
143A PHE* 3.2 9.4 + - - +
145A LYS* 1.3 74.9 - - - +
147A LEU* 1.3 60.8 + - - +
149A VAL* 3.1 14.9 - - - +
151A MET* 3.0 52.5 + - - +
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Residues in contact with LEU 147 (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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110A PHE* 4.1 13.5 - - + -
143A PHE* 3.1 40.2 + - + +
144A GLN* 3.6 13.7 - - - +
146A CYS* 1.3 75.9 - - - +
148A SER* 1.3 67.5 + - - +
150A GLY* 3.0 14.4 + - - -
151A MET 4.0 17.5 + - - +
153A LEU* 4.2 25.8 - - + -
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Residues in contact with SER 148 (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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144A GLN 2.8 17.5 + - - -
145A LYS* 3.4 11.6 - - - +
147A LEU* 1.3 78.2 - - - +
149A VAL* 1.3 65.1 + - - +
150A GLY* 3.2 1.2 + - - -
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Residues in contact with VAL 149 (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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87A PRO* 3.6 42.0 - - + +
88A VAL* 3.6 18.6 - - + -
100A LEU* 3.5 16.7 - - + +
145A LYS* 2.8 31.7 + - + +
146A CYS* 3.1 17.7 - - - +
148A SER* 1.3 73.9 - - - +
150A GLY* 1.3 56.2 + - - +
151A MET* 4.3 8.7 - - + +
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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