Contacts of the helix formed by residues 136 - 148 (chain A) in PDB entry 2A1X
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 LEU 136 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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73A VAL* 4.1 36.3 - - + -
74A PRO* 5.0 0.9 - - + -
77A ASP* 3.9 22.7 - - + +
81A PHE* 5.2 3.1 - - + -
132A ARG* 2.9 31.5 + - - +
133A TYR* 3.5 13.9 - - + +
134A CYS 3.3 2.8 - - - -
135A THR* 1.3 77.1 - - - +
137A PRO* 1.3 75.0 - - + +
138A GLU* 3.2 30.1 - - + +
139A ILE* 3.0 22.3 + - + +
140A LEU* 3.1 12.5 + - - +
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Residues in contact with PRO 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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135A THR 3.3 8.3 - - - +
136A LEU* 1.3 92.8 - - + +
138A GLU* 1.3 73.5 + - - +
140A LEU* 4.1 9.4 - - + +
141A LYS* 3.1 26.5 + - - +
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Residues in contact with GLU 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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72A LEU* 3.6 36.1 - - + +
74A PRO* 4.7 17.4 - - + +
77A ASP* 4.9 0.5 - - - +
136A LEU* 3.2 30.5 - - + +
137A PRO* 1.3 88.7 - - - +
139A ILE* 1.3 61.4 + - - +
140A LEU 3.6 0.2 + - - -
141A LYS* 4.1 3.8 + - - +
142A TYR* 3.5 24.4 - - - -
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Residues in contact with ILE 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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72A LEU* 4.4 7.9 - - + -
73A VAL* 4.0 14.4 - - + -
133A TYR* 3.8 47.8 - - + +
136A LEU* 3.0 23.2 + - + +
138A GLU* 1.3 79.2 - - - +
140A LEU* 1.3 59.3 + - + +
142A TYR* 3.4 6.4 + - - +
143A VAL* 3.0 45.3 + - + +
192A ALA* 4.3 4.5 - - + -
255A THR* 4.1 19.1 - - + +
257A PHE* 4.2 3.2 - - + -
282A PHE* 3.7 23.1 - - + -
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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
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134A CYS 3.5 16.2 - - - +
135A THR* 3.8 21.5 - - - +
136A LEU 3.1 11.7 + - - +
137A PRO* 3.3 7.7 + - + +
139A ILE* 1.3 73.5 - - + +
141A LYS* 1.3 62.9 + - - +
142A TYR 3.0 5.2 - - - -
143A VAL* 4.1 7.4 - - + +
144A GLU* 3.0 29.6 + - - +
151A ILE* 4.2 20.4 - - + +
282A PHE* 4.3 14.1 - - + -
331A VAL* 3.6 33.4 - - + +
332A LYS* 4.2 14.1 - - + -
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Residues in contact with LYS 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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53A LEU* 3.3 38.4 - - + +
137A PRO 3.1 16.5 + - - +
138A GLU* 4.3 6.5 - - - +
139A ILE 3.6 0.2 - - - -
140A LEU* 1.3 75.3 - - - +
142A TYR* 1.3 59.3 + - + +
144A GLU* 4.5 8.4 - - - +
145A CYS* 3.7 8.3 + - - -
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Residues in contact with TYR 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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53A LEU* 4.3 29.8 + - + +
54A THR* 4.3 18.4 - - - -
57A GLN* 5.5 0.8 + - - -
67A LEU* 5.5 3.1 - - + -
69A ILE* 3.5 49.6 - - + +
72A LEU* 4.2 13.2 - - + -
138A GLU 3.5 20.6 - - - -
139A ILE 3.4 2.6 + - - +
140A LEU 3.0 0.6 - - - -
141A LYS* 1.3 82.1 - - + +
143A VAL* 1.3 66.8 + - - +
144A GLU 3.2 1.6 - - - -
145A CYS* 2.9 25.1 + - - +
146A PHE* 3.2 14.3 - + + -
257A PHE* 3.6 25.6 - + + -
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Residues in contact with VAL 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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139A ILE* 3.0 29.1 + - + +
140A LEU* 3.1 11.6 + - + +
142A TYR* 1.3 75.8 - - - +
144A GLU* 1.3 62.7 + - - +
146A PHE* 2.9 22.4 + - - +
147A THR* 3.0 28.4 + - + +
151A ILE* 3.9 9.0 - - + -
190A VAL* 3.8 7.0 - - + -
257A PHE* 4.4 8.3 - - + -
282A PHE* 3.5 57.7 - - + -
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Residues in contact with GLU 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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48A LEU* 3.6 4.5 - - - +
140A LEU 3.0 16.8 + - - +
141A LYS* 4.5 9.0 - - - +
143A VAL* 1.3 77.4 - - - +
145A CYS* 1.3 59.9 + - - +
147A THR* 3.7 8.5 - - - -
148A GLY* 2.8 40.3 + - - +
149A PRO* 3.3 29.3 - - + +
151A ILE* 4.1 9.0 - - + +
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Residues in contact with CYS 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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47A THR* 3.5 7.1 - - + -
48A LEU* 2.7 39.4 + - - +
49A ASP 5.5 1.3 - - - -
50A ASN 3.5 25.8 - - - +
53A LEU* 3.7 33.9 - - - -
54A THR* 4.7 7.6 - - + -
141A LYS 3.7 7.0 - - - -
142A TYR* 2.9 16.4 + - - +
144A GLU* 1.3 78.3 - - - +
146A PHE* 1.3 66.5 + - + +
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Residues in contact with PHE 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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46A TYR 3.6 25.4 - - - +
47A THR* 3.9 13.6 - - + +
48A LEU* 4.2 5.2 - - - +
61A TYR* 3.3 41.1 - + + -
67A LEU* 5.3 8.1 - - + -
142A TYR* 3.2 28.3 - + + -
143A VAL* 2.9 10.6 + - - +
145A CYS* 1.3 83.1 - - + +
147A THR* 1.3 60.0 + - + +
148A GLY 3.7 0.7 - - - -
187A ASP 3.7 14.1 - - - +
188A LEU* 3.5 20.1 - - - +
189A ILE 5.2 1.6 - - - +
190A VAL* 3.8 24.9 - - + -
257A PHE* 3.8 36.1 - + + -
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Residues in contact with THR 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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48A LEU* 4.1 2.4 - - - +
143A VAL* 3.0 36.5 + - + +
146A PHE* 1.3 80.3 - - - +
148A GLY* 1.3 69.2 + - - +
151A ILE* 3.7 8.8 - - + +
188A LEU* 3.4 31.8 - - - +
190A VAL* 4.2 6.7 - - + -
282A PHE* 4.2 6.3 - - + +
283A ALA* 4.1 10.5 - - - +
284A SER* 3.2 40.4 + - - +
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Residues in contact with GLY 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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48A LEU* 3.4 16.8 - - - +
144A GLU* 2.8 30.0 + - - +
147A THR* 1.3 85.7 + - - +
149A PRO* 1.3 73.5 - - - +
150A ASN 3.3 3.8 + - - +
151A ILE* 3.3 8.8 - - - +
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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