Contacts of the helix formed by residues 145 - 158 (chain A) in PDB entry 1R88
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 ALA 145 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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67A ALA* 3.9 7.9 - - + -
68A PHE* 3.8 7.6 - - + -
144A ALA* 1.3 71.5 - - - +
146A GLN* 1.3 66.1 + - - +
148A GLY 3.1 8.5 + - - +
149A TYR* 3.3 9.7 + - - +
168A MET 3.0 12.5 + - - -
169A SER 3.2 14.7 + - - -
170A GLY* 3.6 8.1 - - - -
171A PHE* 3.7 11.9 + - - -
241A ALA 3.3 26.7 - - - +
242A MET* 3.8 15.9 - - - -
283A TRP* 4.5 1.9 - - + -
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Residues in contact with GLN 146 (chain A).
Click here for Legend to table.
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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66A ASP 3.3 8.1 - - - +
67A ALA 3.0 27.9 + - - -
68A PHE* 3.5 38.9 - - + +
100A GLY 2.9 24.8 + - - -
102A TYR 3.7 2.8 + - - +
103A SER 3.1 10.8 + - - -
104A MET* 2.9 35.3 + - - +
105A TYR* 3.4 23.6 + - + -
145A ALA* 1.3 79.2 - - - +
147A GLY* 1.3 59.6 + - - +
149A TYR* 3.5 8.3 + - - +
150A GLY* 2.9 23.9 + - - -
171A PHE* 5.2 0.4 - - - -
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Residues in contact with GLY 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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65A LEU* 3.6 23.3 - - - +
66A ASP 3.2 15.0 + - - -
105A TYR* 3.9 4.5 - - - -
143A GLY* 3.4 10.1 - - - -
144A ALA 2.9 11.8 + - - -
146A GLN* 1.3 75.4 - - - +
148A GLY* 1.3 58.8 + - - +
151A ALA* 2.9 28.9 + - - +
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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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143A GLY 3.3 22.7 - - - -
144A ALA 3.5 1.0 - - - +
145A ALA 3.1 8.4 + - - -
147A GLY* 1.3 73.9 - - - +
149A TYR* 1.3 64.2 + - - +
151A ALA* 3.5 1.6 + - - +
152A MET 3.3 15.2 + - - -
166A GLY 4.5 0.9 - - - -
167A SER* 3.5 26.9 - - - -
170A GLY* 4.2 3.1 - - - -
172A LEU* 3.5 10.8 - - - +
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Residues in contact with TYR 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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104A MET* 3.2 44.4 - - + -
105A TYR 5.1 1.1 - - - -
106A THR* 4.4 5.2 + - - -
145A ALA 3.3 9.5 + - - +
146A GLN* 3.5 9.0 - - - +
148A GLY* 1.3 74.5 - - - +
150A GLY* 1.3 66.8 + - - +
152A MET* 3.2 3.5 + - - +
153A ALA* 2.9 37.4 + - + +
171A PHE* 3.4 26.8 - - + +
172A LEU* 4.0 11.3 - - - +
174A PRO* 3.9 14.8 - - + -
199A TRP* 3.2 29.8 - + - -
210A HIS* 2.6 34.2 + - - +
212A PRO* 3.6 18.4 - - + -
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Residues in contact with GLY 150 (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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65A LEU* 3.9 13.5 - - - -
104A MET 4.3 5.2 - - - -
105A TYR* 4.4 8.2 - - - +
146A GLN 2.9 15.2 + - - -
147A GLY 3.4 2.2 + - - -
148A GLY 3.2 0.4 - - - -
149A TYR* 1.3 89.0 - - - +
151A ALA* 1.3 57.8 + - - +
153A ALA* 3.5 1.7 + - - +
154A LEU* 3.0 34.9 + - - +
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Residues in contact with ALA 151 (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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65A LEU* 3.7 3.7 - - + +
141A ALA* 3.4 43.4 - - + +
142A VAL* 3.9 2.7 - - - +
147A GLY 2.9 17.5 + - - +
148A GLY 3.9 1.8 - - - +
149A TYR 3.3 0.2 - - - -
150A GLY* 1.3 77.1 - - - +
152A MET* 1.3 62.1 + - - +
154A LEU* 3.5 2.6 + - - +
155A ALA* 3.3 17.0 + - - +
165A ALA* 3.5 10.6 - - - +
166A GLY 3.4 19.1 - - - +
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Residues in contact with MET 152 (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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148A GLY 3.3 11.2 + - - +
149A TYR 3.2 4.5 + - - +
151A ALA* 1.3 76.1 - - - +
153A ALA* 1.3 60.5 + - - +
155A ALA* 3.5 0.9 + - - +
156A ALA* 3.1 28.6 + - - +
165A ALA* 3.8 31.8 - - + +
167A SER* 4.1 16.4 - - - -
172A LEU* 3.8 11.9 - - + -
212A PRO* 3.7 22.4 - - + -
219A LEU* 3.8 17.9 - - + +
226A VAL* 3.9 12.1 - - + -
228A VAL* 3.9 28.5 - - + -
256A PHE* 3.8 22.0 - - + -
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Residues in contact with ALA 153 (chain A).
Click here for Legend to table.
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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117A ASP* 5.2 4.7 - - - +
149A TYR* 2.9 49.3 + - + +
150A GLY* 3.9 3.8 - - - +
152A MET* 1.3 75.0 - - - +
154A LEU* 1.3 64.7 + - + +
156A ALA* 3.4 2.0 + - - -
157A PHE* 3.1 42.2 + - + +
158A HIS* 4.8 0.5 - - - -
210A HIS 4.2 5.6 - - - +
212A PRO* 4.4 4.4 - - + +
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Residues in contact with LEU 154 (chain A).
Click here for Legend to table.
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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63A TYR* 5.6 1.6 - - + -
65A LEU* 4.0 13.7 - - + -
105A TYR 5.4 3.4 - - - +
117A ASP* 3.7 23.3 - - - +
120A LEU* 4.0 38.8 - - + -
121A SER* 4.0 23.1 - - - -
141A ALA* 4.4 7.9 - - + -
150A GLY* 3.0 25.0 + - - +
151A ALA* 3.8 4.3 - - - +
153A ALA* 1.3 77.2 - - - +
155A ALA* 1.3 57.3 + - - +
158A HIS* 2.9 38.8 + - + +
162A PHE* 3.8 26.9 - - + -
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Residues in contact with ALA 155 (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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151A ALA 3.3 4.9 + - - +
152A MET 4.0 0.2 - - - +
153A ALA 3.3 0.2 - - - -
154A LEU* 1.3 77.7 - - - +
156A ALA* 1.3 65.3 + - - +
158A HIS 4.4 0.7 - - - -
159A PRO* 3.4 24.1 - - - +
162A PHE* 4.0 22.6 - - + +
164A PHE 4.6 0.7 - - - +
165A ALA* 3.7 29.4 - - + -
219A LEU* 4.0 5.4 - - + -
222A ASN* 4.9 0.7 + - - -
224A THR* 3.8 25.0 + - + -
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Residues in contact with ALA 156 (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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152A MET 3.1 19.5 + - - +
153A ALA* 3.7 6.5 - - - +
154A LEU 3.3 0.2 - - - -
155A ALA* 1.3 80.7 - - - +
157A PHE* 1.3 76.2 + - + +
159A PRO* 3.9 6.6 - - - +
212A PRO* 4.8 5.4 - - + -
215A HIS 4.6 8.7 - - - +
218A LEU* 3.6 23.1 - - + +
219A LEU* 3.7 27.3 - - + +
222A ASN* 4.1 4.0 + - - -
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Residues in contact with PHE 157 (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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117A ASP* 5.6 3.4 - - - -
153A ALA* 3.1 34.6 + - + +
156A ALA* 1.3 80.0 - - + +
158A HIS* 1.3 82.1 + - + +
159A PRO* 3.4 6.9 - - - +
209A TRP 3.3 21.8 - - - -
210A HIS* 3.7 30.1 - - + -
211A ASP 4.0 3.8 - - - -
215A HIS* 3.8 26.0 - + + -
218A LEU* 3.6 27.6 - - + -
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Residues in contact with HIS 158 (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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117A ASP* 2.9 34.3 + - - -
121A SER* 3.4 37.9 + - - -
154A LEU* 2.9 27.8 + - + +
155A ALA 3.8 0.4 - - - -
157A PHE* 1.3 95.2 + - + +
159A PRO* 1.3 60.4 - - - +
160A ASP* 3.1 15.8 + - - +
161A ARG* 3.0 24.2 + - + +
162A PHE* 3.2 10.0 + - + +
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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