Contacts of the helix formed by residues 145 - 158 (chain B) 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 B).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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67B ALA* 4.0 8.3 - - + -
68B PHE* 3.9 7.9 - - + -
144B ALA* 1.3 69.6 - - - +
146B GLN* 1.3 65.6 + - - +
148B GLY 3.1 8.7 + - - +
149B TYR* 3.3 9.2 + - - +
168B MET 3.0 13.3 + - - -
169B SER* 3.3 16.2 + - - -
170B GLY* 3.6 8.5 - - - -
171B PHE* 3.7 11.9 + - + -
241B ALA 3.3 26.2 - - - +
242B MET* 3.8 15.5 - - - -
283B TRP* 4.5 1.3 - - + -
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Residues in contact with GLN 146 (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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66B ASP 3.3 7.4 - - - +
67B ALA 3.0 26.8 + - - -
68B PHE* 3.5 38.5 - - + +
100B GLY 2.8 27.3 + - - -
102B TYR 3.6 2.8 + - - +
103B SER 3.1 10.2 + - - -
104B MET* 3.0 35.8 + - - +
105B TYR* 3.5 21.7 + - + -
145B ALA* 1.3 79.9 - - - +
147B GLY* 1.3 59.6 + - - +
149B TYR* 3.4 8.7 + - - +
150B GLY* 2.9 24.1 + - - -
171B PHE* 5.2 0.2 - - - -
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Residues in contact with GLY 147 (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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65B LEU* 3.6 23.4 - - - +
66B ASP 3.5 10.1 - - - -
105B TYR* 3.8 4.0 - - - -
143B GLY* 3.4 14.9 - - - -
144B ALA 2.9 11.6 + - - -
146B GLN* 1.3 80.5 - - - +
148B GLY* 1.3 58.2 + - - +
150B GLY* 3.6 0.6 - - - -
151B ALA* 3.0 24.9 + - - +
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Residues in contact with GLY 148 (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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143B GLY* 3.3 22.3 - - - -
144B ALA 3.5 1.2 - - - +
145B ALA 3.1 8.3 + - - -
147B GLY* 1.3 74.6 - - - +
149B TYR* 1.3 64.7 + - - +
151B ALA* 3.6 1.0 + - - +
152B MET 3.4 13.7 + - - -
166B GLY 4.4 0.4 - - - -
167B SER* 3.5 28.5 - - - -
170B GLY* 4.3 3.1 - - - -
172B LEU* 3.5 9.9 - - - +
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Residues in contact with TYR 149 (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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104B MET* 3.2 42.0 - - + -
105B TYR 5.1 1.1 - - - -
106B THR* 4.4 5.2 + - - -
145B ALA 3.3 9.7 + - - +
146B GLN* 3.5 8.1 - - - +
148B GLY* 1.3 73.3 - - - +
150B GLY* 1.3 70.0 + - - +
152B MET* 3.2 3.8 + - - +
153B ALA* 2.9 35.7 + - + +
170B GLY* 4.3 1.2 - - - -
171B PHE* 3.5 26.2 - - + +
172B LEU* 4.0 11.5 - - - +
174B PRO* 3.8 15.7 - - + -
199B TRP* 3.1 30.4 - + - -
210B HIS* 2.7 33.3 + - - +
212B PRO* 3.7 19.1 - - + -
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Residues in contact with GLY 150 (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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65B LEU* 3.9 14.4 - - - -
104B MET 4.4 0.2 - - - -
105B TYR* 4.3 13.6 - - - +
146B GLN 2.9 16.3 + - - -
147B GLY 3.4 1.8 + - - -
148B GLY 3.2 0.4 - - - -
149B TYR* 1.3 89.6 - - - +
151B ALA* 1.3 56.5 + - - +
153B ALA* 3.8 1.7 - - - +
154B LEU* 2.9 34.2 + - - +
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Residues in contact with ALA 151 (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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65B LEU* 3.7 4.1 - - + +
141B ALA* 3.3 44.9 - - + +
142B VAL* 3.8 2.5 - - - +
147B GLY 3.0 15.1 + - - +
148B GLY 4.0 1.3 - - - +
150B GLY* 1.3 74.0 - - - +
152B MET* 1.3 62.4 + - - +
154B LEU* 3.5 3.2 + - - +
155B ALA* 3.2 18.0 + - - +
165B ALA* 3.6 10.2 - - - +
166B GLY 3.5 22.0 - - - +
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Residues in contact with MET 152 (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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148B GLY 3.4 11.5 + - - +
149B TYR 3.2 4.5 + - - +
151B ALA* 1.3 78.4 - - - +
153B ALA* 1.3 57.3 + - - +
155B ALA* 3.5 2.1 + - - +
156B ALA* 3.0 29.3 + - - +
165B ALA* 3.7 31.6 - - + +
167B SER* 4.1 17.3 - - - -
172B LEU* 3.9 10.8 - - + -
212B PRO* 3.7 22.4 - - + -
219B LEU* 3.8 16.6 - - + +
226B VAL* 4.0 10.8 - - + -
227B TRP 4.4 0.2 - - - +
228B VAL* 3.8 28.7 - - + -
256B PHE* 3.8 21.8 - - + -
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Residues in contact with ALA 153 (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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117B ASP* 5.4 4.5 - - - +
149B TYR* 2.9 49.1 + - + +
150B GLY* 3.8 3.4 - - - +
152B MET* 1.3 74.6 - - - +
154B LEU* 1.3 65.3 + - + +
156B ALA* 4.3 3.1 - - - -
157B PHE* 3.1 40.8 + - + +
158B HIS* 4.8 0.3 - - - -
210B HIS 4.0 6.7 - - - +
212B PRO* 4.4 4.8 - - + +
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Residues in contact with LEU 154 (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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63B TYR* 5.6 1.8 - - + -
65B LEU* 4.0 22.2 - - + -
105B TYR 5.4 3.6 - - - +
117B ASP* 3.7 23.3 - - - +
120B LEU* 4.0 34.3 - - + -
121B SER* 4.0 19.3 - - - +
141B ALA* 4.4 7.6 - - + -
150B GLY* 2.9 25.3 + - - +
151B ALA 3.7 4.7 - - - +
153B ALA* 1.3 77.0 - - - +
155B ALA* 1.3 55.7 + - - +
158B HIS* 2.9 39.1 + - + +
162B PHE* 3.9 28.0 - - + -
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Residues in contact with ALA 155 (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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151B ALA 3.2 14.4 + - - +
152B MET 4.0 1.6 - - - +
154B LEU* 1.3 77.3 - - - +
156B ALA* 1.3 65.2 + - - +
158B HIS 4.4 0.4 - - - -
159B PRO* 3.4 23.9 - - - +
162B PHE* 3.9 24.4 - - + +
164B PHE 4.6 0.7 - - - +
165B ALA* 3.7 20.2 - - + -
219B LEU* 4.0 3.8 - - + -
222B ASN* 4.9 0.9 + - - -
224B THR* 3.8 24.0 + - + -
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Residues in contact with ALA 156 (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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152B MET 3.0 18.2 + - - +
153B ALA* 3.7 7.0 - - - +
154B LEU 3.3 0.4 - - - -
155B ALA* 1.3 78.9 - - - +
157B PHE* 1.3 77.6 + - + +
159B PRO* 3.9 6.4 - - - +
212B PRO* 4.8 4.9 - - + -
215B HIS 4.7 8.7 - - - +
218B LEU* 3.5 23.3 - - + +
219B LEU* 3.7 27.1 - - + +
222B ASN* 4.2 3.9 + - - +
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Residues in contact with PHE 157 (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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117B ASP* 5.7 2.9 - - - -
153B ALA* 3.1 33.8 + - + +
156B ALA* 1.3 81.3 - - + +
158B HIS* 1.3 80.8 + - + +
159B PRO* 3.4 7.1 - - - +
209B TRP 3.3 22.2 - - - -
210B HIS* 3.6 29.6 - - + -
211B ASP 4.0 4.0 - - - -
215B HIS* 3.8 25.8 - + + -
218B LEU* 3.6 27.6 - - + -
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Residues in contact with HIS 158 (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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117B ASP* 2.8 35.0 + - - -
121B SER* 3.4 37.5 + - - -
154B LEU* 2.9 27.9 + - + +
155B ALA 3.8 0.4 - - - -
157B PHE* 1.3 98.2 + - + +
159B PRO* 1.3 64.2 - - - +
160B ASP* 3.2 16.3 + - - +
161B ARG* 3.0 18.3 + - + +
162B PHE* 3.2 12.1 + - + +
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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