Contacts of the strand formed by residues 185 - 197 (chain B) in PDB entry 1UIR
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 185 (chain B).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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151B ARG* 4.2 7.3 - - - -
152B TYR 3.2 13.7 - - - +
153B ASP 4.0 5.8 - - - +
155B VAL* 3.7 24.7 - - + -
181B VAL* 3.7 11.4 - - + +
182B LYS* 3.1 17.8 + - + +
183B ALA 4.8 1.0 - - - +
184B HIS* 1.3 80.1 - - - +
186B ASN* 1.3 69.8 + - - +
189B GLY* 4.1 15.7 - - - +
190B VAL 4.0 26.2 - - - +
191B MET* 4.5 3.1 - - + +
217B PHE* 3.8 35.0 - - + -
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Residues in contact with ASN 186 (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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80B ARG* 5.3 6.1 + - - +
151B ARG* 3.1 34.7 - - - +
152B TYR 2.7 15.5 + - - +
153B ASP* 3.1 31.8 - - - +
185B LEU* 1.3 79.2 - - - +
187B PRO* 1.3 81.0 - - + +
188B GLY 3.4 3.4 - - - +
189B GLY* 2.9 13.2 + - - +
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Residues in contact with PRO 187 (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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186B ASN* 1.3 94.9 - - + +
188B GLY* 1.3 57.4 + - - +
189B GLY 3.4 1.7 + - - +
241B ASP* 5.9 0.7 - - - +
242B ALA* 3.4 17.7 + - - +
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Residues in contact with GLY 188 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
75B HIS* 3.4 24.8 + - - -
76B PRO* 5.4 1.2 - - - +
186B ASN* 3.2 2.9 + - - +
187B PRO* 1.3 80.5 - - - +
189B GLY* 1.3 64.3 + - - +
242B ALA* 3.8 12.6 - - - -
243B PHE* 3.7 14.9 - - - -
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Residues in contact with GLY 189 (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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153B ASP* 3.1 18.8 - - - -
185B LEU* 4.1 16.9 - - - +
186B ASN* 2.9 17.9 + - - +
187B PRO 3.2 2.5 + - - +
188B GLY* 1.3 79.6 - - - +
190B VAL* 1.3 58.7 + - - +
240B SER* 2.8 26.0 + - - -
241B ASP 4.8 0.9 + - - -
242B ALA* 4.8 0.3 - - - +
243B PHE* 4.1 0.2 - - - -
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Residues in contact with VAL 190 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
71B ALA* 3.6 25.4 - - + +
74B THR* 4.1 9.4 - - - +
75B HIS* 4.4 9.0 - - + -
153B ASP 3.0 3.4 + - - +
154B VAL* 3.3 20.0 - - + +
155B VAL 3.2 20.0 + - - -
185B LEU* 4.0 6.9 - - - +
189B GLY* 1.3 75.9 - - - +
191B MET* 1.3 72.6 + - - +
238B LEU* 4.1 20.2 - - + -
239B ALA 3.4 15.3 - - - +
240B SER* 4.5 3.4 - - - -
243B PHE* 4.2 13.0 - - + -
245B PRO* 4.7 5.2 - - + -
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Residues in contact with MET 191 (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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155B VAL* 3.3 20.2 - - + +
157B ILE* 3.5 24.7 - - + -
178B TYR* 3.9 11.9 - - + -
181B VAL* 3.7 18.2 - - - -
185B LEU* 4.5 3.3 - - + +
190B VAL* 1.3 78.4 - - - +
192B GLY* 1.3 65.8 + - - +
193B MET* 3.8 22.2 - - - -
213B VAL* 3.8 28.5 - - + -
217B PHE* 3.8 24.7 - - + -
237B LEU* 3.8 2.5 - - + +
238B LEU* 3.2 4.0 - - - -
239B ALA* 2.7 46.1 + - + +
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Residues in contact with GLY 192 (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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67B LEU 4.8 4.3 - - - -
71B ALA* 4.0 12.5 - - - +
155B VAL 2.9 7.0 + - - +
156B ILE* 3.2 13.0 - - - -
157B ILE 3.0 21.7 + - - -
191B MET* 1.3 76.7 - - - +
193B MET* 1.3 61.5 + - - +
223B TYR* 5.3 0.2 - - - -
237B LEU 3.3 9.0 - - - -
238B LEU* 3.8 13.5 - - - -
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Residues in contact with MET 193 (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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67B LEU* 3.8 10.7 + - - +
157B ILE* 3.3 33.4 - - + +
173B TYR* 4.6 8.1 - - + -
178B TYR* 3.6 27.8 - - + +
191B MET* 3.8 17.9 - - + -
192B GLY* 1.3 76.2 - - - +
194B GLN* 1.3 70.8 + - - +
195B THR* 3.2 9.0 - - + -
209B VAL* 3.7 13.9 - - + -
213B VAL* 4.0 10.3 - - - -
223B TYR* 5.1 1.4 + - - -
236B PHE* 3.1 9.1 - - - +
237B LEU* 3.0 62.1 + - + -
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Residues in contact with GLN 194 (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* 3.1 30.4 + - + +
67B LEU* 3.4 6.2 - - + +
157B ILE* 3.2 11.3 + - - +
158B ASP* 4.6 2.4 - - - +
159B LEU 3.1 23.4 + - - +
160B THR* 4.8 2.9 - - - -
161B ASP* 4.1 9.1 + - - +
173B TYR* 4.9 6.7 + - - -
193B MET* 1.3 84.9 - - - +
195B THR* 1.3 62.2 + - - +
196B GLY* 2.7 36.0 - - - +
234B PHE* 3.6 29.5 - - + -
235B GLY 4.1 0.2 - - - +
236B PHE* 3.4 22.4 - - + -
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Residues in contact with THR 195 (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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161B ASP* 5.1 0.2 - - - -
173B TYR* 5.9 1.8 - - - -
193B MET* 3.2 39.7 - - + +
194B GLN* 1.3 72.2 - - - +
196B GLY* 1.3 57.8 + - - +
206B HIS* 2.4 59.0 + - - -
209B VAL* 3.8 24.7 - - + +
235B GLY 2.7 17.5 + - - -
236B PHE 3.1 0.2 + - - -
237B LEU* 3.2 26.0 - - + +
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Residues in contact with GLY 196 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
161B ASP* 3.8 19.2 + - - -
194B GLN* 2.7 24.8 - - - +
195B THR* 1.3 76.9 - - - +
197B MET* 1.3 66.6 + - - +
205B VAL* 4.4 6.1 - - - -
206B HIS* 4.0 1.4 - - - +
234B PHE* 3.8 7.2 - - - -
235B GLY* 2.8 26.5 + - - -
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Residues in contact with MET 197 (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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10B HIS* 5.7 1.3 - - - +
11B VAL* 3.7 23.6 - - - +
12B THR* 4.9 1.3 - - + -
52B ASP* 5.9 2.2 - - - +
161B ASP* 4.6 8.6 + - - +
196B GLY* 1.3 77.2 - - - +
198B ILE* 1.3 63.3 + - - +
199B LEU* 4.1 21.1 - - - -
203B HIS* 3.3 42.1 - - + +
206B HIS* 3.8 11.4 + - - +
232B LEU* 4.1 28.5 - - + -
233B ASN 3.6 9.6 - - - +
234B PHE* 3.7 28.2 - - + -
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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