Contacts of the helix formed by residues 175 - 193 (chain B) in PDB entry 4U1D
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 175 (chain B).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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76B LYS* 4.1 20.0 - - - -
86B LEU* 3.4 34.3 - - + +
89B VAL* 4.2 9.4 - - + -
90B GLY* 4.0 19.1 - - - +
169B LEU* 4.0 27.4 - - + +
172B ASN* 2.8 40.3 + - + +
174B LEU* 1.3 86.9 - - - +
176B GLU* 1.3 56.6 + - - +
177B ILE 3.4 2.5 - - - -
178B THR* 3.4 7.7 + - - +
179B TYR* 2.8 31.0 + - - +
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Residues in contact with GLU 176 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
172B ASN 2.9 19.2 + - - +
173B ALA* 3.4 21.9 + - - +
174B LEU 3.4 2.4 - - - -
175B LEU* 1.3 77.8 - - - +
177B ILE* 1.3 58.6 + - + +
179B TYR* 3.7 8.1 - - - +
180B SER* 2.9 30.8 + - - -
225B VAL* 3.4 29.5 - - + +
226B ASP 4.2 0.9 + - - -
232B THR* 2.8 31.5 + - - +
235B ARG* 2.6 43.1 + - - +
236B TYR* 5.0 7.6 - - + +
239B GLN* 5.2 0.2 + - - -
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Residues in contact with ILE 177 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
173B ALA 5.1 4.5 - - - +
174B LEU* 4.8 11.4 - - - +
176B GLU* 1.3 79.4 - - + +
178B THR* 1.3 64.4 + - - +
180B SER* 3.3 3.7 + - - -
181B GLY* 3.1 19.2 + - - -
235B ARG* 3.7 35.2 - - - +
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Residues in contact with THR 178 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
90B GLY* 3.7 30.2 - - - +
93B ALA* 4.6 2.5 - - + -
94B ARG* 3.8 33.3 + - + +
169B LEU* 3.6 17.3 - - + -
174B LEU 5.2 1.4 + - - -
175B LEU* 3.4 13.0 + - - +
176B GLU 3.3 0.4 - - - -
177B ILE* 1.3 76.1 - - - +
179B TYR* 1.3 63.7 + - - +
181B GLY* 3.2 2.9 + - - -
182B VAL* 3.1 31.0 + - + +
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Residues in contact with TYR 179 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
166B LEU* 3.4 41.3 - - + +
169B LEU* 3.6 34.4 - - + +
170B ARG* 3.8 8.1 - - - -
171B ASN 5.4 2.2 - - - -
175B LEU 2.8 19.5 + - - +
176B GLU* 3.7 7.0 - - - +
178B THR* 1.3 75.7 - - - +
180B SER* 1.3 64.3 + - - +
182B VAL* 3.3 4.5 + - - +
183B VAL* 3.1 41.9 + - + +
206B LEU* 4.0 15.9 - - - +
209B HIS* 2.8 34.7 + + + +
236B TYR* 4.2 19.0 - + - -
239B GLN* 3.9 19.0 + - - -
240B ARG* 5.6 1.6 + - - -
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Residues in contact with SER 180 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
176B GLU 2.9 18.8 + - - -
177B ILE* 3.6 5.6 - - - -
178B THR 3.3 0.2 - - - -
179B TYR* 1.3 76.0 - - - +
181B GLY* 1.3 62.2 + - - +
183B VAL* 3.4 4.5 + - - +
184B LYS* 3.3 20.3 + - - +
235B ARG* 3.9 26.6 + - - +
238B ASP* 5.6 1.2 - - - +
239B GLN* 3.1 36.7 + - - +
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Residues in contact with GLY 181 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
177B ILE 3.1 13.0 + - - -
178B THR* 3.2 4.9 + - - -
179B TYR 3.1 0.2 - - - -
180B SER* 1.3 76.2 - - - +
182B VAL* 1.3 64.0 + - - +
184B LYS* 3.2 23.0 + - - -
185B LYS* 3.1 24.0 + - - +
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Residues in contact with VAL 182 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
93B ALA* 5.7 1.8 - - + +
94B ARG* 5.9 3.1 - - + -
97B ILE* 4.0 15.5 - - + -
162B TYR* 4.0 18.6 - - + +
165B VAL* 3.9 30.1 - - + -
166B LEU* 3.9 17.7 - - + -
169B LEU* 4.3 5.4 - - + -
178B THR* 3.1 21.0 + - + +
179B TYR* 3.3 5.6 + - - +
181B GLY* 1.3 72.2 - - - +
183B VAL* 1.3 55.6 - - - +
185B LYS* 3.2 9.1 + - + +
186B THR* 2.6 46.6 + - - +
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Residues in contact with VAL 183 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
166B LEU* 3.6 21.3 - - + -
179B TYR* 3.1 39.2 + - + +
180B SER 3.5 8.3 - - - +
181B GLY 3.2 0.2 - - - -
182B VAL* 1.3 76.3 - - - +
184B LYS* 1.3 63.2 + - - +
186B THR* 3.1 8.4 + - - -
187B MET* 2.9 44.6 + - + +
202B LEU* 5.6 1.6 - - + -
206B LEU* 4.1 9.6 - - + -
239B GLN* 4.0 31.6 - - + +
242B GLN* 5.5 0.2 - - - +
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Residues in contact with LYS 184 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
180B SER 3.3 8.0 + - - +
181B GLY* 3.2 25.5 + - - +
183B VAL* 1.3 79.2 - - - +
185B LYS* 1.3 91.4 + - - +
187B MET 3.4 0.5 + - - -
188B HIS* 3.0 24.0 + - + +
239B GLN* 5.9 0.2 - - - +
242B GLN* 3.4 33.3 + - - +
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Residues in contact with LYS 185 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
97B ILE* 3.9 13.2 - - + -
98B ASP* 4.2 12.1 - - - -
101B GLU* 3.2 37.8 - - - +
162B TYR* 3.9 16.5 + - + -
181B GLY 3.1 16.0 + - - +
182B VAL* 3.5 11.9 - - + +
184B LYS* 1.3 98.9 - - - +
186B THR* 1.3 62.7 + - - +
188B HIS* 3.3 9.7 + - - +
189B PHE* 3.1 22.3 + - - +
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Residues in contact with THR 186 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
159B TRP* 3.7 29.6 - - + -
162B TYR* 3.4 35.3 - - + +
166B LEU* 3.7 10.5 - - + +
182B VAL* 2.6 26.1 + - - +
183B VAL* 3.4 7.6 - - - -
185B LYS* 1.3 77.6 - - - +
187B MET* 1.3 60.4 + - - +
189B PHE* 3.3 5.6 + - - +
190B CYS* 3.2 21.5 + - - -
202B LEU* 3.8 20.2 - - + -
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Residues in contact with MET 187 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
183B VAL* 2.9 22.8 + - + +
186B THR* 1.3 72.5 - - - +
188B HIS* 1.3 65.1 + - - +
189B PHE 3.1 1.8 - - - -
190B CYS* 3.2 6.0 + - - +
191B LEU* 3.1 22.3 + - - +
199B PHE* 4.3 7.4 - - + -
202B LEU* 3.5 25.8 - - + -
203B ALA* 5.7 0.4 - - - -
206B LEU* 3.6 31.4 - - + -
239B GLN 4.0 7.4 - - - +
242B GLN* 3.3 27.8 - - - +
243B GLN* 3.7 47.1 - - + +
246B VAL* 4.0 11.9 - - + +
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Residues in contact with HIS 188 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
101B GLU* 5.9 2.9 - - - -
184B LYS* 3.0 18.6 + - + +
185B LYS* 3.7 7.9 - - - +
186B THR 3.3 0.2 - - - -
187B MET* 1.3 77.3 - - - +
189B PHE* 1.3 59.7 + - - +
191B LEU* 3.8 11.2 - - + +
192B LYS* 2.9 61.6 + - + +
242B GLN* 4.0 5.3 - - - +
246B VAL* 5.7 0.4 - - - -
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Residues in contact with PHE 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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104B ILE* 5.3 2.2 - - + -
155B LEU* 3.8 41.5 - - + -
158B THR* 3.9 14.8 - - + -
159B TRP* 4.1 14.1 - + + -
162B TYR* 3.7 29.2 - + + +
185B LYS 3.1 13.3 + - - +
186B THR 3.3 11.7 - - - +
187B MET 3.1 0.2 - - - -
188B HIS* 1.3 80.7 - - - +
190B CYS* 1.3 70.1 + - - +
192B LYS* 4.6 0.9 - - - -
193B TYR* 3.0 49.6 + + - +
195B ARG* 3.8 23.6 - - + -
198B GLU* 3.6 21.8 - - - -
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Residues in contact with CYS 190 (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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159B TRP* 4.1 19.1 - - - -
186B THR 3.2 16.5 + - - -
187B MET 3.2 6.7 + - - +
189B PHE* 1.3 88.3 - - - +
191B LEU* 1.3 58.0 + - - +
194B GLN* 3.0 9.9 + - - -
195B ARG* 2.9 36.0 + - - +
198B GLU 4.5 0.4 - - - -
199B PHE* 3.8 51.6 - - + -
202B LEU* 4.5 2.9 - - - -
250B LEU* 4.2 5.4 - - + +
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Residues in contact with LEU 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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187B MET 3.1 16.1 + - - +
188B HIS* 3.8 13.5 - - + +
190B CYS* 1.3 77.1 - - - +
192B LYS* 1.3 60.2 + - - +
194B GLN* 3.0 30.3 + - - +
246B VAL* 4.2 17.7 - - + +
249B LYS* 3.6 51.4 - - + +
250B LEU* 3.7 22.4 - - + -
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Residues in contact with LYS 192 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
104B ILE* 5.9 0.2 - - - +
188B HIS* 2.9 48.0 + - + +
191B LEU* 1.3 79.5 - - - +
193B TYR* 1.3 99.1 + - + +
194B GLN* 3.9 3.3 + - - +
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Residues in contact with TYR 193 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
104B ILE* 3.2 26.0 - - + +
108B GLN* 4.1 25.4 - - + +
155B LEU* 3.6 32.8 - - + +
189B PHE* 3.0 35.4 + + + -
192B LYS* 1.3 120.4 + - + +
194B GLN* 1.3 72.4 + - - +
195B ARG* 3.0 32.3 + - + -
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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
------------------------------------------------------------
Atomic class I II III IV V VI VII VIII
------------------------------------------------------------
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