Contacts of the helix formed by residues 176 - 195 (chain D) in PDB entry 4O9U
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 176 (chain D).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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174D ASN* 2.9 29.9 + - - +
175D ASP* 1.3 76.4 - - - +
177D THR* 1.3 64.8 + - - +
178D ALA* 4.2 6.5 - - + +
179D SER* 3.0 24.1 + - - +
180D ILE* 3.1 15.7 + - - +
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Residues in contact with THR 177 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
105D LEU* 3.8 28.4 + - + +
175D ASP 3.8 2.0 + - - -
176D ALA* 1.3 71.8 - - - +
178D ALA* 1.3 61.4 + - - +
180D ILE* 3.3 19.0 + - - +
181D VAL* 3.3 23.3 + - + +
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Residues in contact with ALA 178 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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176D ALA* 3.2 7.1 - - + +
177D THR* 1.3 80.5 - - - +
179D SER* 1.3 60.4 + - - +
180D ILE 3.3 1.0 + - - -
181D VAL* 3.5 12.9 + - - +
182D LEU* 3.6 16.3 + - - +
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Residues in contact with SER 179 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
167D ILE* 3.4 21.2 - - - +
170D SER* 4.0 17.0 + - - -
171D LEU* 3.3 30.1 - - - +
174D ASN* 3.6 24.7 + - - -
176D ALA* 3.0 14.2 + - - +
178D ALA* 1.3 77.9 - - - +
180D ILE* 1.3 59.2 + - - +
182D LEU* 4.7 1.3 - - - -
183D PHE* 3.5 1.7 - - - +
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Residues in contact with ILE 180 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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101D ALA* 4.7 11.0 - - + +
104D LEU* 3.4 41.5 - - + +
105D LEU* 4.0 17.5 - - + -
171D LEU* 3.7 17.5 - - + -
175D ASP 4.2 3.8 - - - +
176D ALA 3.1 18.8 + - - +
177D THR* 3.5 17.9 - - - +
178D ALA 3.2 0.6 - - - -
179D SER* 1.3 77.6 - - - +
181D VAL* 1.3 67.4 + - + +
183D PHE* 3.5 5.8 - - - +
184D PHE* 2.9 52.3 + - + -
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Residues in contact with VAL 181 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
177D THR* 3.3 23.9 + - + +
178D ALA* 3.5 6.0 + - - +
180D ILE* 1.3 75.3 - - + +
182D LEU* 1.3 56.2 + - - +
184D PHE* 3.0 10.9 + - + +
185D LEU* 2.8 52.0 + - + +
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Residues in contact with LEU 182 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
167D ILE* 3.8 25.4 - - + -
178D ALA 3.6 13.7 + - - +
179D SER* 5.4 0.4 - - - -
181D VAL* 1.3 78.3 - - - +
183D PHE* 1.3 57.6 - - - +
185D LEU* 3.3 16.3 + - + +
186D LEU* 2.8 54.3 + - + +
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Residues in contact with PHE 183 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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100D ALA* 6.2 0.4 - - + -
104D LEU* 5.8 3.4 - - + -
119D ILE* 3.5 40.4 - - + -
122D GLY 4.7 2.0 - - - -
123D LEU* 4.0 31.9 - - + -
164D THR* 3.4 27.3 - - - -
165D VAL* 5.6 0.4 - - - -
167D ILE* 3.5 17.1 - - + +
168D GLY* 3.6 20.0 - - - -
171D LEU* 4.4 5.6 - - + -
179D SER 3.5 15.0 + - - +
180D ILE* 3.5 13.4 + - + +
181D VAL 3.2 0.4 - - - -
182D LEU* 1.3 79.2 - - - +
184D PHE* 1.3 80.9 + + - +
186D LEU* 3.8 3.4 - - - +
187D ALA* 3.0 30.7 + - + +
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Residues in contact with PHE 184 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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97D ALA* 3.3 31.4 - - + -
100D ALA* 4.1 11.4 - - + -
101D ALA* 3.6 25.1 - - + -
104D LEU* 5.0 3.4 - - + -
122D GLY 4.6 4.9 - - - -
126D SER* 3.2 25.1 - - - -
180D ILE* 2.9 45.0 + - + -
181D VAL* 3.0 9.9 + - + +
183D PHE* 1.3 95.8 - + - +
185D LEU* 1.3 55.6 + - + +
187D ALA* 3.2 4.1 + - - +
188D LEU* 2.7 49.2 + - + +
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Residues in contact with LEU 185 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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181D VAL* 2.8 39.8 + - + +
182D LEU* 3.5 21.3 - - + +
184D PHE* 1.3 73.2 - - + +
186D LEU* 1.3 52.0 + - + +
188D LEU* 3.3 12.8 + - + +
189D LEU* 2.6 36.1 + - - +
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Residues in contact with LEU 186 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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160D VAL* 3.8 7.3 - - + +
163D LEU* 3.7 17.0 - - + -
164D THR* 3.2 35.1 - - + +
167D ILE* 3.4 23.1 - - + -
182D LEU* 2.8 38.9 + - + +
183D PHE 3.8 2.7 - - - +
185D LEU* 1.3 73.0 - - + +
187D ALA* 1.3 55.3 + - - +
189D LEU* 3.4 25.1 - - + +
190D PHE* 2.7 36.0 + - - +
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Residues in contact with ALA 187 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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122D GLY 4.9 0.2 - - - +
123D LEU* 4.3 21.5 - - + +
126D SER* 3.7 20.0 - - - -
127D VAL* 3.2 17.4 - - + +
164D THR* 4.0 8.2 - - - +
183D PHE* 3.0 25.4 + - + +
184D PHE* 3.5 6.5 - - - +
186D LEU* 1.3 75.2 - - - +
188D LEU* 1.3 57.6 + - - +
190D PHE* 4.7 1.8 - - - -
191D GLY* 3.0 23.2 + - - -
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Residues in contact with LEU 188 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
126D SER* 3.4 33.0 - - - +
129D PHE* 3.8 18.8 - - + -
130D THR* 3.3 33.1 + - - +
184D PHE* 2.7 35.2 + - + +
185D LEU* 3.4 13.5 - - + +
187D ALA* 1.3 69.6 - - - +
189D LEU* 1.3 63.2 + - - +
192D VAL* 3.3 13.3 - - - +
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Residues in contact with LEU 189 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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160D VAL* 4.0 17.7 - - + -
185D LEU 2.6 20.5 + - - +
186D LEU* 3.2 28.2 + - + +
188D LEU* 1.3 73.1 - - - +
190D PHE* 1.3 59.9 + - - +
192D VAL* 3.1 8.1 + - + +
193D LEU* 2.8 51.1 + - + +
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Residues in contact with PHE 190 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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123D LEU* 6.4 2.0 - - + -
127D VAL* 4.0 15.3 - - + -
157D ASN* 3.5 40.2 - - + -
158D ALA* 5.6 0.2 - - - -
160D VAL* 3.8 14.7 - - + +
161D LEU* 3.5 41.5 - - + +
164D THR* 4.7 4.0 - - + -
186D LEU 2.7 20.4 + - - +
187D ALA* 4.2 2.7 - - - +
189D LEU* 1.3 73.4 - - - +
191D GLY* 1.3 57.1 + - - +
193D LEU* 4.3 4.5 - - + -
194D MET* 2.7 80.4 + - + +
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Residues in contact with GLY 191 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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127D VAL* 3.7 23.1 - - - -
130D THR* 3.6 17.0 - - - -
131D GLY* 3.4 8.7 - - - -
187D ALA 3.0 19.0 + - - -
189D LEU 3.3 0.2 - - - -
190D PHE* 1.3 77.3 - - - +
192D VAL* 1.3 56.1 + - - +
194D MET* 4.0 1.6 - - - +
195D THR* 3.2 21.1 + - - +
210D TYR* 3.5 6.8 + - - -
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Residues in contact with VAL 192 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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130D THR* 3.0 28.0 - - + +
134D ILE* 3.7 32.5 - - + -
188D LEU 3.3 9.5 + - - +
189D LEU* 3.1 9.9 + - + +
190D PHE 3.1 0.4 - - - -
191D GLY* 1.3 72.9 - - - +
193D LEU* 1.3 57.2 + - + +
194D MET 2.9 3.8 - - - -
195D THR* 2.7 32.3 + - - +
196D LEU* 3.1 24.4 - - + +
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Residues in contact with LEU 193 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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150D PHE* 3.8 14.8 - - + -
153D GLN* 5.1 0.3 - - - +
156D VAL* 4.7 4.0 - - + +
157D ASN* 2.7 46.5 + - - +
160D VAL* 3.8 24.9 - - + -
189D LEU* 2.8 42.3 + - + +
190D PHE* 3.9 6.3 - - + +
192D VAL* 1.3 73.1 - - + +
194D MET* 1.3 57.0 + - - +
196D LEU* 3.3 43.3 - - + +
197D PRO* 3.6 2.3 - - - +
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Residues in contact with MET 194 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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127D VAL* 3.8 19.1 - - + -
157D ASN* 3.7 7.3 + - - -
190D PHE* 2.7 66.1 + - + +
191D GLY 4.0 1.8 - - - +
192D VAL 2.8 0.6 + - - -
193D LEU* 1.3 71.1 - - - +
195D THR* 1.3 54.8 + - - +
196D LEU 3.1 5.2 - - - -
197D PRO* 3.0 18.1 - - - +
198D ILE* 3.7 9.9 - - + +
209D PHE* 4.5 20.2 - - + -
210D TYR* 3.5 29.4 - - - -
213D PHE* 4.9 7.9 - - + -
260D LEU* 4.5 17.6 - - + +
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Residues in contact with THR 195 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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131D GLY* 3.6 15.8 + - - -
134D ILE* 3.5 35.1 - - + +
135D ALA* 4.1 6.4 + - - +
138D LYS* 2.9 19.5 + - - -
191D GLY 3.2 16.4 + - - +
192D VAL* 2.7 23.2 + - - +
194D MET* 1.3 71.4 - - - +
196D LEU* 1.3 57.7 + - - +
198D ILE* 3.8 16.1 - - - +
203D MET* 4.4 12.1 - - - +
210D TYR* 3.3 16.7 - - - -
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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
------------------------------------------------------------
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