Contacts of the helix formed by residues 177 - 195 (chain D) in PDB entry 1L9W
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 SER 177 (chain D).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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193C GLN* 6.1 1.8 - - - -
175D PRO* 3.5 1.5 - - - +
176D GLN* 1.4 83.0 - - - +
178D LYS* 1.3 66.4 + - - +
179D HIS* 3.3 10.0 + - - +
180D ASP* 3.2 32.3 + - - +
181D VAL* 3.5 11.4 + - - +
208D GLU* 3.3 16.3 - - - +
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Residues in contact with LYS 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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189C LEU* 4.1 26.6 - - + +
192C GLN* 4.5 15.1 - - - +
193C GLN* 4.4 14.6 - - - +
217C GLU 4.5 10.5 - - - -
218C VAL* 3.4 31.4 - - + +
219C PHE* 4.3 4.0 - - + -
177D SER* 1.3 75.2 - - - +
179D HIS* 1.3 61.3 + - - +
181D VAL* 3.1 23.0 + - - +
182D LEU* 3.4 6.1 + - - +
208D GLU* 3.5 12.8 + - + +
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Residues in contact with HIS 179 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
186C THR* 6.0 1.8 - - - +
189C LEU* 3.8 23.5 - - + +
193C GLN* 4.8 11.2 + - - +
177D SER* 3.3 9.0 + - - +
178D LYS* 1.3 77.9 - - - +
180D ASP* 1.3 59.4 + - - +
182D LEU* 3.1 16.6 + - + +
183D THR* 2.8 46.6 + - - -
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Residues in contact with ASP 180 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
148D THR* 3.6 37.9 + - - +
175D PRO* 3.6 8.1 - - + +
176D GLN* 2.6 38.9 + - - +
177D SER* 3.2 18.5 + - - +
179D HIS* 1.3 74.8 + - - +
181D VAL* 1.3 66.7 + - - +
183D THR* 3.1 10.5 + - - -
184D LEU* 3.0 22.9 + - - +
204D SER* 5.0 0.7 - - - -
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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
----------------------------------------------------------
218C VAL* 4.7 3.6 - - + -
219C PHE* 4.3 10.5 - - + -
175D PRO* 3.7 22.0 - - + -
177D SER 3.5 8.0 + - - +
178D LYS* 3.1 11.1 + - - +
180D ASP* 1.3 77.0 - - - +
182D LEU* 1.3 61.7 + - - +
184D LEU* 3.2 12.5 + - - +
185D LEU* 3.3 16.9 + - + +
204D SER* 3.8 14.8 - - - +
208D GLU* 3.4 28.3 - - + +
209D GLY* 4.4 5.8 - - - +
211D ILE* 3.7 28.9 - - + -
212D SER* 5.2 2.0 - - - +
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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
----------------------------------------------------------
182C LEU* 3.6 30.7 - - + -
185C LEU* 4.4 13.2 - - + -
186C THR* 4.1 30.1 - - + +
189C LEU* 3.7 22.4 - - + -
219C PHE* 3.8 28.2 - - + -
178D LYS 3.4 2.5 + - - +
179D HIS* 3.1 26.8 + - + +
181D VAL* 1.3 79.4 - - - +
183D THR* 1.3 62.6 + - - +
185D LEU* 3.5 5.9 + - + -
186D THR* 2.8 31.1 + - - +
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Residues in contact with THR 183 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
148D THR* 4.6 2.5 - - - -
149D PRO 4.1 7.9 - - - +
150D SER* 4.6 1.3 - - - -
151D ALA* 3.7 32.0 - - + +
154D MET* 3.9 9.9 - - + -
179D HIS* 2.8 34.0 + - - -
180D ASP* 3.1 13.5 + - - -
182D LEU* 1.3 77.9 - - - +
184D LEU* 1.3 57.1 + - - +
186D THR* 3.1 5.6 + - - -
187D ALA* 2.9 30.0 + - - +
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Residues in contact with LEU 184 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
148D THR* 5.0 0.2 - - + -
154D MET* 3.8 28.9 - - + +
171D ILE* 4.3 7.6 - - + -
173D VAL* 3.8 17.7 - - + -
180D ASP 3.0 11.3 + - - +
181D VAL 3.2 7.2 + - - +
183D THR* 1.3 75.6 - - - +
185D LEU* 1.4 63.0 + - + +
187D ALA* 3.7 2.5 - - + +
188D THR* 2.7 34.6 + - - +
202D THR* 3.7 30.5 - - + +
203D MET 4.0 27.4 - - - +
204D SER* 4.1 10.3 - - - -
212D SER* 4.1 17.9 - - - -
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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
----------------------------------------------------------
182C LEU* 4.4 9.1 - - + +
185C LEU* 5.0 2.0 - - + -
219C PHE* 4.0 30.1 - - + -
181D VAL* 3.3 13.2 + - + +
182D LEU* 3.9 10.1 - - + +
183D THR 3.3 0.2 - - - -
184D LEU* 1.4 78.2 - - + +
186D THR* 1.3 57.7 + - - +
188D THR* 3.6 7.2 - - + +
189D LEU* 3.0 28.4 + - - +
211D ILE* 4.6 12.1 - - + -
212D SER* 4.0 32.8 - - - +
215D ALA* 5.1 3.4 - - + -
219D PHE* 3.9 45.9 - - + +
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Residues in contact with THR 186 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
179C HIS* 5.3 5.2 - - - +
182C LEU* 3.7 29.6 - - + +
186C THR* 5.4 0.5 + - - -
151D ALA* 5.1 9.4 - - + -
182D LEU* 2.8 25.2 + - - +
183D THR* 3.7 6.0 - - - -
185D LEU* 1.3 73.1 - - - +
187D ALA* 1.3 63.0 + - - +
189D LEU* 3.2 1.6 + - - +
190D GLU* 2.9 34.9 + - + +
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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
----------------------------------------------------------
151D ALA* 3.8 18.0 - - - +
154D MET* 3.8 24.0 - - + -
155D VAL* 3.7 24.0 - - + +
158D LEU* 5.3 3.8 - - + -
183D THR 2.9 16.2 + - - +
184D LEU* 3.9 2.5 - - + +
186D THR* 1.3 71.5 - - - +
188D THR* 1.3 67.0 + - - +
190D GLU* 3.2 4.4 + - - +
191D MET* 3.0 25.4 + - - +
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Residues in contact with THR 188 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
158D LEU* 5.5 0.2 - - - -
184D LEU* 2.7 31.2 + - - +
185D LEU* 3.6 10.5 - - + -
187D ALA* 1.3 74.8 - - - +
189D LEU* 1.3 55.8 + - - +
191D MET* 3.4 5.9 + - - +
192D GLN* 3.0 24.8 + - - +
200D VAL* 6.0 2.0 - - + -
202D THR* 2.5 45.6 + - + +
219D PHE* 3.1 23.3 - - + +
220D GLY 3.8 19.7 - - - +
221D SER* 4.0 3.1 - - - +
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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
----------------------------------------------------------
178C LYS* 4.0 22.7 - - + +
179C HIS* 3.7 48.0 - - + +
182C LEU* 3.8 13.9 - - + -
185D LEU 3.0 18.4 + - - +
186D THR 3.2 3.1 + - - +
188D THR* 1.3 72.6 - - - +
190D GLU* 1.3 65.7 + - - +
192D GLN* 4.0 11.4 - - - +
193D GLN* 2.9 53.8 + - + +
218D VAL 4.2 0.2 - - - +
219D PHE* 3.5 29.8 - - + +
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Residues in contact with GLU 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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151D ALA* 4.6 14.0 - - - +
152D GLU* 5.2 2.8 + - - -
155D VAL* 4.1 20.1 - - + +
186D THR* 2.9 19.5 + - + +
187D ALA* 3.5 8.2 - - - +
189D LEU* 1.3 77.4 - - - +
191D MET* 1.4 60.3 + - - +
193D GLN* 5.0 0.4 - - - -
194D HIS* 2.8 56.0 + - + +
195D TYR* 3.6 25.0 + - - -
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Residues in contact with MET 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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155D VAL* 4.2 9.0 - - + -
158D LEU* 3.9 51.6 - - + +
159D ARG* 3.9 26.7 - - + +
162D GLN* 4.2 11.4 - - - +
169D PRO* 5.3 0.7 - - + -
187D ALA 3.0 14.2 + - - +
188D THR* 3.5 4.7 - - - +
190D GLU* 1.4 83.3 - - - +
192D GLN* 1.3 63.2 + - - +
195D TYR* 3.2 16.1 + - + +
196D ALA* 2.9 48.9 + - + +
200D VAL* 4.1 21.3 - - + -
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Residues in contact with GLN 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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178C LYS* 4.2 16.8 - - - +
1D MET* 3.6 34.4 + - + +
188D THR 3.0 14.6 + - - +
189D LEU* 3.8 17.1 - - + +
191D MET* 1.3 78.0 - - - +
193D GLN* 1.3 79.0 + - + +
196D ALA* 3.8 18.5 - - - +
200D VAL* 6.1 1.8 - - + -
219D PHE 4.2 2.9 - - - +
220D GLY* 4.0 31.2 - - - +
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Residues in contact with GLN 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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177C SER* 5.8 3.0 - - - -
178C LYS* 4.7 14.9 - - - +
179C HIS* 4.7 12.4 - - - +
189D LEU* 2.9 46.5 + - + +
192D GLN* 1.3 92.8 - - + +
194D HIS* 1.3 79.7 + - + +
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Residues in contact with HIS 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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190D GLU* 2.8 39.8 + - + +
193D GLN* 1.3 95.8 + - + +
195D TYR* 1.3 83.0 + + + +
196D ALA 3.9 0.9 - - - -
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Residues in contact with TYR 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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155D VAL* 3.9 20.6 - - + -
159D ARG* 3.3 49.4 + - + +
162D GLN* 3.2 15.0 - - - +
190D GLU* 3.6 28.2 + - - -
191D MET* 3.2 20.2 + - + -
194D HIS* 1.3 99.3 - + + +
196D ALA* 1.3 65.0 + - - +
197D ASP* 3.5 2.4 + - - +
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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