Contacts of the helix formed by residues 182 - 195 (chain D) in PDB entry 3LSG
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 182 (chain D).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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222A TYR* 3.8 36.6 - - - +
233A VAL* 6.5 0.2 - - - -
184B GLY* 3.7 20.4 + - - -
188B ILE* 5.3 2.9 - - - +
181D LEU* 1.3 76.8 - - - +
183D SER* 1.3 59.2 + - - +
184D GLY 3.7 3.2 + - - -
185D TYR* 3.2 17.1 + - - +
186D LEU* 2.9 25.5 + - - +
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Residues in contact with SER 183 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
222A TYR* 4.9 2.4 - - - -
231C GLU* 4.0 20.4 + - - +
232C ASP* 4.4 1.4 - - - +
172D LEU* 3.9 17.9 - - - +
173D SER* 4.1 17.7 + - - -
176D SER* 3.2 17.2 + - - -
182D SER* 1.3 70.4 - - - +
184D GLY* 1.3 60.6 + - - +
186D LEU* 4.3 2.5 - - - -
187D SER* 2.9 32.9 + - - -
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Residues in contact with GLY 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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182B SER* 3.8 18.3 + - - -
184B GLY* 4.3 4.2 - - - -
185B TYR* 3.6 19.6 - - - +
232C ASP* 5.8 1.3 - - - -
182D SER* 3.2 5.3 + - - -
183D SER* 1.3 79.7 - - - +
185D TYR* 1.3 62.9 + - - +
187D SER* 3.8 6.2 - - - -
188D ILE* 3.6 11.3 - - - +
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Residues in contact with TYR 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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184B GLY 3.7 10.8 - - - +
185B TYR* 3.5 38.7 - + - +
188B ILE* 3.5 33.9 - - + -
189B MSE 4.4 6.7 - - + -
181D LEU* 4.1 18.2 - - + -
182D SER* 3.2 17.8 + - - +
184D GLY* 1.3 73.8 - - - +
186D LEU* 1.3 67.9 + - - +
188D ILE* 3.2 6.9 + - - +
189D MSE 3.1 50.2 + - + +
215E LEU 3.4 10.3 + - - -
216E THR* 3.3 39.3 + - + -
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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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157D ILE* 4.8 2.2 - - + -
172D LEU* 3.7 20.9 - - + -
175D LEU* 3.6 32.3 - - + -
176D SER* 3.4 28.3 - - - +
179D LEU* 3.8 14.8 - - + -
181D LEU* 4.5 5.4 - - + +
182D SER 2.9 20.2 + - - +
183D SER* 4.1 2.5 - - - +
185D TYR* 1.3 79.6 - - - +
187D SER* 1.3 56.3 + - - +
189D MSE 3.6 25.6 - - + +
190D PHE* 2.7 48.9 + - + +
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Residues in contact with SER 187 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
232C ASP* 2.7 42.8 + - - +
233C VAL* 4.1 2.2 + - - +
234C ASN* 3.5 17.8 + - - +
172D LEU* 4.9 6.7 - - - +
183D SER 2.9 20.6 + - - -
184D GLY* 3.8 7.2 - - - -
186D LEU* 1.3 78.8 - - - +
188D ILE* 1.3 66.4 + - - +
190D PHE* 4.0 4.0 - - - +
191D LYS* 3.4 18.7 + - - +
197D PRO* 5.9 1.6 - - - +
198D PHE* 6.0 0.4 + - - -
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Residues in contact with ILE 188 (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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181B LEU* 5.7 6.7 - - + -
182B SER* 5.7 0.2 - - - +
185B TYR* 3.4 52.3 - - + +
233C VAL* 4.3 15.5 - - + -
234C ASN* 3.9 24.2 - - - +
184D GLY 3.6 11.2 - - - +
185D TYR 3.2 1.2 + - - +
187D SER* 1.3 80.6 - - - +
189D MSE 1.3 65.9 + - - +
191D LYS* 3.3 5.7 + - - +
192D LYS* 3.0 22.9 + - + +
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Residues in contact with MSE 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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185B TYR* 5.5 1.1 - - + -
153D ALA* 5.7 1.6 - - - -
157D ILE* 3.9 24.5 - - + -
179D LEU* 4.5 1.1 - - + -
181D LEU* 3.9 21.8 - - + -
185D TYR* 3.1 32.8 + - + +
186D LEU* 3.6 24.5 - - + +
188D ILE* 1.3 77.0 - - - +
190D PHE* 1.3 67.4 + - - +
192D LYS* 3.3 12.0 + - + +
193D ASN* 2.9 47.4 + - - +
215E LEU* 3.6 35.0 - - + +
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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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157D ILE* 4.0 11.4 - - + -
161D ILE* 4.0 18.4 - - + -
175D LEU* 4.6 5.2 - - + -
186D LEU* 2.7 30.6 + - + +
187D SER* 4.0 4.5 - - - +
189D MSE 1.3 79.2 - - - +
191D LYS* 1.3 58.1 + - - +
193D ASN* 3.0 2.3 + - - -
194D PHE* 2.8 76.2 + + + -
196D ILE 3.2 24.9 - - - -
197D PRO* 3.8 1.6 - - + -
198D PHE* 3.4 38.6 - + + +
201D TYR* 3.7 24.5 - + + -
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Residues in contact with LYS 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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234C ASN* 2.8 35.5 + - - +
238C THR* 4.2 15.4 - - - +
187D SER 3.4 8.2 + - - +
188D ILE 3.3 8.4 + - - +
190D PHE* 1.3 79.5 - - - +
192D LYS* 1.3 60.2 + - - +
195D GLY* 2.7 55.7 + - - +
196D ILE 3.9 15.0 - - - +
197D PRO* 4.5 12.3 - - + -
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Residues in contact with LYS 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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185B TYR* 5.9 0.6 + - - -
192B LYS* 6.2 2.2 - - - +
188D ILE* 3.0 16.7 + - + +
189D MSE 3.4 17.7 - - + +
190D PHE 3.1 0.2 - - - -
191D LYS* 1.3 77.8 - - - +
193D ASN* 1.3 69.5 + - - +
195D GLY* 4.5 1.0 + - - -
218E GLU* 4.4 27.7 + - - +
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Residues in contact with ASN 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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151D SER* 3.4 22.5 + - - -
153D ALA* 4.6 6.3 - - - +
154D LYS* 3.8 31.6 + - + +
157D ILE* 5.7 0.4 - - - -
189D MSE 2.9 48.4 + - - +
190D PHE* 3.0 4.2 + - - +
192D LYS* 1.3 87.3 - - - +
194D PHE* 1.3 76.1 + - + +
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Residues in contact with PHE 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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154D LYS* 3.7 41.1 - - + +
157D ILE* 3.7 28.9 - - + -
158D GLN* 3.8 21.5 - - + -
190D PHE* 2.8 61.9 + + + +
193D ASN* 1.3 83.7 - - + +
195D GLY* 1.3 58.4 + - - +
196D ILE* 3.2 16.1 + - + +
201D TYR* 3.7 34.1 - + + -
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Residues in contact with GLY 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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191D LYS* 2.7 43.1 + - - -
192D LYS 4.5 0.8 + - - -
193D ASN 3.7 0.8 - - - -
194D PHE* 1.3 71.1 - - - +
196D ILE* 1.3 65.1 + - - +
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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