Contacts of the helix formed by residues 197 - 218 (chain A) in PDB entry 3LRA
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 GLU 197 (chain A).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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195A LEU 3.8 0.7 + - - +
196A GLY* 1.3 70.7 - - - -
198A PRO* 1.3 83.1 - - + +
199A VAL* 2.9 44.8 + - - +
200A ARG* 3.3 17.8 + - + +
201A LEU* 3.2 20.3 + - - +
249A TYR* 4.0 18.9 + - + +
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Residues in contact with PRO 198 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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196A GLY 3.2 3.8 - - - +
197A GLU* 1.3 94.3 - - - +
199A VAL* 1.3 58.9 + - + +
201A LEU* 3.6 6.2 + - + +
202A GLU* 3.1 26.9 + - - +
242A ARG* 5.4 2.8 + - - +
245A TYR* 3.8 21.8 - - + -
246A GLU* 4.1 23.3 - - + +
249A TYR* 3.2 41.3 - - + -
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Residues in contact with VAL 199 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
197A GLU* 2.9 24.3 + - - +
198A PRO* 1.3 76.8 - - + +
200A ARG* 1.3 66.5 + - - +
202A GLU* 3.3 12.8 + - - +
203A ARG* 2.9 66.8 + - + +
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Residues in contact with ARG 200 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
163A LEU* 6.0 1.8 - - - +
166A LYS* 3.9 17.1 - - - +
168A ASN* 5.0 3.1 - - - +
197A GLU* 3.3 23.5 + - + +
199A VAL* 1.3 79.7 - - - +
201A LEU* 1.3 53.4 + - - +
203A ARG* 3.0 11.9 + - - +
204A ASP* 2.7 68.1 + - - +
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Residues in contact with LEU 201 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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168A ASN* 3.4 45.0 - - + +
172A LEU* 4.3 13.7 - - + -
195A LEU* 3.7 38.1 - - + +
197A GLU 3.2 10.2 + - - +
198A PRO* 3.7 9.0 - - + +
199A VAL 3.2 0.4 - - - -
200A ARG* 1.3 79.1 - - - +
202A GLU* 1.3 58.2 + - - +
204A ASP* 3.1 3.1 + - - +
205A ILE* 2.9 45.1 + - + +
242A ARG* 4.3 18.6 - - + -
245A TYR* 4.5 11.2 - - + -
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Residues in contact with GLU 202 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
198A PRO 3.1 14.9 + - - +
199A VAL* 3.8 15.3 - - - +
200A ARG 3.3 0.2 - - - -
201A LEU* 1.3 80.1 - - - +
203A ARG* 1.3 62.5 + - + +
205A ILE* 4.1 5.8 - - + +
206A CYS* 3.1 36.4 + - - -
242A ARG* 3.9 36.0 + - - +
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Residues in contact with ARG 203 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
199A VAL* 2.9 44.3 + - - +
200A ARG* 3.5 11.4 - - - +
201A LEU 3.0 0.2 - - - -
202A GLU* 1.3 83.1 + - + +
204A ASP* 1.3 65.6 + - - +
206A CYS* 3.5 5.0 + - - +
207A ARG* 3.2 22.9 + - - +
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Residues in contact with ASP 204 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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163A LEU* 3.3 21.8 - - + +
166A LYS* 2.4 41.1 + - - +
168A ASN* 3.3 13.5 + - - +
169A VAL* 4.6 10.3 - - + -
200A ARG* 2.7 50.7 + - - +
201A LEU 3.7 4.0 - - - +
203A ARG* 1.3 74.4 - - - +
205A ILE* 1.3 59.8 + - - +
207A ARG* 3.4 4.9 + - - +
208A ALA* 3.0 22.7 + - - +
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Residues in contact with ILE 205 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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169A VAL* 4.1 30.1 - - + -
172A LEU* 3.6 31.6 - - + -
201A LEU* 2.9 32.3 + - + +
202A GLU* 4.1 7.2 - - - +
204A ASP* 1.3 75.6 - - - +
206A CYS* 1.3 72.3 + - - +
208A ALA* 3.1 7.8 + - + +
209A ILE* 3.0 37.3 + - + +
233A LEU* 4.0 25.5 - - + +
238A CYS* 6.4 0.2 - - - -
239A ASN* 6.0 0.2 - - - +
242A ARG* 4.8 14.6 - - - +
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Residues in contact with CYS 206 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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202A GLU* 3.1 33.4 + - - +
203A ARG* 3.9 6.3 - - - +
204A ASP 3.4 0.4 - - - -
205A ILE* 1.3 84.6 - - - +
207A ARG* 1.3 57.1 + - - +
209A ILE* 3.1 15.0 + - - +
210A GLU* 3.0 36.7 + - - +
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Residues in contact with ARG 207 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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159A GLU* 2.8 43.4 + - - +
163A LEU* 4.2 9.6 - - + -
203A ARG 3.2 11.3 + - - +
204A ASP* 3.6 10.3 - - - +
205A ILE 3.2 0.4 - - - -
206A CYS* 1.3 79.3 - - - +
208A ALA* 1.3 61.9 + - - +
210A GLU* 3.3 31.2 + - - +
211A LEU* 3.0 39.3 + - + +
214A LYS* 3.6 19.4 - - - +
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Residues in contact with ALA 208 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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160A LEU* 3.9 16.1 - - + +
163A LEU* 3.7 18.4 - - + +
164A LEU* 5.3 5.8 - - + -
169A VAL* 6.0 4.0 - - + -
204A ASP 3.0 14.7 + - - +
205A ILE* 3.2 14.1 - - + +
207A ARG* 1.3 78.7 - - - +
209A ILE* 1.3 56.1 + - - +
211A LEU* 3.5 3.0 + - - +
212A LEU* 2.9 32.3 + - + +
233A LEU* 4.1 15.3 - - + -
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Residues in contact with ILE 209 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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205A ILE* 3.0 21.7 + - + +
206A CYS* 3.1 14.8 + - - +
208A ALA* 1.3 74.1 - - - +
210A GLU* 1.3 59.5 + - + +
212A LEU* 3.2 8.3 + - - +
213A GLU* 2.9 44.0 + - - +
230A GLN* 3.8 13.5 - - + +
233A LEU* 3.8 33.9 - - + +
234A GLN* 3.6 44.0 - - + +
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Residues in contact with GLU 210 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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206A CYS* 3.0 23.6 + - - +
207A ARG* 3.4 42.7 + - - +
208A ALA 3.3 0.4 - - - -
209A ILE* 1.3 75.5 - - + +
211A LEU* 1.3 57.7 + - - +
212A LEU 3.1 0.3 + - - -
213A GLU* 3.2 16.4 + - - +
214A LYS* 2.9 34.2 + - - +
217A ARG* 4.9 2.1 + - - +
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Residues in contact with LEU 211 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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156A GLU* 4.0 25.9 - - + +
159A GLU* 3.5 42.0 - - + +
160A LEU* 3.8 40.2 - - + +
163A LEU* 4.4 5.2 - - + -
207A ARG* 3.0 43.8 + - + +
208A ALA 3.9 2.5 - - - +
210A GLU* 1.3 79.0 - - - +
212A LEU* 1.3 61.4 + - - +
214A LYS* 3.8 9.3 - - - +
215A LEU* 3.1 31.4 + - - +
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Residues in contact with LEU 212 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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144A LEU* 4.2 18.6 - - + -
160A LEU* 3.6 29.6 - - + -
208A ALA* 2.9 18.8 + - + +
209A ILE* 3.3 7.9 - - - +
210A GLU 3.0 0.2 - - - -
211A LEU* 1.3 76.4 - - - +
213A GLU* 1.3 64.6 + - - +
215A LEU* 3.6 4.1 + - - +
216A GLN* 3.0 28.0 + - - +
226A LEU* 3.5 25.7 - - + +
229A LEU* 3.8 16.4 - - + +
230A GLN* 3.4 37.7 - - + +
233A LEU* 4.3 10.5 - - + -
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Residues in contact with GLU 213 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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209A ILE* 2.9 29.1 + - - +
210A GLU* 3.7 14.6 - - - +
212A LEU* 1.3 73.0 - - - +
214A LYS* 1.3 59.9 + - - +
216A GLN* 3.2 13.0 + - - +
217A ARG* 2.9 56.0 + - - +
230A GLN* 3.2 23.3 + - - +
234A GLN* 3.8 16.6 + - - -
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Residues in contact with LYS 214 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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156A GLU* 3.5 41.1 + - + +
207A ARG* 3.6 27.5 - - - +
210A GLU* 2.9 20.3 + - - +
211A LEU* 3.8 7.5 - - - +
213A GLU* 1.3 78.1 - - - +
215A LEU* 1.3 62.2 + - - +
217A ARG* 3.1 32.1 + - + +
218A SER* 3.1 17.3 + - - +
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Residues in contact with LEU 215 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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148A LEU* 4.4 8.7 - - + -
154A ASN* 4.4 12.1 - - - +
156A GLU* 3.6 31.4 - - + +
157A ILE* 4.2 26.5 - - + -
160A LEU* 3.8 25.1 - - + -
211A LEU 3.1 19.5 + - - +
212A LEU 3.6 0.6 + - - +
213A GLU 3.4 0.2 - - - -
214A LYS* 1.3 78.4 - - - +
216A GLN* 1.3 61.1 + - - +
218A SER* 3.7 20.1 + - - +
219A GLY* 4.0 0.9 + - - -
220A GLU* 4.3 1.7 + - - +
221A VAL* 3.8 21.9 - - + +
222A PRO* 5.5 0.5 - - - +
226A LEU* 3.5 24.5 - - + -
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Residues in contact with GLN 216 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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212A LEU 3.0 20.2 + - - +
213A GLU* 3.2 8.0 + - - +
214A LYS 3.1 0.4 - - - -
215A LEU* 1.3 77.2 - - - +
217A ARG* 1.3 66.1 + - + +
218A SER 3.1 0.2 - - - -
219A GLY* 3.1 15.1 + - - -
222A PRO* 5.5 7.0 - - - +
223A PRO 4.9 5.9 + - - +
226A LEU* 3.8 18.4 - - + +
227A GLN* 2.7 53.6 + - - +
230A GLN* 3.1 21.1 - - - +
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Residues in contact with ARG 217 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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210A GLU* 4.9 1.6 + - - +
213A GLU* 2.9 40.9 + - - +
214A LYS* 3.1 30.4 + - + +
216A GLN* 1.3 76.8 - - - +
218A SER* 1.3 57.2 + - - +
219A GLY 3.3 3.2 + - - -
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Residues in contact with SER 218 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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154A ASN* 5.5 3.8 + - - -
214A LYS* 3.1 16.7 + - - +
215A LEU* 3.7 14.2 + - - +
216A GLN 3.1 0.2 - - - -
217A ARG* 1.3 77.0 - - - +
219A GLY* 1.3 65.1 + - - +
220A GLU* 2.8 26.0 + - - +
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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