Contacts of the helix formed by residues 203 - 222 (chain A) in PDB entry 5LSW
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 TYR 203 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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202A THR* 1.3 71.9 - - - +
204A GLU* 1.3 72.1 + - - +
206A PHE* 3.8 28.8 - + - +
207A SER* 2.8 48.7 + - - -
244A ARG* 3.5 24.2 - - + +
248A ALA* 4.7 10.8 - - + +
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Residues in contact with GLU 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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202A THR* 3.2 19.0 - - + +
203A TYR* 1.3 88.6 + - + +
205A ARG* 1.3 62.3 + - + +
207A SER* 3.0 17.5 + - - +
208A HIS* 3.1 15.1 + - - +
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Residues in contact with ARG 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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198A TYR* 3.2 67.5 + - - -
199A ILE* 3.4 16.4 - - + +
201A GLN* 3.0 31.2 - - - +
202A THR* 3.3 24.0 + - + +
203A TYR 3.3 0.6 - - - -
204A GLU* 1.3 79.8 - - + +
206A PHE* 1.3 62.6 + - - +
208A HIS* 3.4 5.9 + - - +
209A VAL* 3.2 26.5 + - - +
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Residues in contact with PHE 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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199A ILE* 3.2 17.0 + - - +
200A CYS* 4.5 9.9 - - - +
202A THR 3.2 11.0 + - - +
203A TYR* 3.4 24.4 + + - +
205A ARG* 1.3 79.1 - - - +
207A SER* 1.3 60.9 + - - +
209A VAL* 3.2 3.4 + - + +
210A ALA* 2.8 41.8 + - + +
239A LEU* 3.9 31.9 - - + -
244A ARG* 5.1 1.6 - - + -
245A ALA* 3.4 44.9 - - + -
248A ALA* 3.4 26.9 - - + -
249A LEU* 4.3 10.1 - - + -
252A CYS* 5.1 1.8 - - - -
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Residues in contact with SER 207 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
203A TYR* 2.8 46.7 + - - -
204A GLU* 3.0 16.6 + - - +
206A PHE* 1.3 76.7 - - - +
208A HIS* 1.3 59.8 + - - +
210A ALA* 3.8 7.4 - - - +
211A MET* 2.7 46.9 + - - +
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Residues in contact with HIS 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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165A PRO* 5.6 7.6 - - + +
168A LEU* 3.6 24.4 - - + +
169A ARG* 5.2 15.6 + - - -
204A GLU 3.1 18.5 + - - +
205A ARG* 3.6 5.8 - - - +
207A SER* 1.3 78.1 + - - +
209A VAL* 1.3 60.7 + - - +
211A MET* 3.5 20.2 + - + +
212A ILE* 3.2 52.1 + - + +
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Residues in contact with VAL 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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164A ILE* 5.0 4.0 - - + -
168A LEU* 4.0 27.1 - - + +
186A LEU* 4.3 20.0 - - + -
190A LEU* 5.2 2.9 - - + -
199A ILE* 3.6 29.2 - - + -
205A ARG 3.2 13.0 + - - +
206A PHE* 3.2 8.1 + - + +
208A HIS* 1.3 76.8 - - - +
210A ALA* 1.3 56.7 + - - +
212A ILE* 3.3 2.9 + - - +
213A LEU* 3.0 47.1 + - + +
239A LEU* 4.2 14.4 - - + -
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Residues in contact with ALA 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 PHE* 2.8 43.2 + - + +
207A SER* 3.8 6.7 - - - +
209A VAL* 1.3 74.8 - - - +
211A MET* 1.3 58.7 + - + +
213A LEU* 3.3 8.4 + - - +
214A GLY* 2.7 28.8 + - - -
236A TYR* 4.0 4.3 + - + -
239A LEU* 5.5 0.7 - - + -
249A LEU* 5.0 4.7 - - + -
252A CYS* 4.6 16.6 - - - -
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Residues in contact with MET 211 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
207A SER* 2.7 33.5 + - - +
208A HIS* 3.8 25.4 - - + +
210A ALA* 1.3 73.2 - - + +
212A ILE* 1.3 64.3 + - + +
214A GLY* 3.4 1.9 + - - +
215A LYS* 3.0 49.6 + - - +
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Residues in contact with ILE 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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168A LEU* 3.9 36.8 - - + +
171A MET* 4.0 21.3 - - + -
172A GLU* 3.7 42.2 - - + +
208A HIS* 3.2 39.2 + - + +
209A VAL 3.3 3.8 + - - +
211A MET* 1.3 78.6 - - + +
213A LEU* 1.3 64.3 + - - +
215A LYS* 3.2 10.0 + - + +
216A MET* 3.1 31.4 + - + +
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Residues in contact with LEU 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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171A MET* 3.7 27.8 - - + -
183A THR* 5.2 0.2 - - + -
186A LEU* 4.8 1.3 - - + -
209A VAL* 3.0 39.0 + - + +
210A ALA* 3.8 1.8 - - - +
212A ILE* 1.3 76.5 - - - +
214A GLY* 1.3 63.1 + - - +
216A MET* 3.2 18.1 + - - +
217A VAL* 3.2 17.7 + - - +
232A VAL* 4.2 21.1 - - + +
235A CYS* 4.1 25.8 - - + -
236A TYR* 3.2 30.7 - - + +
239A LEU* 4.0 18.2 - - + -
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Residues in contact with GLY 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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210A ALA 2.7 20.9 + - - -
211A MET* 3.8 1.8 - - - -
213A LEU* 1.3 74.5 - - - +
215A LYS* 1.3 59.9 + - - +
217A VAL* 3.4 12.0 + - - +
218A LEU* 3.6 15.6 + - - +
236A TYR* 3.0 11.9 + - - -
252A CYS 5.6 2.7 - - - -
254A PRO* 4.2 13.1 - - - +
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Residues in contact with LYS 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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172A GLU* 4.2 25.4 - - + +
211A MET* 3.0 45.3 + - - +
212A ILE* 3.7 9.1 - - + +
213A LEU 3.2 0.2 - - - -
214A GLY* 1.3 74.7 - - - +
216A MET* 1.3 66.6 + - + +
218A LEU* 3.2 24.1 + - + +
219A GLN* 3.3 18.4 + - + +
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Residues in contact with MET 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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171A MET* 3.6 55.2 - - + +
172A GLU* 5.3 1.8 - - - -
179A LYS* 4.5 4.0 - - + +
183A THR* 3.4 22.2 - - - +
212A ILE* 3.1 18.0 + - + +
213A LEU* 3.2 13.9 + - - +
215A LYS* 1.3 73.3 - - + +
217A VAL* 1.3 65.9 + - - +
219A GLN* 3.3 14.9 + - - +
220A LEU* 3.0 31.7 + - + +
228A LEU* 3.8 21.3 - - + -
232A VAL* 3.7 22.9 - - + -
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Residues in contact with VAL 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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213A LEU 3.2 15.3 + - - +
214A GLY 3.6 7.0 - - - +
215A LYS 3.2 0.4 - - - -
216A MET* 1.3 76.2 - - - +
218A LEU* 1.3 62.2 + - + +
220A LEU* 3.2 11.6 + - + +
221A SER* 3.0 19.6 + - - -
229A LEU* 5.7 1.3 - - + -
232A VAL* 4.2 9.9 - - + -
236A TYR* 4.0 15.7 - - + -
254A PRO* 3.6 35.4 - - + -
256A GLN* 4.0 8.7 - - + +
257A LEU* 4.1 11.7 - - + -
262A PHE* 3.7 25.7 - - + -
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Residues in contact with LEU 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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214A GLY 3.6 13.4 + - - +
215A LYS* 3.2 15.1 + - + +
217A VAL* 1.3 78.4 - - + +
219A GLN* 1.3 61.9 + - + +
221A SER* 2.3 27.5 + - - +
222A LYS* 3.4 17.2 + - - +
254A PRO* 5.7 1.8 - - + -
256A GLN* 3.4 33.7 - - - +
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Residues in contact with GLN 219 (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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172A GLU 4.1 14.7 + - - -
179A LYS* 3.5 28.7 + - - +
215A LYS* 3.3 13.5 + - - +
216A MET* 3.3 14.7 + - - +
218A LEU* 1.3 76.6 - - + +
220A LEU* 1.3 54.4 + - + +
222A LYS* 2.9 10.3 + - + +
223A GLU* 2.7 48.6 + - - +
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Residues in contact with LEU 220 (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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216A MET 3.0 23.7 + - - +
217A VAL* 3.2 11.2 + - - +
219A GLN* 1.3 76.8 - - + +
221A SER* 1.3 61.4 + - - +
222A LYS 3.4 0.2 + - - -
223A GLU 3.6 5.6 - - - +
224A PRO* 3.4 23.7 - - - +
225A SER* 3.8 40.8 - - - +
228A LEU* 4.1 18.6 - - + -
229A LEU* 3.8 36.3 - - + +
232A VAL* 4.4 14.1 - - + -
262A PHE* 3.6 20.0 - - + -
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Residues in contact with SER 221 (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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217A VAL 3.0 10.1 + - - -
218A LEU* 2.3 31.9 + - - +
220A LEU* 1.3 78.4 - - - +
222A LYS* 1.3 63.1 + - - +
224A PRO* 5.3 1.1 - - - +
256A GLN* 4.1 26.0 + - - +
261A THR* 4.3 13.6 - - - +
262A PHE* 3.9 7.8 - - - -
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Residues in contact with LYS 222 (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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218A LEU* 3.6 18.6 - - - +
219A GLN* 2.9 8.4 + - + +
221A SER* 1.3 83.2 - - - +
223A GLU* 1.3 81.6 + - - +
224A PRO* 3.3 11.4 - - - +
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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
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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