Contacts of the helix formed by residues 216 - 235 (chain A) in PDB entry 5LUQ
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 LYS 216 (chain A).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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168A ASP* 5.3 15.5 + - - +
207A GLN* 3.9 26.7 + - - +
211A ALA* 5.9 1.8 - - - +
212A VAL* 3.5 34.8 - - + +
214A GLU 4.2 5.4 - - - +
215A PRO* 1.3 75.6 - - - +
217A LEU* 1.3 64.1 + - - +
218A PRO* 4.4 11.9 - - + -
219A VAL* 5.2 7.9 - - + +
220A LEU* 3.1 31.7 + - - +
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Residues in contact with LEU 217 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
215A PRO* 5.2 7.0 - - + +
216A LYS* 1.3 71.0 - - - +
218A PRO* 1.3 74.4 - - + +
220A LEU* 3.5 3.3 + - + -
221A ALA* 2.9 25.7 + - - +
258A PRO* 4.5 25.8 - - + -
259A GLN 4.7 8.3 - - - +
260A ILE* 6.0 1.6 - - + -
261A ASP* 4.1 17.0 - - - +
264A ARG* 3.6 39.5 - - + +
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Residues in contact with PRO 218 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
168A ASP* 4.1 28.5 - - + +
169A THR* 5.5 2.5 - - - -
172A GLU* 3.5 22.1 + - + +
216A LYS* 3.7 9.4 - - + -
217A LEU* 1.3 95.0 - - + +
219A VAL* 1.3 65.8 + - + +
221A ALA* 3.3 20.4 - - + +
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Residues in contact with VAL 219 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
168A ASP* 3.8 25.8 - - + +
171A LEU* 3.7 42.8 - - + -
172A GLU 4.9 0.4 - - - +
175A TYR* 3.9 8.5 - - + -
204A LEU* 3.5 33.4 - - + -
207A GLN* 5.0 9.0 - - - +
216A LYS* 4.1 9.9 + - + +
217A LEU 3.4 0.2 - - - -
218A PRO* 1.3 78.5 - - + +
220A LEU* 1.3 62.1 + - - +
221A ALA 3.2 0.7 - - - -
222A GLY 4.6 0.4 - - - +
223A CYS* 2.8 33.1 + - - +
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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
----------------------------------------------------------
204A LEU* 5.9 0.9 - - + -
208A MSE 3.5 40.8 - - + -
215A PRO* 3.8 26.7 - - + -
216A LYS 3.1 27.7 + - - +
217A LEU* 3.9 6.1 - - + +
219A VAL* 1.3 76.9 - - - +
221A ALA* 1.3 67.9 + - - +
223A CYS* 4.3 2.7 - - + -
224A LEU* 2.9 54.0 + - + +
248A ILE* 5.0 7.4 - - + -
251A PHE* 4.8 9.4 - - + -
264A ARG* 4.1 10.5 - - + -
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Residues in contact with ALA 221 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
172A GLU* 4.0 17.0 - - - +
217A LEU 2.9 14.0 + - - +
218A PRO* 3.3 15.5 - - + +
220A LEU* 1.3 78.8 - - - +
222A GLY* 1.3 66.4 + - - +
224A LEU* 4.2 1.0 - - - +
225A LYS* 3.0 28.2 + - - +
264A ARG* 3.3 34.0 + - - +
267A VAL* 4.8 1.3 - - - +
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Residues in contact with GLY 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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172A GLU* 3.3 38.5 - - - +
175A TYR* 3.0 11.6 - - - +
218A PRO 3.7 0.2 + - - -
219A VAL 3.6 2.2 + - - -
220A LEU 3.4 0.2 - - - -
221A ALA* 1.3 77.9 - - - +
223A CYS* 1.3 53.9 + - - +
225A LYS* 2.6 32.4 + - - +
226A GLY 2.8 11.1 + - - -
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Residues in contact with CYS 223 (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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175A TYR* 3.2 18.1 - - - -
201A LEU* 4.3 24.0 - - - +
204A LEU* 3.4 38.4 - - + -
205A LYS* 6.3 0.4 - - - -
208A MSE 5.0 4.9 - - - -
219A VAL 2.8 24.4 + - - +
220A LEU* 3.9 4.7 - - + +
222A GLY* 1.3 69.9 - - - +
224A LEU* 1.3 69.4 + - + +
226A GLY* 3.3 1.0 + - - -
227A LEU* 3.0 28.9 + - - +
244A THR* 6.4 2.2 - - - -
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Residues in contact with LEU 224 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
208A MSE 4.9 4.5 - - + -
220A LEU* 2.9 48.9 + - + +
223A CYS* 1.3 79.8 - - - +
225A LYS* 1.3 66.5 + - - +
227A LEU* 4.5 7.1 - - + +
228A SER* 2.9 27.0 + - - -
244A THR* 5.2 8.7 - - + -
248A ILE* 3.5 50.7 - - + -
264A ARG* 4.3 3.1 - - - +
267A VAL* 3.6 26.8 - - + +
268A PRO* 4.9 3.8 - - + +
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Residues in contact with LYS 225 (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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139A ARG* 3.8 16.6 - - - +
172A GLU* 4.2 7.3 + - - -
175A TYR 4.3 1.8 - - - -
176A GLU* 3.3 47.6 + - + -
221A ALA* 3.0 24.4 + - - +
222A GLY* 2.6 16.6 + - - +
224A LEU* 1.3 70.4 - - - +
226A GLY* 1.3 58.4 + - - +
228A SER* 2.3 25.7 + - - -
229A SER* 2.9 13.4 + - - -
264A ARG* 4.1 18.5 - - - +
267A VAL* 3.9 22.4 - - + +
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Residues in contact with GLY 226 (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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175A TYR* 3.3 29.8 + - - -
179A GLY* 4.4 4.4 - - - -
197A PHE* 5.1 2.7 - - - -
222A GLY 2.8 13.7 + - - -
223A CYS 3.6 3.4 - - - -
225A LYS* 1.3 71.0 - - - +
227A LEU* 1.3 58.8 + - - +
229A SER* 2.8 19.8 + - - -
230A LEU* 3.0 25.6 + - - +
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Residues in contact with LEU 227 (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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197A PHE* 5.7 0.2 - - - -
201A LEU* 3.9 40.7 - - + +
223A CYS* 3.0 19.0 + - - +
224A LEU* 4.5 6.5 - - + +
226A GLY* 1.3 71.4 - - - -
228A SER* 1.3 60.7 + - - +
230A LEU* 3.7 12.9 - - + +
231A LEU* 3.3 40.8 + - + +
240A GLU* 4.8 8.3 - - + +
241A ASP* 3.6 20.4 - - - +
244A THR* 4.0 27.1 - - + +
275A PHE* 3.2 14.1 - - + -
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Residues in contact with SER 228 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
224A LEU 2.9 16.4 + - - -
225A LYS* 2.3 31.9 + - - -
227A LEU* 1.3 77.7 - - - +
229A SER* 1.3 62.5 + - - +
232A CYS* 3.7 2.6 - - - -
267A VAL* 4.0 12.4 + - - +
268A PRO* 5.8 0.4 - - - -
270A ALA* 5.9 0.7 - - - -
271A GLY* 4.0 19.5 - - - -
274A LEU* 3.4 11.7 - - - +
275A PHE* 2.9 32.3 - - - -
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Residues in contact with SER 229 (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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176A GLU 5.4 0.9 - - - -
179A GLY* 2.7 40.7 + - - +
180A LEU 3.7 0.2 + - - -
183A GLU* 2.7 43.9 - - - +
225A LYS 3.3 13.9 - - - -
226A GLY 2.8 8.7 + - - -
228A SER* 1.3 78.5 + - - +
230A LEU* 1.3 58.1 + - - -
231A LEU 3.5 0.2 - - - -
232A CYS* 4.5 7.4 + - - -
233A ASN* 4.2 5.0 + - - -
274A LEU* 6.3 0.4 - - - -
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Residues in contact with LEU 230 (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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178A LEU 5.0 1.3 - - - +
179A GLY* 4.7 6.5 - - - -
182A GLY* 5.3 5.4 - - - -
194A GLU* 3.2 26.7 - - + +
197A PHE* 3.4 66.6 - - + -
201A LEU* 5.8 0.4 - - + -
226A GLY* 3.0 29.7 + - - +
227A LEU* 3.7 13.0 - - + -
229A SER* 1.3 76.5 - - - +
231A LEU* 1.3 79.9 + - + +
232A CYS 3.4 1.1 - - - -
233A ASN* 3.3 9.7 + - - +
234A PHE* 3.0 20.9 + - + +
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Residues in contact with LEU 231 (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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227A LEU* 3.3 29.0 + - + +
228A SER 4.0 0.2 + - - -
229A SER 3.5 0.6 - - - -
230A LEU* 1.3 83.1 - - + +
232A CYS* 1.3 60.3 + - - +
233A ASN 3.1 1.6 - - - -
234A PHE* 3.2 37.5 - - + -
235A THR* 2.8 33.7 + - - +
237A SER* 3.5 15.7 - - - +
240A GLU* 6.4 0.4 - - + -
241A ASP* 3.3 37.2 - - - +
275A PHE* 3.2 29.9 - - + -
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Residues in contact with CYS 232 (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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183A GLU* 5.9 3.1 - - + -
228A SER 3.7 6.5 - - - -
229A SER* 4.6 8.1 - - - +
230A LEU 3.4 0.4 - - - -
231A LEU* 1.3 77.4 - - - +
233A ASN* 1.3 64.5 + - - +
235A THR* 3.9 13.4 - - - +
274A LEU* 3.4 39.0 - - - +
275A PHE* 3.2 24.3 - - - -
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Residues in contact with ASN 233 (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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182A GLY 2.4 37.4 + - - -
183A GLU* 3.3 16.4 - - - +
184A VAL 4.8 2.5 - - - +
185A HIS* 5.4 4.9 + - - -
190A ILE* 3.5 19.3 - - + +
194A GLU* 3.1 17.8 - - - +
229A SER 4.2 7.9 + - - -
230A LEU 3.3 3.7 + - - +
231A LEU 3.1 0.2 - - - -
232A CYS* 1.3 83.1 - - - +
234A PHE* 1.3 62.4 + - - +
235A THR* 4.3 3.8 - - - +
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Residues in contact with PHE 234 (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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194A GLU* 2.9 50.5 + - + +
195A ASN* 4.3 13.2 - - - -
198A ARG* 5.4 12.1 - - - -
230A LEU* 3.0 8.2 + - + +
231A LEU* 3.0 31.6 + - + -
233A ASN* 1.3 78.3 - - - +
235A THR* 1.3 95.6 + - - +
236A LYS* 4.8 10.8 - - + +
237A SER* 5.6 0.9 - - - -
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Residues in contact with THR 235 (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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231A LEU* 2.8 19.1 + - - +
232A CYS 3.9 16.6 - - - +
233A ASN 4.3 4.4 + - - +
234A PHE* 1.3 106.3 + - - +
236A LYS* 1.3 82.0 + - - +
237A SER* 3.1 6.1 + - - -
277A LEU* 5.3 15.5 - - + -
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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