Contacts of the helix formed by residues 217 - 236 (chain B) in PDB entry 3L2V
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 217 (chain B).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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119B GLN* 6.2 2.0 - - - -
126B PHE* 4.0 13.9 - - - -
148B GLY 4.6 5.8 + - - -
216B SER* 1.3 79.1 - - - +
218B GLY* 1.3 66.1 + - - +
219B LYS* 3.4 15.9 + - - +
220B VAL* 3.0 21.5 + - - +
221B GLU* 2.9 25.0 + - - +
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Residues in contact with GLY 218 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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216B SER 3.8 1.6 + - - -
217B SER* 1.3 73.5 + - - +
219B LYS* 1.3 62.6 + - - +
221B GLU* 3.4 7.0 + - - +
222B ARG* 3.3 20.1 + - - +
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Residues in contact with LYS 219 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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148B GLY 4.5 8.7 - - - +
149B MET 3.5 19.5 - - - +
150B THR 3.4 29.3 + - - -
151B GLY* 4.0 8.5 - - - +
217B SER* 3.3 9.9 + - - +
218B GLY* 1.3 75.3 - - - +
220B VAL* 1.3 57.8 + - + +
222B ARG* 3.7 5.6 + - - +
223B LYS* 3.1 26.1 + - + +
258B SER* 3.7 23.3 + - - +
260B VAL* 6.0 0.2 - - - +
261B LEU* 3.4 29.6 - - + +
263B TYR 5.4 0.4 + - - -
265B PRO* 5.8 2.4 - - - +
268B LEU* 4.5 1.2 - - - +
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Residues in contact with VAL 220 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
126B PHE* 3.5 47.8 - - + -
146B VAL* 4.5 16.4 - - + -
147B ASP 4.8 0.4 - - - +
148B GLY* 4.3 14.4 - - - +
151B GLY* 6.0 0.9 - - - -
216B SER* 4.3 11.0 - - - +
217B SER* 3.0 20.3 + - - +
219B LYS* 1.3 77.1 - - + +
221B GLU* 1.3 56.2 + - - +
223B LYS* 3.2 6.2 + - - +
224B ASN* 2.6 56.3 + - + +
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Residues in contact with GLU 221 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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216B SER* 4.6 9.8 + - - +
217B SER 2.9 15.0 + - - +
218B GLY* 3.7 7.2 - - - +
220B VAL* 1.3 76.5 - - - +
222B ARG* 1.3 52.7 + - - +
224B ASN* 3.2 6.7 + - - +
225B SER* 2.8 36.2 + - - -
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Residues in contact with ARG 222 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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218B GLY 3.3 9.1 + - - +
219B LYS* 3.8 9.2 - - - +
220B VAL 3.2 0.4 - - - -
221B GLU* 1.3 77.5 - - - +
223B LYS* 1.3 63.5 + - - +
225B SER* 2.8 19.5 + - - -
226B ASP* 2.9 22.5 + - - +
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Residues in contact with LYS 223 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
146B VAL* 4.4 10.5 - - + -
151B GLY* 2.9 33.0 + - - +
153B THR* 3.5 20.8 + - - +
219B LYS* 3.1 17.1 + - + +
220B VAL* 3.7 5.8 - - - +
222B ARG* 1.3 76.7 - - - +
224B ASN* 1.3 62.7 + - - +
226B ASP* 3.2 21.3 + - + +
227B ILE* 3.1 32.2 + - + +
253B LEU* 3.1 44.2 + - + +
254B ASN* 3.6 2.4 + - - -
256B THR* 5.4 3.8 - - - -
265B PRO* 3.6 15.1 - - - +
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Residues in contact with ASN 224 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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126B PHE* 5.4 5.1 + - - +
127B ILE 6.3 0.4 - - - -
128B ASP* 5.1 15.5 - - - +
130B ILE* 5.6 6.2 - - - +
144B VAL* 4.4 14.8 + - - +
146B VAL* 4.0 17.0 - - - +
220B VAL* 2.6 38.1 + - + +
221B GLU* 3.5 7.6 - - - +
223B LYS* 1.3 72.7 - - - +
225B SER* 1.3 61.6 + - - +
227B ILE* 3.9 9.4 + - - +
228B LYS* 3.6 16.8 + - - +
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Residues in contact with SER 225 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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221B GLU 2.8 13.2 + - - -
222B ARG* 2.8 12.5 + - - -
224B ASN* 1.3 75.8 - - - +
226B ASP* 1.3 68.4 + - - -
228B LYS* 3.1 8.9 + - - +
229B ARG* 3.0 22.9 + - - +
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Residues in contact with ASP 226 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
222B ARG* 2.9 23.1 + - - +
223B LYS* 3.2 22.4 + - + +
225B SER* 1.3 79.0 + - - +
227B ILE* 1.3 52.6 + - - +
229B ARG* 3.3 6.5 + - - +
230B LEU* 2.7 39.8 + - + +
253B LEU* 4.4 13.5 - - + -
256B THR* 5.9 2.8 - - - +
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Residues in contact with ILE 227 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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130B ILE* 3.9 21.5 - - + -
144B VAL* 3.6 32.3 - - + -
146B VAL* 4.3 6.7 - - + -
153B THR* 4.0 18.4 - - + +
155B LEU* 4.5 10.5 - - + -
223B LYS* 3.1 19.3 + - + +
224B ASN* 3.9 13.9 - - - +
225B SER 3.2 0.2 - - - -
226B ASP* 1.3 74.6 - - - +
228B LYS* 1.3 52.9 + - - +
230B LEU* 3.2 3.3 + - - +
231B LEU* 2.7 48.5 + - + +
249B VAL* 5.7 0.8 - - + +
253B LEU* 3.8 28.0 - - + +
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Residues in contact with LYS 228 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
130B ILE* 4.8 12.5 - - + +
224B ASN 3.6 9.7 + - - +
225B SER* 3.1 11.0 + - - +
227B ILE* 1.3 79.8 - - - +
229B ARG* 1.3 56.2 + - - +
231B LEU* 3.4 6.2 + - - +
232B THR* 2.8 33.6 + - - -
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Residues in contact with ARG 229 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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225B SER* 3.0 14.3 + - - +
226B ASP* 3.7 9.2 - - - +
228B LYS* 1.3 74.1 - - - +
230B LEU* 1.3 60.8 + - - +
231B LEU 3.1 0.5 + - - -
232B THR* 3.1 6.4 + - - -
233B LYS* 2.8 39.3 + - + +
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Residues in contact with LEU 230 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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226B ASP* 2.7 22.3 + - + +
227B ILE* 3.7 4.3 - - - +
229B ARG* 1.3 72.0 - - - +
231B LEU* 1.3 62.0 + - - +
233B LYS* 4.0 8.5 - - + -
234B LEU* 3.4 40.7 + - + +
249B VAL* 4.4 20.1 - - + +
252B ALA* 4.7 15.3 - - + -
253B LEU* 3.6 31.6 - - + +
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Residues in contact with LEU 231 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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130B ILE* 3.8 40.2 - - + -
133B LEU* 5.1 7.6 - - + -
142B VAL* 4.8 16.2 - - + -
155B LEU* 5.1 1.6 - - + -
227B ILE* 2.7 28.8 + - + +
228B LYS* 3.7 5.8 - - - +
229B ARG 3.1 0.2 - - - -
230B LEU* 1.3 72.1 - - - +
232B THR* 1.3 52.5 + - - +
234B LEU 3.7 0.2 - - - -
235B LEU* 2.7 49.8 + - + +
242B TRP* 5.9 8.5 - - + +
246B LEU* 4.6 20.2 - - + -
249B VAL* 4.7 20.2 - - + -
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Residues in contact with THR 232 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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228B LYS 2.8 18.1 + - - -
229B ARG* 3.8 5.6 + - - -
231B LEU* 1.3 75.2 - - - +
233B LYS* 1.3 66.1 + - - +
235B LEU* 3.9 13.9 - - + -
236B VAL* 3.2 24.8 + - + +
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Residues in contact with LYS 233 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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229B ARG* 2.8 27.9 + - + +
230B LEU* 3.8 13.2 - - + +
231B LEU 3.2 0.2 - - - -
232B THR* 1.3 80.4 - - - +
234B LEU* 1.3 68.8 + - + +
236B VAL* 3.3 22.2 - - - +
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Residues in contact with LEU 234 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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230B LEU* 3.4 32.9 + - + +
231B LEU 3.7 0.7 - - - +
233B LYS* 1.3 81.9 - - + +
235B LEU* 1.3 64.7 + - - +
236B VAL 3.9 2.7 - - - -
238B ARG* 3.7 43.9 + - - +
242B TRP* 5.7 1.4 - - - +
245B LEU* 4.3 21.2 - - + +
248B VAL* 6.5 1.6 - - + -
249B VAL* 5.3 11.4 - - + -
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Residues in contact with LEU 235 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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133B LEU* 4.7 31.6 - - + -
134B PRO* 4.7 13.7 - - + -
231B LEU* 2.7 33.8 + - + +
232B THR* 3.6 14.1 - - + +
233B LYS 3.2 0.4 - - - -
234B LEU* 1.3 70.9 - - - +
236B VAL* 1.3 72.7 + - + +
238B ARG 3.0 29.7 + - - +
239B PRO* 3.0 24.4 - - + +
242B TRP* 4.8 18.4 - - + -
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Residues in contact with VAL 236 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
232B THR* 3.2 12.3 + - + +
233B LYS* 3.3 21.5 - - - +
234B LEU* 3.8 5.2 - - - +
235B LEU* 1.3 90.5 - - + +
237B GLY* 1.3 62.0 + - - +
238B ARG* 3.2 7.6 + - - -
239B PRO* 4.8 3.8 - - - -
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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
------------------------------------------------------------
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