Contacts of the helix formed by residues 231 - 245 (chain K) in PDB entry 3SWD
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 ASP 231 (chain K).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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18K ILE* 3.6 2.6 - - - +
19K SER* 2.9 18.8 + - - +
20K GLY 3.7 3.6 - - - +
21K ALA* 3.5 15.7 - - - +
22K LYS* 3.1 16.8 + - - +
47K LEU* 6.0 0.2 - - - +
230K PRO* 1.3 70.5 - - - +
232K ARG* 1.3 57.7 + - - +
233K ILE* 3.0 13.0 + - - +
234K GLU* 2.9 34.3 + - + +
235K THR* 3.0 31.2 + - - -
371K ARG* 2.9 27.7 + - - -
398K GLY 5.0 0.3 - - - +
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Residues in contact with ARG 232 (chain K).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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21K ALA* 5.2 0.8 - - - +
188K GLU* 3.2 22.1 + - - +
189K PRO* 3.7 11.9 - - - +
190K GLU* 2.8 42.6 + - - +
230K PRO 3.5 6.0 + - - +
231K ASP* 1.3 72.9 + - - +
233K ILE* 1.3 79.3 + - + +
235K THR* 3.3 5.6 + - - -
236K GLY 3.0 23.2 + - - -
258K THR* 3.3 42.1 + - + -
259K LEU* 3.5 27.3 - - + +
299K HIS* 4.5 9.6 + - - +
303K PRO* 4.2 20.0 - - - +
306K MET* 3.3 5.4 - - - +
501K EPZ 5.5 3.6 + - - -
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Residues in contact with ILE 233 (chain K).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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23K ASN* 5.5 1.6 - - - +
231K ASP* 3.0 8.8 + - - +
232K ARG* 1.3 99.6 - - + +
234K GLU* 1.3 56.7 + - - +
237K THR* 2.7 28.8 + - - -
259K LEU* 6.3 0.2 - - + -
303K PRO* 4.7 4.7 - - + -
305K ASP* 3.3 55.9 - - + +
306K MET* 2.8 31.0 - - + +
309K GLN* 4.1 1.6 - - - +
371K ARG* 3.9 31.4 - - - +
399K TYR* 4.0 9.2 - - - +
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Residues in contact with GLU 234 (chain K).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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18K ILE* 3.7 9.0 - - - +
19K SER* 2.9 34.8 + - - -
231K ASP* 2.9 22.7 + - - +
233K ILE* 1.3 75.6 - - - +
235K THR* 1.3 64.6 + - - +
237K THR* 3.2 5.9 + - - -
238K PHE* 3.1 55.8 + - + -
371K ARG* 5.1 1.3 - - - +
399K TYR* 4.0 24.0 - - + +
400K GLU 4.4 11.2 + - - +
402K ILE* 6.1 0.2 - - - -
405K LYS* 2.9 29.2 + - - +
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Residues in contact with THR 235 (chain K).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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18K ILE* 3.5 27.9 - - + +
230K PRO* 5.1 1.4 - - - +
231K ASP 3.0 16.2 + - - -
232K ARG* 3.6 9.4 - - - -
233K ILE 3.3 0.2 - - - -
234K GLU* 1.3 76.2 - - - +
236K GLY* 1.3 61.6 + - - +
238K PHE* 3.5 2.3 + - - +
239K LEU* 3.0 34.0 + - + +
251K CYS* 4.2 17.0 - - + -
254K ALA* 4.5 9.0 - - + +
255K GLN 5.5 1.1 + - - +
259K LEU* 3.3 24.9 - - + -
280K ILE* 4.0 15.9 - - + -
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Residues in contact with GLY 236 (chain K).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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232K ARG 3.0 12.0 + - - -
235K THR* 1.3 75.3 - - - +
237K THR* 1.3 65.1 + - - +
239K LEU* 2.9 13.8 + - - +
240K VAL* 2.7 27.8 + - - +
259K LEU* 4.5 2.0 - - - +
262K VAL* 4.9 10.3 - - - -
306K MET* 3.3 22.4 - - - -
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Residues in contact with THR 237 (chain K).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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233K ILE 2.7 22.0 + - - -
234K GLU 3.2 5.6 + - - -
236K GLY* 1.3 75.3 - - - +
238K PHE* 1.3 70.3 + - + +
240K VAL* 3.3 5.0 + - - +
241K ALA* 2.9 20.4 + - - +
306K MET* 3.7 1.4 - - - +
309K GLN* 3.3 27.0 + - + -
374K ALA* 4.3 20.0 - - + -
378K LEU* 3.6 26.4 - - + +
399K TYR* 3.3 17.7 + - + -
402K ILE* 5.2 4.5 - - + -
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Residues in contact with PHE 238 (chain K).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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16K VAL* 4.1 20.4 - - + -
18K ILE* 4.7 2.2 - - + -
234K GLU* 3.1 59.5 + - + +
235K THR 4.2 2.9 - - - +
237K THR* 1.3 83.4 - - + +
239K LEU* 1.3 62.8 + - - +
241K ALA* 2.9 19.0 + - + +
242K ALA* 3.1 12.8 + - - +
249K ILE* 3.9 20.4 - - + +
251K CYS* 4.7 1.8 - - - -
378K LEU* 6.3 0.2 - - + -
399K TYR* 5.4 1.6 - + - -
402K ILE* 4.3 19.5 - - + -
405K LYS* 3.8 35.9 - - + -
406K LEU* 3.9 31.2 - - + -
409K LEU* 4.5 12.6 - - + -
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Residues in contact with LEU 239 (chain K).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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235K THR* 3.0 38.4 + - + +
236K GLY* 2.9 9.9 + - - +
238K PHE* 1.3 76.0 - - - +
240K VAL* 1.3 60.5 + - - +
242K ALA* 3.5 2.3 + - - +
243K ALA* 3.3 16.5 + - - +
249K ILE* 4.5 14.4 - - + -
251K CYS* 3.5 24.5 - - - -
259K LEU* 4.3 5.6 - - + -
262K VAL* 5.2 2.0 - - + -
263K LEU* 3.8 28.7 - - + -
266K LEU* 4.3 17.5 - - + -
280K ILE* 3.6 25.1 - - + +
282K LEU* 3.7 23.2 - - + +
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Residues in contact with VAL 240 (chain K).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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236K GLY* 2.7 23.0 + - - +
237K THR 3.6 5.4 - - - +
239K LEU* 1.3 69.0 - - - +
241K ALA* 1.3 67.5 + - - +
242K ALA 3.1 1.8 - - - -
243K ALA* 3.1 6.2 + - - +
244K ILE* 3.1 39.3 + - + +
266K LEU* 4.3 8.7 - - + -
306K MET* 5.5 0.7 - - - -
309K GLN* 3.7 35.0 - - + +
310K PHE* 3.7 36.1 - - + -
312K LEU* 5.7 1.3 - - + -
313K LEU* 4.9 4.9 - - + -
378K LEU* 4.5 7.6 - - + -
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Residues in contact with ALA 241 (chain K).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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12K LEU* 3.2 30.0 - - + +
237K THR 2.9 12.6 + - - +
238K PHE* 2.9 17.8 + - + +
240K VAL* 1.3 74.9 - - - +
242K ALA* 1.3 59.6 + - - +
244K ILE* 3.3 16.7 - - - +
245K SER* 2.8 19.1 + - - -
249K ILE* 5.8 1.6 - - + -
378K LEU* 4.0 16.6 - - + -
406K LEU* 4.8 7.9 - - + -
409K LEU* 6.1 1.1 - - + -
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Residues in contact with ALA 242 (chain K).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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12K LEU* 4.4 12.3 - - + +
238K PHE 3.1 5.9 + - - +
239K LEU 3.8 4.9 - - - +
240K VAL 3.1 0.6 - - - -
241K ALA* 1.3 78.3 - - - +
243K ALA* 1.3 61.8 + - - +
244K ILE 3.4 0.3 + - - -
245K SER* 3.6 4.4 + - - -
246K ARG 3.5 1.6 + - - -
247K GLY* 3.1 26.3 + - - +
248K LYS 4.4 2.5 - - - +
249K ILE* 3.4 42.8 - - + +
282K LEU* 4.0 10.1 - - + -
284K MET* 3.7 3.3 - - - +
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Residues in contact with ALA 243 (chain K).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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239K LEU 3.3 12.9 + - - +
240K VAL 3.1 6.0 + - - +
242K ALA* 1.3 78.2 - - - +
244K ILE* 1.3 60.3 + - - +
246K ARG 4.2 1.8 + - - -
266K LEU* 4.0 22.2 - - + -
269K ALA* 6.4 0.4 - - + -
271K ALA* 4.8 0.7 - - + -
282K LEU* 4.2 4.5 - - + -
284K MET* 3.6 33.0 - - + +
287K LYS 4.7 0.2 - - - +
289K PRO* 3.5 23.4 - - - +
313K LEU* 4.3 10.8 - - + -
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Residues in contact with ILE 244 (chain K).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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12K LEU* 5.5 1.8 - - + -
240K VAL* 3.3 21.8 - - + +
241K ALA* 3.3 16.4 - - - +
243K ALA* 1.3 78.8 - - - +
245K SER* 1.3 63.7 + - - +
246K ARG* 3.4 6.1 + - - +
289K PRO* 4.8 8.9 - - + +
312K LEU* 3.9 21.3 - - + -
313K LEU* 4.0 33.0 - - + +
316K VAL* 4.5 11.5 - - + +
378K LEU* 3.9 32.1 - - + +
382K ILE* 3.9 33.2 - - + +
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Residues in contact with SER 245 (chain K).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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10K THR 3.7 13.8 - - - +
11K LYS* 3.7 14.4 + - - +
12K LEU* 3.0 37.8 + - - +
241K ALA 2.8 20.8 + - - -
242K ALA* 3.6 4.7 + - - -
243K ALA 3.5 0.2 - - - -
244K ILE* 1.3 80.0 - - - +
246K ARG* 1.3 68.4 + - - +
247K GLY 3.0 5.0 + - - -
382K ILE* 3.7 12.8 - - - -
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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
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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