Contacts of the helix formed by residues 229 - 246 (chain K) in PDB entry 3EXG
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 229 (chain K).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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9K ILE* 4.8 2.1 - - - +
10K LYS 5.3 1.0 + - - -
226K ASP* 3.3 28.4 + - - +
227K GLY 3.2 0.2 - - - -
228K MET* 1.3 78.2 - - - +
230K ILE* 1.3 54.7 + - - +
231K LEU* 2.3 58.7 + - - +
232K CYS* 3.1 21.3 + - - -
233K VAL* 3.3 12.5 + - - +
290K LEU* 4.6 12.7 - - + +
294K ARG* 2.9 33.5 + - - -
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Residues in contact with ILE 230 (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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35K TYR* 4.2 19.0 - - + -
39K MET* 3.8 33.7 - - + -
70K ALA* 3.8 19.9 - - - +
73K VAL* 3.6 24.0 - - + -
74K GLY* 3.5 30.7 - - - +
228K MET 3.6 5.7 + - - -
229K ASP* 1.3 69.7 - - - +
231K LEU* 1.3 73.2 + - + +
232K CYS 3.7 0.2 - - - -
233K VAL* 4.0 2.7 - - - -
234K ARG* 3.4 20.5 + - + +
287K PRO* 5.5 2.5 + - - +
291K LEU* 4.4 18.2 - - + -
294K ARG* 5.4 1.6 - - - +
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Residues in contact with LEU 231 (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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7K PHE* 4.0 25.1 - - + -
9K ILE* 3.8 10.0 - - + +
25K THR* 4.2 12.9 - - + +
27K LEU* 4.7 16.6 - - + -
35K TYR* 5.3 4.0 - - + -
229K ASP* 2.3 31.3 + - - +
230K ILE* 1.3 84.1 - - + +
232K CYS* 1.3 57.9 + - - +
234K ARG* 3.7 33.2 + - + +
235K GLU* 3.1 27.0 + - - +
291K LEU* 5.6 5.4 - - + -
294K ARG* 3.0 29.6 - - - +
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Residues in contact with CYS 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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9K ILE* 3.9 26.2 - - + -
10K LYS 4.4 12.6 - - - +
12K CYS* 5.7 5.6 - - - -
225K VAL* 4.3 11.4 - - + -
226K ASP* 3.9 22.9 - - - +
229K ASP* 3.8 23.6 - - - -
231K LEU* 1.3 72.2 - - - +
233K VAL* 1.3 72.0 + - - +
234K ARG 2.8 1.6 - - - -
235K GLU* 2.4 22.8 + - + -
236K ALA* 2.7 15.9 + - + +
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Residues in contact with VAL 233 (chain K).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
70K ALA 3.5 27.4 - - - +
71K CYS* 3.8 6.5 - - - +
74K GLY* 3.7 9.9 - - - -
75K LEU* 3.5 28.5 - - + +
225K VAL* 4.5 11.0 - - + -
226K ASP 3.8 12.6 - - - +
227K GLY* 4.0 15.3 - - - -
229K ASP 3.3 18.1 + - - +
230K ILE 4.0 0.9 - - - +
232K CYS* 1.3 83.1 - - - +
234K ARG* 1.3 53.6 + - - +
236K ALA* 4.1 1.0 - - - +
237K THR* 2.6 34.6 + - - +
253K MET* 5.2 0.2 - - - +
255K LEU* 4.7 9.0 - - + -
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Residues in contact with ARG 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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25K THR* 2.9 27.3 + - - -
26K VAL 3.1 25.5 + - - -
27K LEU* 4.2 6.3 - - - +
31K ASP* 3.8 12.3 + - - -
35K TYR* 3.4 37.8 + - + -
74K GLY* 3.4 10.7 + - - +
77K ALA* 3.4 27.1 - - + +
230K ILE* 3.4 17.7 + - + +
231K LEU* 3.9 20.8 + - + +
232K CYS 2.7 3.2 + - - -
233K VAL* 1.3 77.8 - - - +
235K GLU* 1.3 63.7 + - - +
237K THR* 3.8 1.6 - - - -
238K ARG* 2.9 61.1 + - - +
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Residues in contact with GLU 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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9K ILE* 3.3 32.5 - - + -
21K PRO* 4.4 8.5 - - + -
22K PRO* 3.3 28.6 - - + +
25K THR* 2.7 29.8 + - - +
231K LEU 3.1 14.6 + - - +
232K CYS* 2.4 17.8 + - + +
234K ARG* 1.3 66.5 + - - +
236K ALA* 1.3 68.3 + - - +
238K ARG* 2.9 42.0 + - - +
239K PHE* 3.0 12.1 + - - +
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Residues in contact with ALA 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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12K CYS* 4.8 1.1 - - - -
21K PRO* 4.1 17.7 - - + +
223K LEU* 3.9 11.2 - - + +
225K VAL* 3.6 32.1 - - + -
232K CYS* 2.7 17.8 + - + +
233K VAL* 4.1 2.2 - - - +
235K GLU* 1.3 74.0 - - - +
237K THR* 1.3 64.0 + - - +
239K PHE* 3.2 3.3 + - - +
240K ALA* 2.8 26.2 + - - +
253K MET* 4.1 8.9 - - - +
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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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74K GLY 4.6 0.7 - - - -
75K LEU* 3.2 32.8 - - + +
78K GLY* 3.5 27.8 - - - -
79K ILE* 3.8 15.9 - - + -
162K LEU* 5.1 3.6 - - + -
190K ILE* 4.5 4.7 - - + +
192K ILE* 6.3 0.2 - - + -
233K VAL 2.6 25.0 + - - -
234K ARG* 3.8 4.3 - - - -
235K GLU 3.1 0.2 + - - -
236K ALA* 1.3 75.6 - - - +
238K ARG* 1.3 57.4 + - - +
240K ALA* 3.5 1.7 + - - +
241K ALA* 2.9 28.6 + - - +
253K MET* 3.8 12.7 - - + +
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Residues in contact with ARG 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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25K THR* 4.2 0.4 + - - -
26K VAL 4.9 2.0 + - - +
31K ASP* 5.5 1.4 + - - -
35K TYR* 5.1 0.8 + - - -
77K ALA 3.8 8.8 + - - -
78K GLY* 3.8 23.1 - - - +
234K ARG* 2.9 66.9 + - - +
235K GLU* 2.9 28.9 + - - +
237K THR* 1.3 72.7 - - - +
239K PHE* 1.3 54.1 + - - +
241K ALA* 3.6 2.4 - - - +
242K ALA* 2.7 35.7 + - - +
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Residues in contact with PHE 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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17K LEU* 4.6 14.4 - - + -
19K GLU* 3.5 24.0 - - + -
20K GLY* 3.9 15.7 - - - -
21K PRO* 3.9 35.2 - - + -
22K PRO* 5.7 1.8 - - + -
223K LEU* 3.9 26.0 - - + -
235K GLU* 3.0 10.5 + - - +
236K ALA 3.4 8.7 - - - +
238K ARG* 1.3 79.4 - - - +
240K ALA* 1.3 60.6 + - - +
242K ALA* 3.3 8.3 - - + +
243K TYR* 3.0 35.2 + + + +
251K ILE* 4.6 6.7 - - + -
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Residues in contact with ALA 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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190K ILE* 3.9 17.3 - - + -
223K LEU* 5.2 1.1 - - + -
236K ALA 2.8 17.1 + - - +
237K THR 3.8 2.7 - - - +
239K PHE* 1.3 79.8 - - + +
241K ALA* 1.3 54.7 + - - +
243K TYR* 3.2 9.4 + - - +
244K CYS* 2.7 36.7 + - - +
251K ILE* 4.1 22.2 - - + -
253K MET* 4.1 16.4 - - - -
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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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78K GLY 4.3 6.5 - - - +
79K ILE* 5.1 3.8 - - + -
160K VAL* 4.4 5.2 - - + -
190K ILE* 3.6 15.1 - - + +
237K THR 2.9 18.8 + - - +
238K ARG* 3.6 7.0 - - - +
240K ALA* 1.3 70.8 - - - +
242K ALA* 1.3 56.6 + - - +
244K CYS* 3.1 4.0 + - - +
245K ARG* 2.7 67.7 + - - +
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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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238K ARG 2.7 22.4 + - - +
239K PHE* 3.3 10.1 - - + +
241K ALA* 1.3 72.5 - - - +
243K TYR* 1.3 63.2 + - - +
245K ARG* 3.0 10.4 + - - +
246K SER* 2.9 25.2 + - - -
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Residues in contact with TYR 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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17K LEU* 4.6 18.4 - - + -
221K PRO* 3.4 22.7 - - + +
239K PHE* 3.0 20.5 + + + +
240K ALA* 3.3 9.6 - - - +
242K ALA* 1.3 76.7 - - - +
244K CYS* 1.3 66.3 + - - +
246K SER* 3.0 21.6 + - - -
248K LYS* 3.2 63.4 + - + +
249K GLY 3.6 9.0 - - - -
250K PRO 3.3 22.9 + - - -
251K ILE* 4.2 22.2 - - + -
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Residues in contact with CYS 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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160K VAL* 3.7 20.0 - - + -
188K PRO* 3.8 19.0 - - - +
189K CYS 3.8 19.5 - - - -
190K ILE* 3.8 23.8 - - + -
240K ALA 2.7 17.9 + - - +
241K ALA* 3.6 4.9 - - - +
243K TYR* 1.3 73.9 - - - +
245K ARG* 1.3 61.5 + - - +
247K GLY* 3.3 13.7 + - - -
248K LYS 4.4 0.9 + - - -
249K GLY 3.2 25.6 + - - +
251K ILE* 4.0 11.0 - - - -
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Residues in contact with ARG 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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78K GLY 4.7 1.6 + - - -
79K ILE* 4.5 4.9 - - - +
80K ASN* 3.9 17.1 + - - +
83K ASP* 2.8 41.3 + - - -
158K ASP* 2.7 72.3 + - - +
160K VAL* 3.6 15.9 - - + +
188K PRO* 5.6 0.7 - - - -
241K ALA* 2.7 41.5 + - - +
242K ALA* 3.6 6.6 - - - +
244K CYS* 1.3 68.2 - - - +
246K SER* 1.3 56.9 + - - +
247K GLY 3.1 8.8 + - - -
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Residues in contact with SER 246 (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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242K ALA 2.9 11.8 + - - -
243K TYR* 3.0 19.8 + - - -
245K ARG* 1.3 74.8 - - - +
247K GLY* 1.3 59.5 + - - +
248K LYS* 3.3 24.9 + - - +
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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