Contacts of the helix formed by residues 238 - 256 (chain K) in PDB entry 6T9L
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 ALA 238 (chain K).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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147K PHE* 4.1 19.3 - - + +
150K SER* 5.0 1.1 - - - +
151K ILE* 3.9 23.8 - - + +
236K GLN 3.8 1.0 + - - -
237K ASP* 1.3 75.4 + - - +
239K HIS* 1.3 66.5 + - - +
241K PHE* 3.3 4.7 + - - +
242K TRP* 3.1 20.8 + - - +
417K VAL* 5.5 1.3 - - + -
428K TYR* 3.5 36.3 + - + -
461K TYR* 5.0 4.5 - - + -
462K LEU* 5.3 3.4 - - + -
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Residues in contact with HIS 239 (chain K).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
237K ASP* 3.0 11.6 + - - +
238K ALA* 1.3 79.5 - - - +
240K GLU* 1.3 60.3 + - - +
242K TRP* 3.2 24.1 + + - +
243K GLN* 3.2 37.4 + - - +
305K ASP* 2.8 23.5 + - + -
359K VAL* 6.5 0.7 - - + -
361K GLN* 2.9 47.1 + - + +
461K TYR* 3.8 13.2 - - + +
462K LEU* 4.5 13.0 - - + -
42O ARG* 3.2 26.5 + - - -
44O ILE* 4.7 6.5 - - + -
70O VAL* 5.2 1.1 - - + -
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Residues in contact with GLU 240 (chain K).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
230K LEU* 5.1 19.6 - - + +
236K GLN* 4.9 5.4 - - - +
237K ASP* 2.8 25.4 + - + +
238K ALA 3.3 0.4 - - - -
239K HIS* 1.3 76.4 + - - +
241K PHE* 1.3 61.0 + - - +
243K GLN* 3.7 2.1 + - - +
244K PHE* 3.3 22.6 + - + +
42O ARG* 3.5 27.2 + - - +
49O GLN* 3.4 34.7 + - - +
72O ARG* 3.4 30.0 + - - -
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Residues in contact with PHE 241 (chain K).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
147K PHE* 4.0 22.0 - + + -
148K MET* 4.1 40.8 - - + -
151K ILE* 3.8 35.9 - - + -
152K LEU* 4.2 15.5 - - + -
219K LEU* 4.6 7.4 - - + -
223K ALA* 5.7 2.9 - - + -
230K LEU* 4.8 18.3 - - + +
237K ASP 3.4 12.0 + - - +
238K ALA* 3.3 8.5 + - - +
240K GLU* 1.3 75.9 - - - +
242K TRP* 1.3 64.3 - - - +
244K PHE* 3.8 24.6 - + - +
245K ILE* 3.3 34.0 + - + +
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Residues in contact with TRP 242 (chain K).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
151K ILE* 3.8 27.6 - - + -
154K CYS* 5.3 1.1 - - - -
155K LEU* 3.8 33.7 - - + -
238K ALA 3.1 12.1 + - - +
239K HIS* 3.2 20.8 + + + +
241K PHE* 1.3 77.0 - - - +
243K GLN* 1.3 78.8 + - + +
244K PHE 3.2 0.9 + - - -
245K ILE* 3.3 6.1 - - + +
246K ILE* 3.3 65.4 + - + +
279K PHE* 4.7 31.2 - + + -
304K LEU* 5.3 2.6 + - - +
305K ASP* 4.8 7.1 + - + +
359K VAL* 4.8 22.5 - - + +
462K LEU* 5.5 6.1 - - + -
464K PHE* 5.0 24.0 - + - -
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Residues in contact with GLN 243 (chain K).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
239K HIS* 3.2 25.8 + - - +
240K GLU 3.7 3.3 + - - +
242K TRP* 1.3 89.3 - - + +
244K PHE* 1.3 60.7 + - - +
246K ILE* 3.6 13.4 - - + +
247K ASN* 3.5 22.7 + - - +
304K LEU* 6.2 0.4 - - + -
305K ASP* 2.4 40.1 + - - +
42O ARG* 4.0 4.1 + - - +
44O ILE* 3.4 37.0 - - - +
47O GLY* 3.6 24.1 + - - +
48O LYS* 5.9 0.5 - - - -
49O GLN* 4.1 9.3 + - + +
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Residues in contact with PHE 244 (chain K).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
183K PHE* 3.9 33.0 - + - -
223K ALA* 4.9 10.1 - - + -
226K ILE* 4.2 22.0 - - + -
227K ASN* 4.7 16.2 - - + -
230K LEU* 3.9 26.2 - - + -
240K GLU* 3.3 18.6 + - + +
241K PHE* 3.8 23.3 - + - +
242K TRP 3.1 1.0 - - - -
243K GLN* 1.3 78.7 - - - +
245K ILE* 1.3 65.7 + - - +
247K ASN* 3.6 4.2 + - - +
248K GLN* 3.3 43.3 + - + +
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Residues in contact with ILE 245 (chain K).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
151K ILE* 4.9 6.7 - - + -
152K LEU* 4.3 23.6 - - + -
155K LEU* 5.1 10.8 - - + -
183K PHE* 4.2 18.6 - - + -
187K LEU* 4.6 22.0 - - + -
219K LEU* 5.0 6.1 - - + -
241K PHE* 3.3 26.6 + - + +
242K TRP* 3.3 16.2 - - + +
244K PHE* 1.3 84.3 - - + +
246K ILE* 1.3 74.6 + - + +
248K GLN* 3.4 6.3 + - - +
249K ILE* 3.2 29.7 + - + +
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Residues in contact with ILE 246 (chain K).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
155K LEU* 5.7 3.1 - - + -
242K TRP* 3.3 70.9 - - + +
243K GLN* 3.6 18.6 - - + +
245K ILE* 1.3 81.0 - - + +
247K ASN* 1.3 63.8 + - + +
249K ILE* 3.7 11.0 + - + -
250K HIS* 3.6 14.9 + - - +
275K VAL* 3.6 33.3 - - + +
279K PHE* 6.2 2.0 - - + -
304K LEU* 4.1 29.2 - - + -
47O GLY 4.9 0.7 - - - +
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Residues in contact with ASN 247 (chain K).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
243K GLN 3.5 17.4 + - - +
244K PHE* 3.9 4.7 - - - +
245K ILE 3.2 0.6 - - - -
246K ILE* 1.3 82.3 - - + +
248K GLN* 1.3 65.7 + - + +
250K HIS* 3.3 14.8 + - - +
251K GLN* 3.1 42.2 + - - +
276K HIS* 5.9 0.2 - - - -
47O GLY 5.8 1.1 - - - +
48O LYS* 4.3 33.7 - - + +
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Residues in contact with GLN 248 (chain K).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
183K PHE* 3.5 39.8 - - + +
226K ILE* 4.5 18.9 - - - +
244K PHE* 3.3 35.9 + - + +
245K ILE 3.4 3.2 + - - +
247K ASN* 1.3 81.4 - - - +
249K ILE* 1.3 60.7 + - - +
251K GLN* 3.2 16.7 + - - +
252K SER* 2.9 29.3 + - - -
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Residues in contact with ILE 249 (chain K).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
155K LEU* 6.0 4.5 - - + -
161K PHE* 5.1 9.4 - - + -
164K HIS* 6.1 1.8 - - + -
183K PHE* 5.1 6.5 - - + -
184K SER* 4.3 14.4 - - - +
187K LEU* 4.1 26.5 - - + -
245K ILE* 3.2 23.8 + - + +
246K ILE* 3.9 15.3 - - + +
247K ASN 3.3 0.6 - - - -
248K GLN* 1.3 77.4 - - - +
250K HIS* 1.3 59.5 + - - +
252K SER* 2.8 18.7 + - - -
253K TYR* 3.1 14.5 + - + +
273K CYS* 4.9 1.7 - - + +
274K ILE* 4.1 25.8 - - + +
275K VAL* 4.3 8.5 - - + -
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Residues in contact with HIS 250 (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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246K ILE 3.6 9.1 + - - +
247K ASN* 3.3 16.9 + - - +
248K GLN 3.2 0.4 - - - -
249K ILE* 1.3 78.5 - - - +
251K GLN* 1.3 81.1 + - - +
253K TYR* 3.4 1.2 + - - +
254K VAL* 3.4 37.7 + - + +
271K CYS* 3.4 19.3 - - + -
273K CYS* 4.0 11.9 - - - -
275K VAL* 4.8 1.5 - - + +
276K HIS* 3.3 20.2 + + + -
505K ZN 2.2 34.5 - - - -
48O LYS* 6.2 3.4 - - + -
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Residues in contact with GLN 251 (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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247K ASN* 3.1 30.0 + - - +
248K GLN* 3.2 22.6 + - - +
250K HIS* 1.3 100.2 + - - +
252K SER* 1.3 60.3 + - - +
254K VAL* 3.2 27.6 - - - +
255K LEU* 3.4 10.9 + - - +
48O LYS* 5.5 5.7 - - - +
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Residues in contact with SER 252 (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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170K HIS* 5.0 1.3 - - - -
182K CYS* 3.8 26.7 - - - -
183K PHE* 5.5 1.5 - - - +
184K SER* 3.2 17.8 + - - -
248K GLN 2.9 13.5 + - - -
249K ILE* 2.8 17.7 + - - -
251K GLN* 1.3 75.0 - - - +
253K TYR* 1.3 62.6 + - - +
255K LEU* 3.6 10.6 + - - +
256K ASP* 3.1 31.2 + - - +
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Residues in contact with TYR 253 (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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164K HIS* 6.2 2.0 - - - -
169K ILE* 6.2 4.3 - - + -
170K HIS* 6.3 0.2 - - - -
249K ILE* 3.1 15.8 + - + +
250K HIS 3.8 4.3 - - - +
251K GLN 3.3 0.6 - - - -
252K SER* 1.3 77.7 - - - +
254K VAL* 1.3 67.5 + - + +
256K ASP* 3.2 16.5 + - + +
257K LEU* 3.3 40.7 + - + +
271K CYS* 3.5 32.5 - - - -
272K GLU* 3.3 32.5 + - + +
273K CYS* 3.7 20.6 - - + -
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Residues in contact with VAL 254 (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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250K HIS* 3.4 36.3 - - + +
251K GLN* 3.2 30.3 - - - +
253K TYR* 1.3 83.6 - - + +
255K LEU* 1.3 62.4 + - + +
257K LEU* 3.5 31.9 + - + +
271K CYS* 4.5 2.7 - - - -
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Residues in contact with LEU 255 (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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175K LYS* 2.9 32.8 + - + +
176K VAL* 6.1 4.7 - - + -
251K GLN 3.4 13.4 + - - +
252K SER* 3.7 11.0 - - - +
253K TYR 3.1 0.6 - - - -
254K VAL* 1.3 84.9 - - - +
256K ASP* 1.3 60.9 + - - +
257K LEU 3.2 1.2 + - - +
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Residues in contact with ASP 256 (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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170K HIS* 3.3 30.7 + - - -
173K ASN* 3.5 29.5 - - + +
174K CYS* 3.9 4.9 - - - -
175K LYS* 3.4 34.5 + - - +
176K VAL* 6.0 0.2 - - - +
252K SER* 3.1 17.9 + - - +
253K TYR* 3.2 11.2 + - + +
255K LEU* 1.3 80.5 - - - +
257K LEU* 1.3 63.7 + - - +
258K PRO* 3.7 3.1 - - - +
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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