Contacts of the helix formed by residues 247 - 259 (chain A) in PDB entry 7CAL
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 TYR 247 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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75A TRP* 3.5 25.8 + + - -
79A PHE* 4.2 20.9 - + - -
83A PHE* 3.5 52.3 - + + -
210A HIS* 3.6 12.1 + + - -
214A CYS* 4.5 9.9 - - - -
244A TRP 4.5 5.2 - - - +
245A ASN* 3.6 12.3 - - - -
246A ARG* 1.3 76.1 - - - +
248A VAL* 1.3 59.0 + - + +
249A THR* 3.1 3.8 - - - -
250A ALA* 3.0 20.9 + - + +
251A LEU* 3.5 41.0 + - + +
701A 3PE 5.0 4.3 - - - +
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Residues in contact with VAL 248 (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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246A ARG* 3.2 51.0 + - + +
247A TYR* 1.3 73.2 - - + +
249A THR* 1.3 57.5 + - - +
251A LEU* 3.4 7.0 + - - +
252A TYR* 2.8 29.2 + - - +
271D PRO* 5.0 10.3 - - + +
274D MET* 4.0 23.1 - - + +
275D LEU* 4.0 19.3 - - + -
278D ILE* 3.8 20.9 - - + -
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Residues in contact with THR 249 (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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230A TRP* 4.0 2.7 - - + -
231A ILE* 4.0 24.7 - - + -
235A TYR* 4.3 14.5 - - + -
246A ARG 5.2 3.0 + - - -
247A TYR* 3.1 2.4 - - - -
248A VAL* 1.3 78.2 - - - +
250A ALA* 1.3 60.3 + - - +
252A TYR* 3.8 3.3 - - - +
253A TRP* 3.2 22.9 + - - +
266A PHE* 3.7 34.9 - - + -
271D PRO* 6.1 0.3 - - - +
274D MET* 3.8 21.0 - - + +
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Residues in contact with ALA 250 (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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83A PHE* 4.1 16.2 - - + -
213A GLY* 3.3 35.9 - - - +
217A TYR* 4.7 7.4 - - + -
230A TRP* 3.8 21.1 - - + -
231A ILE* 5.8 0.4 - - + +
247A TYR* 3.0 13.8 + - + +
249A THR* 1.3 79.8 - - - +
251A LEU* 1.3 62.6 + - - +
253A TRP* 3.8 4.9 + - - +
254A SER* 3.5 13.7 + - - -
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Residues in contact with LEU 251 (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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209A ILE* 3.8 32.0 - - + +
210A HIS* 4.5 9.0 - - - +
213A GLY* 4.6 5.8 - - - -
247A TYR* 3.5 42.2 + - + +
248A VAL* 3.4 5.9 + - - +
249A THR 3.3 0.2 - - - -
250A ALA* 1.3 80.8 - - - +
252A TYR* 1.3 60.2 + - - +
253A TRP 3.2 0.4 - - - -
254A SER* 3.9 2.8 - - - +
255A ILE* 3.0 32.1 + - - +
701A 3PE 4.0 29.4 - - + -
278D ILE* 3.8 23.3 - - + -
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Residues in contact with TYR 252 (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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248A VAL 2.8 18.8 + - - +
249A THR 3.8 4.0 - - - +
250A ALA 3.4 0.2 - - - -
251A LEU* 1.3 77.8 - - - +
253A TRP* 1.3 55.3 + - - +
255A ILE* 3.5 6.9 - - + +
256A THR* 2.3 38.5 + - + -
263A TYR* 3.2 28.2 - + - -
265A ASP* 4.1 7.6 - - - -
266A PHE* 3.7 35.2 - + - -
267D HIS* 3.7 3.1 - - - +
268D ALA* 3.4 29.7 + - + -
274D MET* 4.0 33.7 - - + -
277D ASP* 3.8 31.8 + - + -
278D ILE* 3.9 4.7 - - + +
281D MET* 4.1 12.1 - - + -
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Residues in contact with TRP 253 (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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212A ALA 3.6 5.2 - - - -
216A ASN* 3.3 44.1 - - + +
230A TRP* 3.8 29.9 - + + +
249A THR 3.2 9.5 + - - +
250A ALA 4.0 5.8 - - - +
251A LEU 3.2 0.2 - - - -
252A TYR* 1.3 81.2 - - - +
254A SER* 1.3 86.8 + - - +
256A THR* 3.3 9.8 + - - -
257A THR* 3.2 34.5 - - + +
266A PHE* 3.5 42.8 + - + -
267A HIS* 4.8 3.6 - - - +
276A PHE* 4.1 3.8 - + - -
277A ASP* 3.3 34.3 + - - -
280A PHE* 4.0 25.4 - + - -
263B TYR* 4.5 2.8 + - - -
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Residues in contact with SER 254 (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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209A ILE* 3.8 26.7 - - - -
212A ALA* 3.1 27.9 + - - +
213A GLY* 3.2 8.7 + - - -
250A ALA 3.5 8.1 + - - -
251A LEU* 3.2 5.2 + - - -
253A TRP* 1.3 87.6 - - - +
255A ILE* 1.3 61.9 + - - +
257A THR* 3.5 3.5 + - - -
258A LEU* 3.1 31.6 + - - +
280A PHE* 4.4 6.1 - - - -
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Residues in contact with ILE 255 (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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209A ILE* 3.7 33.1 - - + +
251A LEU 3.0 21.0 + - - +
252A TYR* 3.5 14.4 - - - +
254A SER* 1.3 77.6 - - - +
256A THR* 1.3 60.4 + - - +
257A THR 3.4 0.2 - - - -
258A LEU* 4.6 3.1 - - + -
259A THR* 2.8 44.0 + - + +
278D ILE* 3.9 22.4 - - + +
281D MET* 3.7 35.9 - - + +
282D MET* 3.8 18.2 - - + -
285D LEU* 4.9 3.1 - - + -
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Residues in contact with THR 256 (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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252A TYR* 2.3 36.1 + - + -
253A TRP* 3.3 8.4 + - - -
254A SER 3.2 1.2 - - - -
255A ILE* 1.3 78.1 - - - +
257A THR* 1.3 60.9 + - + +
259A THR* 4.3 2.0 - - - -
260A THR 3.8 0.2 - - - -
261A THR* 2.9 28.9 + - - -
262A GLY* 3.2 27.9 + - - +
263A TYR* 3.6 35.4 - - + +
265A ASP* 5.7 1.1 - - - +
263B TYR* 5.9 1.3 - - + -
281D MET* 3.9 13.8 - - - +
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Residues in contact with THR 257 (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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253A TRP* 3.2 35.1 + - + +
254A SER 3.7 1.4 + - - -
255A ILE 3.4 0.2 - - - -
256A THR* 1.3 79.4 - - - +
258A LEU* 1.3 65.3 + - - +
259A THR 3.4 0.9 - - - -
260A THR* 3.2 19.8 + - - +
280A PHE* 3.2 29.2 - - - -
281A MET* 5.0 8.3 - - - +
284A ASN* 3.7 9.3 + - - +
261B THR* 4.3 12.5 + - - -
263B TYR* 3.2 32.3 - - + +
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Residues in contact with LEU 258 (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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205A THR* 4.8 3.4 - - - +
208A ALA* 4.0 16.2 - - + -
209A ILE* 3.9 29.2 - - + -
254A SER 3.1 14.7 + - - +
255A ILE* 4.5 2.7 - - + +
257A THR* 1.3 79.9 + - - +
259A THR* 1.3 62.6 + - + +
260A THR* 3.2 3.9 + - - +
280A PHE* 4.2 11.7 - - + -
284A ASN* 3.7 30.3 - - - +
287A LEU* 3.9 26.7 - - + -
288A THR* 3.6 22.5 - - + +
291A LEU* 5.8 0.2 - - + -
285D LEU* 3.8 28.0 - - + -
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Residues in contact with THR 259 (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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255A ILE* 2.8 36.3 + - + +
258A LEU* 1.3 76.3 - - - +
260A THR* 1.3 71.8 + - - +
261A THR* 2.8 21.6 + - - -
288A THR* 5.4 1.3 - - - -
260D THR* 3.6 19.8 + - - +
281D MET* 3.4 29.6 - - - +
284D ASN* 6.3 1.1 - - - -
285D LEU* 3.8 26.2 - - + -
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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