Contacts of the helix formed by residues 239 - 254 (chain A) in PDB entry 6F3T
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 LEU 239 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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221A LEU* 4.2 15.9 - - + -
225A ILE* 4.3 6.5 - - + -
236A LEU* 3.1 23.6 + - + +
237A SER 3.0 1.0 - - - -
238A GLN* 1.3 78.2 - - - +
240A PHE* 1.3 64.5 + - - +
241A TYR 3.4 0.4 - - - -
242A PRO* 3.4 2.0 - - - +
243A LEU* 3.1 39.8 + - + +
307A LEU* 3.6 23.1 - - + -
317A LEU* 3.8 41.1 - - + -
333A VAL* 4.9 4.9 - - + -
337A LEU* 3.4 30.5 - - + -
339A ILE* 4.9 4.3 - - + -
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Residues in contact with PHE 240 (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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218A TYR* 3.0 31.6 + + - +
221A LEU* 5.8 3.1 - - + -
222A LYS* 3.8 43.1 - - + -
225A ILE* 3.8 33.0 - - + -
226A GLU* 4.7 9.9 - - + -
237A SER* 3.2 43.8 + - - +
239A LEU* 1.3 77.9 - - + +
241A TYR* 1.3 58.7 + - - +
243A LEU* 5.0 0.4 - - + -
244A PHE* 2.9 27.4 + - - +
270A ASP* 5.4 11.4 - - + +
271A GLN* 3.3 12.3 - - - +
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Residues in contact with TYR 241 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
237A SER 4.6 1.2 + - - -
238A GLN 4.3 1.3 + - - +
240A PHE* 1.3 78.9 - - - +
242A PRO* 1.3 74.2 - - + +
244A PHE* 3.1 3.0 + + - +
245A VAL* 3.0 49.3 + - + +
271A GLN* 3.1 19.2 + - + +
275A TYR* 3.4 68.4 - + + +
278A ASP* 2.6 35.3 + - + +
279A LEU* 5.2 5.4 - - + -
300A PHE* 4.8 8.6 - + - -
305A PHE* 4.2 21.5 - + - -
358A SER 4.3 5.8 - - - -
359A LEU* 3.8 12.7 - - - +
649A ARG* 4.7 0.2 + - - -
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Residues in contact with PRO 242 (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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238A GLN 3.1 27.6 - - - +
239A LEU* 3.4 10.1 - - - +
241A TYR* 1.3 97.9 - - + +
243A LEU* 1.3 58.1 + - - +
245A VAL* 4.0 0.3 - - - +
246A HIS* 2.9 37.0 + - + -
300A PHE* 4.4 7.6 - - + -
305A PHE* 3.5 43.1 - - + -
307A LEU* 4.3 3.1 - - + -
337A LEU* 3.7 16.4 - - + -
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Residues in contact with LEU 243 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
218A TYR* 4.2 13.0 - - + -
221A LEU* 3.2 35.4 - - + -
239A LEU* 3.1 28.7 + - + +
240A PHE* 4.1 1.6 - - - +
242A PRO* 1.3 74.3 - - - +
244A PHE* 1.3 61.0 + - - +
246A HIS* 4.6 2.7 - - + +
247A MET* 2.9 40.2 + - - +
329A ILE* 4.6 10.5 - - + -
332A ILE* 3.7 28.3 - - + -
333A VAL* 4.0 17.7 - - + -
336A HIS* 6.1 0.2 - - + -
337A LEU* 4.0 25.4 - - + -
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Residues in contact with PHE 244 (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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218A TYR* 3.8 10.0 - - - +
240A PHE 2.9 20.3 + - - +
241A TYR* 3.1 3.1 + + - +
243A LEU* 1.3 78.1 - - - +
245A VAL* 1.3 65.4 + - + +
248A TYR* 2.9 33.7 + - + +
263A PHE* 3.4 36.2 - + - -
264A PHE* 3.6 30.5 - + - -
267A PHE* 3.6 31.6 - - + -
268A HIS* 3.7 16.6 - - + -
271A GLN* 3.7 16.4 - - + +
279A LEU* 3.5 30.1 - - + -
282A LEU* 4.6 5.4 - - + -
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Residues in contact with VAL 245 (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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241A TYR* 3.0 46.3 + - + +
244A PHE* 1.3 82.4 - - + +
246A HIS* 1.3 61.3 + - - +
248A TYR* 3.8 3.4 - - - +
249A LEU* 2.8 46.8 + - + +
282A LEU* 3.9 28.9 - - + -
297A MET* 5.2 4.0 - - + -
300A PHE* 3.4 33.7 - - + -
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Residues in contact with HIS 246 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
242A PRO* 2.9 29.3 + - + +
243A LEU* 4.2 4.9 - - + +
245A VAL* 1.3 76.9 - - - +
247A MET* 1.3 58.7 + - - +
249A LEU* 4.7 1.1 - - - -
250A GLU* 3.1 14.5 + - - +
300A PHE* 3.2 50.0 + + - -
301A ARG* 3.0 38.1 + - - +
303A SER 3.9 5.6 + - - -
305A PHE* 4.4 4.4 - - - +
332A ILE* 5.0 5.2 - - + -
336A HIS* 3.1 66.0 + - + -
337A LEU* 4.5 6.1 - - + -
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Residues in contact with MET 247 (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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214A TYR* 3.4 54.6 - - + +
217A TYR* 4.2 5.8 - - + -
218A TYR* 3.9 17.0 - - - +
243A LEU* 2.9 26.1 + - - +
246A HIS* 1.3 73.4 - - - +
248A TYR* 1.3 65.9 + - - +
250A GLU* 3.4 2.1 + - - +
251A LEU* 3.3 27.6 + - - +
263A PHE* 3.7 15.9 - - + -
329A ILE* 3.7 31.6 - - + -
332A ILE* 4.0 29.6 - - + -
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Residues in contact with TYR 248 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
244A PHE* 2.9 24.8 + + + +
245A VAL* 3.8 3.1 - - - +
247A MET* 1.3 77.7 - - - +
249A LEU* 1.3 67.6 + - + +
251A LEU* 3.2 7.7 + - - +
252A VAL* 3.1 31.8 + - + +
260A ALA* 3.3 40.9 - - + +
261A LYS* 4.6 2.0 + - - -
263A PHE* 3.9 12.2 - + + -
264A PHE* 3.7 28.8 - + + -
282A LEU* 3.0 47.7 + - + -
283A SER* 4.5 1.7 + - - -
285A LEU 2.7 29.3 + - - -
286A THR* 4.1 9.4 - - - +
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Residues in contact with LEU 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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245A VAL* 2.8 37.0 + - + +
246A HIS* 5.3 0.4 - - - -
248A TYR* 1.3 84.0 - - + +
250A GLU* 1.3 58.2 + - - +
252A VAL* 3.7 5.0 - - + +
253A TYR* 2.8 32.4 + - - +
282A LEU* 3.8 23.6 - - + -
285A LEU* 4.2 13.0 - - + -
291A MET* 3.9 28.2 - - + +
297A MET* 4.1 24.9 - - + +
300A PHE* 4.1 16.6 - - + -
301A ARG* 4.0 13.5 - - + +
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Residues in contact with GLU 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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207A GLN* 2.9 34.6 + - - +
208A GLN 4.8 0.2 + - - -
209A GLY 5.6 0.3 + - - -
214A TYR* 3.0 30.1 + - + +
246A HIS 3.1 15.1 + - - +
247A MET* 3.7 6.5 - - - +
248A TYR 3.2 0.4 - - - -
249A LEU* 1.3 78.1 - - - +
251A LEU* 1.3 62.1 + - + +
253A TYR* 4.0 0.6 - - - -
254A ASN* 2.8 48.5 + - - +
301A ARG* 3.0 31.5 + - - +
332A ILE* 5.0 7.4 - - - +
336A HIS* 4.0 13.6 + - - -
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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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211A PRO* 3.6 40.4 - - + +
214A TYR* 3.9 26.5 - - + -
247A MET 3.4 14.8 - - - +
248A TYR* 3.2 6.8 + - - +
250A GLU* 1.3 78.2 - - + +
252A VAL* 1.3 60.8 + - - +
254A ASN 3.7 0.2 - - - -
255A GLN 3.2 2.4 + - - -
256A HIS* 2.8 41.8 + - + +
259A GLU* 4.0 17.3 - - + +
260A ALA* 3.7 27.1 - - + -
263A PHE* 4.0 17.0 - - + -
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Residues in contact with VAL 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 TYR* 3.1 43.6 + - + +
249A LEU* 3.7 10.1 - - + +
251A LEU* 1.3 75.0 - - - +
253A TYR* 1.3 66.4 + - - +
255A GLN* 2.9 15.5 + - - +
256A HIS 5.0 0.9 - - - +
257A GLU* 5.8 0.9 - - - +
260A ALA* 3.8 11.4 - - + -
285A LEU* 3.9 11.4 - - + +
286A THR* 3.8 18.5 - - - +
287A LYS 3.6 27.6 - - - +
288A LYS* 3.9 9.7 + - - +
291A MET* 4.2 14.4 - - + -
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Residues in contact with TYR 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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249A LEU 2.8 21.6 + - - +
250A GLU 4.2 2.5 - - - +
252A VAL* 1.3 73.5 - - - +
254A ASN* 1.3 70.7 + - - +
255A GLN* 3.2 3.2 + - - +
288A LYS* 3.3 53.7 + - + +
291A MET* 3.9 30.1 - - + -
292A LYS* 3.4 33.2 + - + -
298A LEU* 4.7 10.8 - - + -
301A ARG* 4.7 12.1 - - - +
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Residues in contact with ASN 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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207A GLN* 5.6 7.2 - - - +
250A GLU* 2.8 47.0 + - - +
251A LEU 3.7 0.2 - - - -
253A TYR* 1.3 85.4 - - - +
255A GLN* 1.3 71.4 + - - +
256A HIS* 3.3 31.1 + - + +
301A ARG* 4.9 1.8 - - - +
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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