Contacts of the helix formed by residues 340 - 359 (chain F) in PDB entry 2JJD
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 GLY 340 (chain F).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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339F VAL* 1.3 73.2 - - - +
341F ARG* 1.3 59.5 + - - -
343F GLY* 3.6 3.5 - - - +
344F THR* 2.8 27.7 + - - -
377F MET 2.5 19.3 + - - +
378F VAL* 4.5 0.7 - - - -
379F GLN* 3.8 9.9 - - - -
383F GLN* 3.5 28.3 - - - +
1693F CL 4.3 1.8 - - - -
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Residues in contact with ARG 341 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
233F LEU* 2.8 48.9 + - + +
234F THR* 3.8 15.0 + - - +
235F ASN* 4.8 2.8 - - - +
301F TRP* 3.3 64.0 + - + +
302F PRO 3.2 26.1 + - - -
303F ASP* 4.0 11.3 + - - +
305F GLY 5.5 0.2 + - - -
335F CYS* 4.2 13.8 - - + -
339F VAL 4.0 2.0 + - - -
340F GLY* 1.3 70.8 - - - +
342F THR* 1.3 66.0 + - - +
343F GLY 3.0 0.2 + - - -
344F THR* 3.1 2.8 + - - -
345F PHE* 2.9 24.8 + - - +
383F GLN* 3.6 9.9 - - - +
1693F CL 4.1 17.4 - - - +
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Residues in contact with THR 342 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
206F ALA* 4.1 7.8 - - - +
233F LEU* 3.5 12.9 - - - +
333F VAL* 3.3 34.6 + - - +
335F CYS* 3.4 16.8 - - - -
338F GLY* 2.9 41.3 - - - +
339F VAL* 3.2 8.5 - - - +
341F ARG* 1.3 79.4 - - - +
343F GLY* 1.3 64.0 + - - +
345F PHE* 3.7 1.9 + - - +
346F ILE* 3.2 29.9 + - - +
377F MET* 4.4 3.6 - - + -
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Residues in contact with GLY 343 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
340F GLY 3.2 6.1 + - - -
341F ARG 3.0 0.8 - - - -
342F THR* 1.3 80.9 - - - +
344F THR* 1.3 64.9 + - - +
345F PHE 3.0 2.3 + - - -
346F ILE* 3.0 2.8 + - - +
347F VAL* 2.9 31.0 + - - +
370F ILE* 4.9 0.7 - - - -
377F MET* 3.3 35.2 - - - -
378F VAL* 4.4 3.1 - - - -
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Residues in contact with THR 344 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
301F TRP* 4.5 17.9 - - - -
313F MET* 5.3 0.7 - - - -
340F GLY 2.8 18.8 + - - -
341F ARG* 3.8 3.8 - - - -
343F GLY* 1.3 70.5 - - - +
345F PHE* 1.3 57.6 + - - +
347F VAL* 3.6 1.2 + - - +
348F ILE* 3.0 37.4 + - - +
378F VAL* 4.3 3.9 - - - +
383F GLN* 4.5 18.2 - - - -
386F PHE* 5.1 7.4 - - - -
387F ILE* 4.3 23.1 - - - -
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Residues in contact with PHE 345 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
204F PHE* 4.2 21.1 - + - -
231F VAL* 4.1 12.3 - - + -
233F LEU* 3.6 19.1 - - + -
313F MET* 3.4 28.4 - - + +
316F PHE* 3.8 24.7 - + - -
317F LEU* 3.8 32.0 - - + +
320F VAL* 4.2 20.0 - - + -
333F VAL* 4.0 24.5 - - + -
341F ARG 2.9 15.9 + - - +
342F THR 3.7 2.5 - - - +
344F THR* 1.3 74.5 - - - +
346F ILE* 1.3 71.5 + - + +
348F ILE* 3.3 4.2 + - - -
349F ASP* 3.2 20.2 + - + +
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Residues in contact with ILE 346 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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195F ILE* 3.8 33.4 - - + -
196F ASP 4.2 6.3 - - - +
204F PHE* 3.9 47.4 - - + -
206F ALA* 4.3 10.1 - - + -
333F VAL* 4.7 4.3 - - + -
342F THR* 3.2 20.6 + - - +
343F GLY* 3.0 5.4 + - - +
345F PHE* 1.3 81.4 - - + +
347F VAL* 1.3 63.6 + - - +
349F ASP* 3.4 3.5 + - - +
350F ALA* 3.0 21.5 + - + +
366F PHE* 4.3 10.1 - - + -
370F ILE* 4.8 4.0 - - + -
377F MET* 3.9 18.4 - - + -
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Residues in contact with VAL 347 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
343F GLY 2.9 19.2 + - - +
344F THR 3.9 0.4 - - - +
346F ILE* 1.3 75.7 - - - +
348F ILE* 1.3 56.9 + - - +
350F ALA* 3.2 2.1 + - - +
351F MET* 2.9 39.8 + - + +
363F VAL* 4.1 10.3 - - + +
366F PHE* 3.9 17.3 - - + -
367F VAL* 3.9 20.6 - - + -
370F ILE* 3.9 20.2 - - + -
378F VAL* 4.1 3.8 - - + -
387F ILE* 3.4 39.5 - - + -
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Residues in contact with ILE 348 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
313F MET* 4.6 14.1 - - + +
314F LEU* 4.3 13.0 - - + -
317F LEU* 3.9 15.7 - - + -
344F THR 3.0 24.0 + - - +
345F PHE* 3.3 5.8 + - - +
347F VAL* 1.3 75.8 - - - +
349F ASP* 1.3 57.6 + - - +
351F MET* 4.1 4.6 - - - +
352F MET* 3.0 40.9 + - + +
386F PHE* 4.0 24.5 - - + -
387F ILE* 4.1 23.1 - - + +
390F ALA* 3.6 25.8 - - + -
391F LEU* 4.4 5.1 - - + +
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Residues in contact with ASP 349 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
204F PHE* 4.2 20.9 - - + -
317F LEU* 3.8 26.2 - - + +
345F PHE* 3.2 14.4 + - + +
346F ILE 3.7 6.5 - - - +
348F ILE* 1.3 73.2 - - - +
350F ALA* 1.3 67.7 + - - +
352F MET* 3.1 13.9 + - - +
353F ALA* 3.1 13.0 + - - +
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Residues in contact with ALA 350 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
197F GLY* 4.6 2.7 - - - -
198F TYR* 3.3 23.4 - - + +
204F PHE* 5.7 0.8 - - - -
346F ILE 3.0 8.9 + - - +
347F VAL 3.5 3.8 - - - +
349F ASP* 1.3 74.6 - - - +
351F MET* 1.3 67.0 + - + +
353F ALA* 3.1 8.6 - - - +
354F MET 3.0 20.8 + - - -
366F PHE* 3.2 46.2 - - + -
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Residues in contact with MET 351 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
198F TYR* 5.0 1.1 - - + -
347F VAL* 2.9 26.2 + - + +
348F ILE 4.1 0.2 - - - +
350F ALA* 1.3 81.7 - - + +
352F MET* 1.3 65.5 + - - +
354F MET* 3.2 29.1 + - + +
355F MET* 3.0 26.9 + - - +
361F VAL* 3.6 17.7 - - + +
362F ASP 3.7 25.8 - - - +
363F VAL* 3.9 19.3 - - + -
366F PHE* 3.9 28.0 - - + -
391F LEU* 3.4 26.5 - - + -
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Residues in contact with MET 352 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
314F LEU* 3.7 23.6 - - + +
317F LEU* 3.6 31.9 - - + -
318F LYS* 6.1 3.4 - - + +
348F ILE* 3.0 25.5 + - + +
349F ASP* 3.5 4.0 - - - +
351F MET* 1.3 77.2 - - - +
353F ALA* 1.3 61.3 + - - +
355F MET* 3.3 6.5 + - - +
356F HIS* 3.0 26.7 + - - +
391F LEU* 3.9 9.6 - - + +
394F TYR* 3.3 57.3 - - + +
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Residues in contact with ALA 353 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
198F TYR* 3.6 26.0 - - + +
349F ASP 3.1 10.7 + - - +
350F ALA* 3.1 12.6 - - - +
352F MET* 1.3 76.3 - - - +
354F MET* 1.3 63.6 + - - +
356F HIS* 3.1 8.5 + - - +
357F ALA* 3.0 23.9 + - - +
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Residues in contact with MET 354 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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114F PRO* 5.9 0.9 - - - -
198F TYR* 3.6 36.8 - - + -
350F ALA 3.0 5.6 + - - +
351F MET* 3.2 38.5 + - + +
353F ALA* 1.3 79.1 - - - +
355F MET* 1.3 57.3 + - - +
358F GLU* 2.6 45.0 + - + +
360F LYS* 3.3 11.2 - - - +
361F VAL* 3.7 6.1 - - - -
362F ASP* 3.1 42.6 - - + +
365F GLU* 6.3 0.4 - - + -
366F PHE* 5.3 4.7 - - + +
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Residues in contact with MET 355 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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117F VAL* 3.8 21.7 - - + +
120F LEU* 3.9 17.0 - - + -
351F MET 3.0 14.6 + - - +
352F MET 3.5 7.0 - - - +
354F MET* 1.3 75.7 - - - +
356F HIS* 1.3 58.8 + - - +
357F ALA 3.0 5.9 + - - -
359F GLN* 3.0 25.6 + - - +
360F LYS 3.7 5.6 + - - -
361F VAL* 4.3 11.9 - - + -
391F LEU* 3.2 57.2 - - + +
394F TYR* 4.0 25.8 - - + -
395F TYR* 4.3 12.1 - - + -
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Residues in contact with HIS 356 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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352F MET 3.0 12.2 + - - +
353F ALA* 3.1 7.2 + - - +
355F MET* 1.3 79.0 - - - +
357F ALA* 1.3 57.7 + - - +
394F TYR* 2.9 38.5 + + - -
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Residues in contact with ALA 357 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
198F TYR* 3.8 25.1 - - + +
353F ALA 3.0 12.8 + - - +
354F MET 4.0 0.2 - - - +
355F MET 3.0 0.6 + - - -
356F HIS* 1.3 79.5 - - - +
358F GLU* 1.3 63.8 + - - +
359F GLN* 3.5 2.4 + - - +
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Residues in contact with GLU 358 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
198F TYR* 4.3 8.7 - - - +
354F MET* 2.6 28.4 + - + +
357F ALA* 1.3 73.3 - - - +
359F GLN* 1.3 64.7 + - - +
360F LYS* 3.0 20.8 + - + +
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Residues in contact with GLN 359 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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116F PRO* 3.7 5.0 - - - +
117F VAL* 3.0 42.5 + - + +
354F MET 3.5 0.2 + - - -
355F MET 3.0 19.6 + - - +
357F ALA 3.5 1.7 - - - +
358F GLU* 1.3 79.3 - - - +
360F LYS* 1.3 56.5 + - - +
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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