Contacts of the helix formed by residues 347 - 365 (chain P) in PDB entry 3L73
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 PRO 347 (chain P).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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346P HIS* 1.3 102.1 - - + +
348P PHE* 1.3 71.8 + - + +
349P ILE 3.1 3.7 + - - -
350P ILE* 3.0 26.4 + - + +
351P ILE* 3.2 7.4 + - + +
61T TRP* 3.7 28.9 - - + -
62T GLY* 3.6 33.4 - - - +
65T GLU* 4.1 9.2 - - + -
66T PHE* 4.1 20.9 - - + -
69T LEU* 4.6 1.1 - - + -
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Residues in contact with PHE 348 (chain P).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
338P TRP* 3.6 35.2 - + - -
339P ILE* 3.9 21.8 - - + +
342P GLN* 3.3 48.9 - - + -
343P PRO* 3.7 26.2 - - + +
345P GLU 3.0 12.7 + - - +
347P PRO* 1.3 80.1 - - + +
349P ILE* 1.3 55.7 + - - +
351P ILE* 3.4 2.7 + - + +
352P GLY* 2.8 29.1 + - - -
62T GLY 3.8 14.4 - - - -
63T THR* 5.0 2.7 - - - -
66T PHE* 3.8 38.4 - + + -
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Residues in contact with ILE 349 (chain P).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
284P SER* 5.9 0.5 - - - -
344P VAL* 3.5 39.0 - - + +
345P GLU* 3.0 29.0 + - - +
346P HIS* 4.2 5.4 - - + +
347P PRO 3.1 0.8 + - - -
348P PHE* 1.3 77.0 - - - +
350P ILE* 1.3 61.5 + - - +
352P GLY* 3.4 1.6 + - - -
353P GLN* 3.1 40.0 + - + +
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Residues in contact with ILE 350 (chain P).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
346P HIS* 4.3 20.8 + - + +
347P PRO* 3.0 19.2 + - + +
349P ILE* 1.3 75.1 - - - +
351P ILE* 1.3 83.0 + - + +
352P GLY 3.0 1.7 + - - -
353P GLN* 3.2 18.2 + - - +
354P MET* 3.1 49.7 + - + +
61T TRP* 5.9 2.2 - - + -
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Residues in contact with ILE 351 (chain P).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
335P ILE* 4.1 10.1 - - + -
338P TRP* 4.2 19.5 - - + -
339P ILE* 3.8 15.5 - - + -
347P PRO* 3.2 23.7 + - + +
348P PHE* 3.8 7.9 - - - +
350P ILE* 1.3 89.3 - - + +
352P GLY* 1.3 62.4 + - - +
354P MET* 3.2 9.9 + - + +
355P ALA* 3.0 23.1 + - + +
58T LEU* 3.8 45.5 - - + -
61T TRP* 4.0 20.6 - - + -
62T GLY* 4.4 0.2 - - - -
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Residues in contact with GLY 352 (chain P).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
280P ALA 5.9 2.0 - - - -
284P SER* 4.5 5.8 - - - -
336P LEU* 4.1 3.3 - - - +
339P ILE* 4.0 22.9 - - - -
348P PHE 2.8 18.3 + - - -
349P ILE 3.4 2.9 + - - -
350P ILE 3.0 0.4 - - - -
351P ILE* 1.3 76.8 - - - +
353P GLN* 1.3 56.1 + - - +
355P ALA* 3.4 3.4 + - - +
356P SER* 2.9 33.2 + - - -
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Residues in contact with GLN 353 (chain P).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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284P SER* 3.4 30.9 + - - +
286P PRO* 4.5 11.7 - - - +
349P ILE* 3.1 31.3 + - + +
350P ILE* 3.2 26.5 + - - +
352P GLY* 1.3 74.7 - - - +
354P MET* 1.3 70.5 + - + +
356P SER* 3.7 7.0 - - - -
357P LEU* 2.8 31.0 + - - +
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Residues in contact with MET 354 (chain P).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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350P ILE* 3.1 42.7 + - + +
351P ILE* 3.4 10.5 - - + +
352P GLY 3.1 0.2 - - - -
353P GLN* 1.3 89.1 - - + +
355P ALA* 1.3 57.1 + - - +
357P LEU* 3.0 18.9 + - + +
358P SER* 2.7 37.0 + - - -
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Residues in contact with ALA 355 (chain P).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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332P ASN* 2.9 19.6 - - - +
335P ILE* 4.0 23.1 - - + -
336P LEU* 3.6 23.9 - - + +
339P ILE* 5.5 0.2 - - + -
351P ILE* 3.0 16.7 + - + +
352P GLY* 3.9 1.1 - - - +
354P MET* 1.3 75.8 - - - +
356P SER* 1.3 56.4 + - - +
358P SER* 2.8 20.6 + - - -
359P TYR* 3.0 13.0 + - - +
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Residues in contact with SER 356 (chain P).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
281P ILE* 3.5 25.0 - - - +
284P SER* 3.2 33.4 + - - -
285P ILE* 6.2 0.7 - - - -
336P LEU* 3.7 8.6 - - - +
352P GLY 2.9 16.4 + - - -
353P GLN* 3.7 4.7 - - - -
355P ALA* 1.3 75.4 - - - +
357P LEU* 1.3 62.8 + - - +
359P TYR* 3.3 18.4 - - - +
360P PHE* 3.3 19.2 - - - -
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Residues in contact with LEU 357 (chain P).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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353P GLN 2.8 19.7 + - - +
354P MET* 3.0 19.5 + - + +
356P SER* 1.3 76.6 - - - +
358P SER* 1.3 58.9 + - - +
359P TYR 3.3 0.2 + - - -
360P PHE* 3.5 6.2 + - + +
361P THR* 2.5 36.6 + - - +
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Residues in contact with SER 358 (chain P).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
332P ASN* 2.7 26.3 + - - -
354P MET 2.7 18.8 + - - -
355P ALA* 2.8 20.8 + - - -
357P LEU* 1.3 72.9 - - - +
359P TYR* 1.3 53.5 + - - +
361P THR* 3.1 6.9 + - - -
362P ILE* 2.8 42.3 + - - +
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Residues in contact with TYR 359 (chain P).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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277P PHE* 5.6 2.6 - + - -
281P ILE* 4.3 9.0 - - + -
298P SER* 3.1 26.6 + - - -
301P ILE* 3.5 10.5 - - + +
329P LEU* 4.0 16.9 - - + +
332P ASN* 3.7 10.1 - - - +
333P LEU* 3.6 34.1 - - + -
336P LEU* 4.3 8.7 - - + -
355P ALA 3.0 15.8 + - - +
356P SER* 3.3 13.2 - - - +
358P SER* 1.3 78.8 + - - +
360P PHE* 1.3 98.5 + + - +
362P ILE* 3.6 3.1 + - - +
363P LEU* 3.5 41.1 + - + +
3007P PEE 4.0 17.6 - - + +
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Residues in contact with PHE 360 (chain P).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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281P ILE* 4.4 16.2 - - + -
294P ALA* 3.8 13.0 - - + -
297P ALA* 3.9 27.8 - - + -
298P SER* 3.7 23.8 - - - -
301P ILE* 4.5 18.2 - - + -
356P SER* 3.3 23.3 - - - -
357P LEU* 3.5 7.5 + - + +
358P SER 3.4 0.2 - - - -
359P TYR* 1.3 100.0 - + - +
361P THR* 1.3 60.0 - - - +
363P LEU* 4.7 2.2 - - - +
364P LEU* 2.8 50.4 + - + +
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Residues in contact with THR 361 (chain P).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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357P LEU* 2.5 30.0 + - - +
358P SER* 3.1 9.8 + - - -
360P PHE* 1.3 74.9 - - - +
362P ILE* 1.3 61.6 + - - +
365P ILE* 2.8 54.8 + - + +
366P LEU* 2.9 21.7 + - + -
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Residues in contact with ILE 362 (chain P).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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325P LEU* 4.2 18.4 - - + -
328P LEU* 4.3 18.4 - - + -
329P LEU* 4.0 35.9 - - + +
332P ASN* 3.8 20.9 - - - +
358P SER* 2.8 25.0 + - - +
359P TYR 3.8 4.9 - - - +
361P THR* 1.3 75.5 - - - +
363P LEU* 1.3 56.9 + - - +
366P LEU* 3.9 14.4 - - + -
367P PHE* 2.9 53.4 + - + -
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Residues in contact with LEU 363 (chain P).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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103P LEU* 4.5 9.2 - - + -
301P ILE* 4.1 27.4 - - + -
305P ILE* 3.9 25.5 - - + +
308P LEU* 3.2 19.6 - - + +
329P LEU* 3.9 27.1 - - + -
359P TYR* 3.5 47.3 + - + +
360P PHE* 4.2 2.7 - - - +
361P THR 3.2 0.4 - - - -
362P ILE* 1.3 81.4 - - - +
364P LEU* 1.3 63.8 + - - +
367P PHE* 4.1 17.5 - - + +
368P PRO* 3.6 10.4 - - - +
3007P PEE 6.5 0.9 - - + -
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Residues in contact with LEU 364 (chain P).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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301P ILE* 3.5 32.8 - - + -
304P LEU* 4.2 11.4 - - + -
308P LEU* 4.1 22.2 - - + +
360P PHE* 2.8 40.7 + - + +
361P THR* 5.0 0.2 - - - -
363P LEU* 1.3 75.1 - - - +
365P ILE* 1.3 67.6 + - + +
368P PRO* 3.2 15.1 - - - +
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Residues in contact with ILE 365 (chain P).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
361P THR* 2.8 35.9 + - + +
363P LEU 3.5 0.2 - - - -
364P LEU* 1.3 83.2 - - + +
366P LEU* 1.3 79.4 + - + +
368P PRO* 3.2 8.3 - - - +
369P THR* 2.8 31.5 + - + +
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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