Contacts of the helix formed by residues 347 - 361 (chain B) in PDB entry 5WWT
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 347 (chain B).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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325B PRO* 3.8 27.4 - - + +
326B CYS* 3.5 22.4 - - - -
327B SER* 3.6 17.0 - - - -
339B TRP* 3.8 9.7 - + - -
343B GLU 3.6 16.2 - - - -
344B VAL 3.5 15.7 - - - -
345B ALA 3.1 1.4 - - - -
346B SER* 1.3 81.4 - - - +
348B GLN* 1.3 67.7 + - - +
349B PRO* 3.3 2.9 - - - -
350B LEU* 3.0 9.4 + - + +
351B GLN* 2.8 44.0 + - - +
379B GLU* 4.2 5.4 - - - +
3D G 3.5 24.7 - + - -
70D C 2.6 43.5 + + + -
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Residues in contact with GLN 348 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
345B ALA* 3.9 8.1 + - - +
347B TYR* 1.3 77.0 - - - +
349B PRO* 1.4 68.1 - - + +
351B GLN* 3.8 3.5 - - - -
352B ARG* 2.9 59.9 + - - +
378B ALA* 3.0 31.9 + - + +
379B GLU* 5.0 4.4 - - + +
382B GLU* 3.4 18.8 + - - +
383B GLN* 3.2 30.3 + - - +
2D A 4.3 7.7 - - - +
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Residues in contact with PRO 349 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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345B ALA 4.3 4.7 - - - +
346B SER 4.2 6.1 - - - +
347B TYR 3.4 9.2 - - - +
348B GLN* 1.4 94.1 - - + +
350B LEU* 1.3 56.3 + - - +
352B ARG* 3.2 7.6 + - + +
353B LYS* 2.9 34.3 + - - +
2D A 3.5 55.6 - - + +
3D G 3.6 25.4 - - - +
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Residues in contact with LEU 350 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
267B LYS* 6.2 1.3 - - - +
293B ASP* 5.8 0.2 - - - +
295B THR* 3.7 25.8 - - + -
325B PRO* 3.7 25.4 - - + -
347B TYR* 3.0 11.9 + - + +
349B PRO* 1.3 76.0 - - - +
351B GLN* 1.3 60.1 + - - +
353B LYS* 3.2 7.6 + - + +
354B LEU* 2.9 43.1 + - + +
3D G 3.7 61.1 + - + +
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Residues in contact with GLN 351 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
322B LEU* 4.1 3.6 - - - +
324B ALA* 4.1 13.2 - - + -
325B PRO* 3.0 30.2 + - + +
326B CYS* 3.9 4.0 - - - +
347B TYR* 2.8 25.2 + - - +
348B GLN* 3.8 1.6 - - - -
350B LEU* 1.3 76.7 - - - +
352B ARG* 1.3 56.9 + - - +
354B LEU* 3.5 7.1 + - - +
355B PHE* 2.9 30.5 + - - +
370B TYR* 3.1 23.5 + - + +
372B THR* 4.6 2.2 - - - +
379B GLU* 3.2 38.2 + - - +
383B GLN* 2.8 27.0 + - - +
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Residues in contact with ARG 352 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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348B GLN* 2.9 51.0 + - - +
349B PRO* 3.5 4.7 - - + +
351B GLN* 1.3 74.1 - - - +
353B LYS* 1.3 61.6 + - + +
355B PHE 3.3 0.2 + - - -
356B THR* 2.9 33.4 + - - -
382B GLU* 4.9 6.7 + - - +
383B GLN* 2.9 23.4 + - - +
386B TRP* 3.4 58.7 - - + +
2D A 2.8 50.9 + - + +
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Residues in contact with LYS 353 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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295B THR* 3.9 25.8 - - + +
349B PRO* 2.9 19.9 + - - +
350B LEU* 3.2 14.6 + - + +
352B ARG* 1.3 76.1 - - + +
354B LEU* 1.3 58.0 + - - +
356B THR* 3.2 9.4 + - - -
357B ALA* 2.9 28.4 + - - +
2D A 6.3 1.1 - - - -
3D G 2.9 54.4 + - + +
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Residues in contact with LEU 354 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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241B LEU* 3.3 17.9 - - + +
242B CYS* 3.7 17.9 - - - -
294B GLY* 3.6 15.0 - - - +
295B THR* 3.5 34.8 - - + +
322B LEU* 3.8 15.7 - - + -
325B PRO* 3.7 31.2 - - + -
350B LEU* 2.9 31.4 + - + +
351B GLN* 3.8 4.5 - - - +
353B LYS* 1.3 75.9 - - - +
355B PHE* 1.3 58.0 + - - +
357B ALA* 3.5 4.1 + - - +
358B ALA* 2.9 24.1 + - - +
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Residues in contact with PHE 355 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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322B LEU* 3.6 9.1 - - + +
351B GLN 2.9 17.8 + - - +
352B ARG 3.5 5.8 - - - +
353B LYS 3.2 0.2 - - - -
354B LEU* 1.3 76.0 - - - +
356B THR* 1.3 60.3 + - - +
358B ALA* 3.1 4.8 + - - +
359B VAL* 2.9 41.3 + - + +
368B LEU* 3.6 18.8 - - + -
370B TYR* 3.6 48.7 - + + -
383B GLN* 5.2 4.9 - - + -
386B TRP* 3.8 22.9 - + + -
387B ALA* 3.5 29.4 - - + -
391B PHE* 4.0 4.0 - + - -
394B LEU* 3.6 20.2 - - + -
463B PHE* 3.7 15.5 - + - -
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Residues in contact with THR 356 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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352B ARG 2.9 15.3 + - - -
353B LYS* 3.5 10.2 - - - -
355B PHE* 1.3 76.0 - - - +
357B ALA* 1.3 63.0 + - - +
359B VAL* 3.1 3.5 + - - +
360B GLN* 2.9 46.4 + - + +
386B TRP* 3.9 6.6 - - - -
390B LYS* 4.4 8.8 - - - -
391B PHE* 3.4 32.3 - - + -
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Residues in contact with ALA 357 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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241B LEU* 4.6 2.5 - - + -
294B GLY 3.5 24.7 - - - +
295B THR* 4.3 9.6 - - - +
297B ALA* 5.3 2.2 - - + -
298B VAL* 3.9 20.9 - - + +
353B LYS 2.9 16.1 + - - +
354B LEU* 3.6 6.3 - - - +
356B THR* 1.3 76.5 - - - +
358B ALA* 1.3 62.8 + - - +
360B GLN* 3.5 3.0 + - - +
361B LEU* 3.2 31.1 + - - +
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Residues in contact with ALA 358 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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241B LEU* 3.9 11.2 - - + +
320B ILE* 3.2 44.6 - - + +
322B LEU* 4.9 4.3 - - + -
354B LEU 2.9 15.8 + - - +
355B PHE* 3.1 12.3 + - - +
357B ALA* 1.3 73.8 - - - +
359B VAL* 1.3 64.4 + - - +
361B LEU* 3.1 10.3 + - - -
362B LEU* 3.3 4.8 + - - +
368B LEU* 3.9 15.7 - - + -
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Residues in contact with VAL 359 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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355B PHE* 2.9 39.6 + - + +
356B THR 3.1 5.8 + - - +
358B ALA* 1.3 75.0 - - - +
360B GLN* 1.3 64.1 + - + +
362B LEU* 3.3 13.2 + - - +
368B LEU* 4.0 6.7 - - + -
391B PHE* 3.8 31.0 - - + -
393B CYS* 4.4 12.3 - - - -
394B LEU* 3.6 33.2 - - + -
465B LYS* 3.0 26.8 + - - +
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Residues in contact with GLN 360 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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298B VAL* 3.3 36.3 - - + +
300B LEU* 5.9 0.5 - - - +
314B PRO* 3.3 13.6 - - + +
315B GLU* 3.0 23.2 + - - +
356B THR* 2.9 40.1 + - + +
357B ALA* 3.8 5.4 - - - +
358B ALA 3.2 0.2 - - - -
359B VAL* 1.3 78.7 - - + +
361B LEU* 1.3 57.3 + - - +
362B LEU 3.2 1.0 + - - -
391B PHE* 6.0 2.0 - - + -
465B LYS* 4.3 2.1 + - - +
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Residues in contact with LEU 361 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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239B LEU* 4.5 18.4 - - + -
241B LEU* 4.8 2.7 - - + -
297B ALA* 3.9 31.0 - - + +
298B VAL* 4.2 8.7 - - + -
312B PHE* 3.3 42.6 - - + +
313B LEU 3.3 15.5 - - - +
314B PRO* 4.2 2.0 - - + -
315B GLU 3.6 4.7 - - - +
316B SER* 3.4 5.1 + - - +
317B PHE* 3.3 32.7 + - + +
320B ILE* 3.7 13.7 - - + -
357B ALA 3.2 21.0 + - - +
358B ALA 3.1 2.9 + - - -
360B GLN* 1.3 76.5 - - - +
362B LEU* 1.3 57.2 + - - +
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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