Contacts of the helix formed by residues 328 - 341 (chain B) in PDB entry 3TVX
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 ARG 328 (chain B).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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558A ARG* 4.2 7.5 - - - +
561A GLU* 2.8 42.5 + - - +
562A ARG* 5.5 0.6 - - - +
296B VAL* 3.6 24.5 - - + -
325B ALA* 3.5 17.3 + - - +
326B GLY 3.2 7.2 - - - +
327B GLY* 1.3 74.5 - - - +
329B SER* 1.3 62.6 + - - +
330B LEU 3.3 2.9 - - - -
331B THR* 3.6 1.2 + - - -
332B CYS* 3.1 23.7 + - - +
359B LEU* 3.6 24.2 + - + +
362B GLU* 3.4 30.9 - - - +
363B ASP* 2.6 39.2 + - - +
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Residues in contact with SER 329 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
318B ILE* 4.5 3.8 - - - -
321B VAL* 4.6 5.8 - - - +
322B SER* 3.8 34.3 + - - +
325B ALA* 4.5 1.2 - - - +
327B GLY 2.9 10.9 + - - -
328B ARG* 1.3 73.0 - - - +
330B LEU* 1.3 59.1 + - - +
332B CYS* 4.0 4.1 - - - +
333B ILE* 3.1 32.4 + - - +
362B GLU* 3.9 1.7 + - - -
374B SER* 4.0 1.2 + - - -
375B LEU* 3.4 34.3 - - - +
378B ALA* 3.6 5.9 - - - +
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Residues in contact with LEU 330 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
329B SER* 1.3 77.9 + - - +
331B THR* 1.3 65.7 + - - +
333B ILE* 3.8 0.3 - - - +
334B MET* 2.9 32.8 + - + +
358B MET* 5.3 1.8 - - + +
361B LEU* 3.9 22.0 - - + -
362B GLU* 3.0 25.8 + - + +
365B TYR* 3.9 31.2 - - + -
374B SER* 3.8 10.8 - - - +
377B ALA* 3.9 10.1 - - + -
378B ALA* 3.8 21.5 - - - +
381B LEU* 3.9 22.0 - - + -
410B ALA* 4.0 11.7 - - + +
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Residues in contact with THR 331 (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 GLY 4.8 3.4 - - - +
296B VAL* 4.2 14.8 - - + -
328B ARG* 4.1 4.0 - - - -
330B LEU* 1.3 76.0 - - - +
332B CYS* 1.3 63.7 + - - +
335B TYR* 3.1 26.6 + - + +
355B VAL* 4.5 8.3 - - + +
358B MET* 3.4 49.6 + - + +
359B LEU* 3.8 25.9 + - + +
362B GLU* 2.6 25.7 + - - +
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Residues in contact with CYS 332 (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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294B PHE* 3.4 21.2 - - - +
296B VAL* 3.9 22.8 - - + +
304B LEU* 4.4 15.7 - - - -
308B LEU* 4.4 17.7 - - - -
321B VAL* 4.3 17.5 - - + -
325B ALA* 4.3 4.3 - - + -
328B ARG 3.1 17.6 + - - +
329B SER* 4.0 3.4 - - - +
331B THR* 1.3 80.5 - - - +
333B ILE* 1.3 63.2 + - - +
335B TYR* 3.4 3.3 - - - +
336B MET* 3.0 26.4 + - - +
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Residues in contact with ILE 333 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
308B LEU* 3.8 26.2 - - + -
311B LEU* 4.1 14.8 - - + -
316B LEU* 4.4 9.6 - - + -
318B ILE* 3.9 21.1 - - + -
321B VAL* 4.2 14.8 - - + -
329B SER 3.1 18.8 + - - +
330B LEU 3.8 4.0 - - - +
332B CYS* 1.3 76.7 - - - +
334B MET* 1.3 63.8 + - - +
336B MET* 3.8 3.0 - - - +
337B ILE* 3.0 38.4 + - + +
378B ALA* 3.9 26.2 - - + +
381B LEU* 3.9 12.8 - - + -
382B GLN* 4.3 11.9 - - + -
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Residues in contact with MET 334 (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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330B LEU* 2.9 23.8 + - - +
333B ILE* 1.3 74.8 - - - +
335B TYR* 1.3 61.9 + - - +
337B ILE* 3.3 2.9 + - - +
338B PHE* 2.8 58.8 + - + -
354B MET* 3.9 15.9 - - + -
357B TYR* 5.2 3.4 - - + -
358B MET* 3.5 30.7 - - + -
361B LEU* 4.8 8.7 - - + -
381B LEU* 3.7 20.2 - - + -
406B LEU 4.8 1.1 - - - +
407B PHE* 4.5 22.2 - - + -
410B ALA* 3.7 29.8 - - + -
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Residues in contact with TYR 335 (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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291B ILE* 3.6 21.9 - - + +
292B PRO 4.2 0.5 + - - -
293B ARG 3.4 24.9 + - - -
294B PHE 3.6 4.9 - - - -
295B GLY* 3.5 27.8 - - - -
331B THR 3.1 18.9 + - - +
332B CYS 3.4 2.9 - - - +
334B MET* 1.3 76.9 - - - +
336B MET* 1.3 65.9 + - - +
338B PHE* 3.3 6.3 + - + +
339B GLN* 2.8 69.3 + - + +
344B LEU* 4.9 5.8 - - + +
351B VAL* 3.9 23.0 - - + +
354B MET* 5.5 2.7 - - + -
355B VAL* 4.5 5.4 - - + -
358B MET* 3.7 21.2 - - + -
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Residues in contact with MET 336 (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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293B ARG 4.7 0.7 - - - +
294B PHE* 3.5 43.3 - - + +
308B LEU* 3.9 26.9 - - + +
311B LEU* 3.7 31.4 - - + +
332B CYS* 3.0 21.0 + - - +
333B ILE 3.8 2.7 - - - +
334B MET 3.2 0.2 - - - -
335B TYR* 1.3 95.0 - - - +
337B ILE* 1.3 51.7 + - - +
339B GLN* 3.1 10.9 + - + +
340B GLU* 2.8 34.8 + - - +
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Residues in contact with ILE 337 (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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311B LEU* 4.2 11.0 - - + -
333B ILE* 3.0 26.0 + - + +
334B MET* 3.7 4.0 - - - +
336B MET* 1.3 74.5 - - - +
338B PHE* 1.3 62.5 + - + +
340B GLU* 3.4 7.4 + - - +
341B ARG* 3.0 29.8 + - - +
343B LEU* 4.5 0.2 - - - +
381B LEU* 3.9 27.4 - - + -
382B GLN* 3.9 25.8 - - + -
385B HIS* 3.9 33.4 - - + +
406B LEU* 3.9 30.7 - - + -
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Residues in contact with PHE 338 (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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334B MET* 2.8 48.2 + - + +
335B TYR* 3.7 6.7 - - - +
337B ILE* 1.3 81.6 - - + +
339B GLN* 1.3 59.8 + - - +
342B ASP* 3.0 5.0 + - - -
343B LEU* 2.9 53.5 + - + -
344B LEU* 3.6 29.9 + - + +
349B ILE* 4.2 5.8 - - + -
354B MET* 3.4 35.9 - - + -
381B LEU* 5.5 0.2 - - + -
403B LEU* 3.7 32.8 - - + -
406B LEU* 4.4 18.4 - - + -
407B PHE* 5.3 2.5 - + + -
460B ILE* 5.5 4.0 - - + -
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Residues in contact with GLN 339 (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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335B TYR* 2.8 62.9 + - + +
336B MET* 3.5 13.5 - - + +
338B PHE* 1.3 73.8 - - - +
340B GLU* 1.3 66.2 + - - +
342B ASP* 3.0 23.7 + - - +
344B LEU* 4.4 19.5 - - + +
351B VAL* 5.3 1.6 - - - +
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Residues in contact with GLU 340 (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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311B LEU* 3.6 17.9 - - + +
312B ASN* 3.2 37.8 + - - +
336B MET 2.8 19.6 + - - +
337B ILE* 3.6 7.0 - - - +
339B GLN* 1.3 74.1 - - - +
341B ARG* 1.3 60.9 + - + +
342B ASP* 3.3 1.3 + - - +
385B HIS* 4.3 9.4 - - + -
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Residues in contact with ARG 341 (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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337B ILE 3.0 15.0 + - - +
340B GLU* 1.3 77.3 - - + +
342B ASP* 1.3 63.9 + - - +
343B LEU* 3.2 16.1 + - + +
346B LYS* 2.8 32.4 + - - +
385B HIS* 2.7 58.6 + - + +
388B LEU* 3.6 20.6 + - - +
389B ALA* 3.6 17.4 - - - +
402B ILE* 3.8 38.7 - - - +
406B LEU* 4.1 13.5 - - - +
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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
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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