Contacts of the helix formed by residues 328 - 341 (chain A) 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 A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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296A VAL* 3.8 14.1 - - + +
322A SER 4.4 0.4 + - - -
325A ALA* 3.1 16.6 + - - +
326A GLY 4.4 6.5 - - - +
327A GLY* 1.3 81.1 - - - +
329A SER* 1.3 63.5 - - - +
330A LEU 3.4 2.0 - - - -
331A THR* 3.6 2.3 + - - -
332A CYS* 3.1 22.2 + - - +
359A LEU* 3.5 23.4 + - - +
362A GLU* 3.4 36.7 - - - +
363A ASP* 2.9 32.0 + - - -
558B ARG* 3.8 13.7 - - - +
561B GLU* 2.5 43.7 + - - +
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Residues in contact with SER 329 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
318A ILE* 4.3 2.9 - - - -
321A VAL* 4.2 18.3 - - - +
322A SER* 4.1 23.1 + - - +
325A ALA* 4.9 0.7 - - - -
327A GLY* 3.6 3.3 + - - -
328A ARG* 1.3 75.2 - - - +
330A LEU* 1.3 55.5 + - - +
332A CYS* 3.2 2.1 + - - +
333A ILE* 2.8 37.8 + - - +
362A GLU* 3.3 2.5 + - - -
374A SER* 3.8 1.4 + - - -
375A LEU* 3.5 26.5 + - - +
378A ALA* 3.3 20.2 - - - +
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Residues in contact with LEU 330 (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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329A SER* 1.3 79.2 + - - +
331A THR* 1.3 60.3 + - - +
333A ILE* 4.1 0.6 - - - +
334A MET* 3.1 32.6 + - + +
358A MET* 5.2 3.5 - - + +
361A LEU* 4.2 11.0 - - + -
362A GLU* 2.9 30.8 + - + +
365A TYR* 3.8 33.7 - - + -
374A SER* 3.6 12.3 - - - +
377A ALA* 3.9 14.1 - - + +
378A ALA* 3.6 25.6 - - - +
381A LEU* 4.2 8.1 - - + -
410A ALA* 4.1 23.6 - - + +
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Residues in contact with THR 331 (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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295A GLY* 4.6 7.8 - - - +
296A VAL* 3.8 20.9 - - + -
328A ARG* 4.5 0.4 - - - -
329A SER 3.3 0.2 - - - -
330A LEU* 1.3 72.9 - - - +
332A CYS* 1.3 67.1 + - - +
335A TYR* 3.2 21.7 + - - +
355A VAL* 4.6 3.4 - - + +
358A MET* 3.3 48.0 + - + +
359A LEU* 3.7 26.7 + - + +
362A GLU* 2.5 24.8 + - - -
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Residues in contact with CYS 332 (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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294A PHE* 3.7 24.1 - - - +
296A VAL* 3.8 12.7 - - + +
304A LEU* 4.4 11.9 - - - -
308A LEU* 4.3 31.2 - - - -
321A VAL* 4.3 12.1 - - + -
325A ALA* 4.3 5.2 - - + -
328A ARG 3.1 18.3 + - - +
329A SER* 3.5 5.8 - - - +
331A THR* 1.3 76.6 - - - +
333A ILE* 1.3 64.7 + - - +
335A TYR* 3.2 6.4 + - - +
336A MET* 3.0 24.8 + - - +
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Residues in contact with ILE 333 (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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308A LEU* 3.9 25.1 - - + -
311A LEU* 4.1 15.5 - - + -
316A LEU* 4.6 8.3 - - + -
318A ILE* 3.9 21.3 - - + -
321A VAL* 4.0 17.5 - - + -
329A SER 2.8 19.7 + - - +
330A LEU 4.1 2.0 - - - +
332A CYS* 1.3 73.6 - - - +
334A MET* 1.3 60.3 + - - +
336A MET* 3.3 3.5 + - - +
337A ILE* 2.9 40.7 + - + +
378A ALA* 3.9 20.6 - - - +
381A LEU* 3.7 20.6 - - + -
382A GLN* 4.1 14.4 - - + -
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Residues in contact with MET 334 (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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330A LEU* 3.1 19.7 + - - +
333A ILE* 1.3 80.2 - - - +
335A TYR* 1.3 58.0 - - - +
337A ILE* 3.9 2.0 - - - +
338A PHE* 3.0 68.3 + - + +
354A MET* 4.0 6.5 - - + -
357A TYR* 5.4 2.9 - - + -
358A MET* 3.4 30.5 - - - -
361A LEU* 4.9 8.5 - - + -
381A LEU* 3.6 18.4 - - + -
406A LEU 4.1 8.5 - - - +
407A PHE* 4.3 17.3 - - + -
410A ALA* 3.7 31.4 - - + -
460A ILE* 5.3 1.3 - - + -
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Residues in contact with TYR 335 (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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291A ILE* 3.7 29.4 - - + +
292A PRO 4.5 0.5 + - - -
293A ARG* 3.6 15.6 + - - -
294A PHE* 3.6 4.7 - - - -
295A GLY* 3.5 31.6 - - - -
331A THR 3.2 17.6 + - - +
332A CYS 3.2 3.5 + - - +
334A MET* 1.3 78.5 - - - +
336A MET* 1.3 72.3 + - - +
338A PHE* 3.3 5.5 + - - +
339A GLN* 3.0 60.9 + - + +
344A LEU* 4.6 9.4 - - + -
351A VAL* 4.6 7.0 - - + +
354A MET* 5.4 3.6 - - + -
355A VAL* 4.3 10.3 - - + -
358A MET* 3.6 21.4 - - + -
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Residues in contact with MET 336 (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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293A ARG 4.7 0.9 - - - +
294A PHE* 3.6 39.7 - - + -
308A LEU* 3.8 29.8 - - + -
311A LEU* 3.8 28.1 - - + +
332A CYS* 3.0 18.8 + - - +
333A ILE 3.6 7.2 - - - +
335A TYR* 1.3 94.5 - - - +
337A ILE* 1.3 52.1 + - - +
339A GLN* 3.2 10.0 + - + +
340A GLU* 2.7 35.2 + - - +
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Residues in contact with ILE 337 (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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311A LEU* 4.0 10.3 - - + -
333A ILE* 2.9 40.6 + - + +
334A MET* 3.9 4.0 - - - +
336A MET* 1.3 71.3 - - - +
338A PHE* 1.3 60.4 + - + +
340A GLU* 3.3 8.2 + - - +
341A ARG* 3.0 30.6 + - - +
381A LEU* 3.9 20.9 - - + -
382A GLN* 4.0 10.1 - - + -
385A HIS* 3.6 48.9 - - + +
406A LEU* 3.8 27.6 - - + -
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Residues in contact with PHE 338 (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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334A MET* 3.0 58.5 + - + +
335A TYR* 3.8 4.5 - - - +
337A ILE* 1.3 82.9 - - + +
339A GLN* 1.3 58.4 + - - +
341A ARG 3.6 0.2 + - - -
342A ASP* 3.1 4.9 + - - -
343A LEU* 2.8 58.4 + - + -
344A LEU* 3.9 16.1 + - + -
349A ILE* 4.3 9.9 - - + -
354A MET* 3.6 32.8 - - + -
381A LEU* 5.5 0.2 - - + -
403A LEU* 3.6 33.4 - - + -
406A LEU* 4.2 20.9 - - + -
407A PHE* 5.3 1.6 - - + -
460A ILE* 5.2 4.0 - - + -
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Residues in contact with GLN 339 (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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335A TYR* 3.0 56.6 + - + +
336A MET* 3.6 11.7 - - + +
338A PHE* 1.3 74.0 - - - +
340A GLU* 1.3 57.5 + - - +
342A ASP* 2.8 32.3 + - - +
344A LEU* 3.5 24.2 - - + +
345A LYS* 5.7 3.5 + - - +
351A VAL* 4.4 6.5 - - - +
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Residues in contact with GLU 340 (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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311A LEU* 3.9 16.6 - - + +
312A ASN* 3.0 41.3 + - - +
336A MET 2.7 21.2 + - - +
337A ILE* 3.4 7.4 - - - +
339A GLN* 1.3 72.3 - - - +
341A ARG* 1.3 59.9 + - + +
342A ASP* 5.2 0.7 - - - +
385A HIS* 4.1 11.9 - - + +
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Residues in contact with ARG 341 (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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337A ILE 3.0 17.3 + - - +
340A GLU* 1.3 79.0 - - + +
342A ASP* 1.3 65.7 + - - +
343A LEU* 3.1 15.0 + - + +
346A LYS* 3.0 29.0 + - - +
385A HIS* 2.8 54.9 + - + -
388A LEU* 3.4 23.8 - - - +
389A ALA* 3.8 13.9 - - - +
402A ILE* 3.9 29.9 - - - +
406A LEU* 3.9 24.9 - - - +
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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