Contacts of the helix formed by residues 332 - 350 (chain A) in PDB entry 6T8B
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 SER 332 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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330A SER* 4.1 2.9 + - - -
331A TYR* 1.3 73.6 - - - +
333A PRO* 1.3 71.1 - - - +
334A GLU* 3.2 21.0 + - - +
335A SER* 2.9 29.4 + - - -
336A LEU* 3.1 8.5 + - - +
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Residues in contact with PRO 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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331A TYR 3.7 3.0 - - - +
332A SER* 1.3 85.8 - - - +
334A GLU* 1.3 68.5 + - - +
336A LEU* 3.7 16.5 - - + +
337A GLU* 2.9 41.9 + - + +
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Residues in contact with GLU 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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332A SER* 3.2 24.3 + - - +
333A PRO* 1.3 85.7 - - - +
335A SER* 1.3 58.0 + - - +
337A GLU* 3.8 8.6 - - - +
338A ALA* 2.9 28.7 + - - +
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Residues in contact with SER 335 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
331A TYR* 5.2 12.7 - - - -
332A SER* 2.9 20.4 + - - -
334A GLU* 1.3 78.6 - - - +
336A LEU* 1.3 59.8 + - - +
338A ALA* 3.3 8.4 + - - +
339A MET* 2.9 37.6 + - - +
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Residues in contact with LEU 336 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
331A TYR* 3.7 48.7 - - + +
332A SER 3.1 9.1 + - - +
333A PRO* 3.7 16.8 - - + +
334A GLU 3.3 0.4 - - - -
335A SER* 1.3 76.9 - - - +
337A GLU* 1.3 56.9 + - + +
339A MET* 3.4 6.2 + - - +
340A SER* 2.8 32.8 + - - -
359A VAL* 4.3 26.2 - - + -
361A PRO* 4.3 24.2 - - + -
366A THR* 4.5 10.3 - - + -
368A PHE* 4.0 8.5 - - + -
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Residues in contact with GLU 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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333A PRO* 2.9 27.3 + - + +
334A GLU* 3.8 7.1 - - - +
336A LEU* 1.3 74.8 - - + +
338A ALA* 1.3 66.5 + - - +
340A SER* 3.2 7.0 + - - -
341A ARG* 3.0 44.9 + - - +
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Residues in contact with ALA 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 GLU 2.9 19.0 + - - +
335A SER* 3.6 9.0 - - - +
337A GLU* 1.3 77.2 - - - +
339A MET* 1.3 56.1 + - - +
341A ARG* 3.4 4.1 + - - +
342A LEU* 2.9 30.0 + - - +
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Residues in contact with MET 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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331A TYR* 4.9 21.3 - - + +
335A SER* 2.9 24.3 + - - +
336A LEU* 3.8 5.2 - - - +
338A ALA* 1.3 72.6 - - - +
340A SER* 1.3 60.1 + - - +
342A LEU* 3.7 9.0 - - + +
343A LEU* 2.8 28.3 + - - +
368A PHE* 3.7 31.9 - - + -
392A LEU* 4.0 23.7 - - + +
393A ALA* 6.1 2.2 - - + +
394A VAL* 4.6 13.2 - - + -
413A ILE* 4.3 16.2 - - + -
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Residues in contact with SER 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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336A LEU 2.8 24.0 + - - -
337A GLU* 3.2 8.9 + - - -
339A MET* 1.3 76.7 - - - +
341A ARG* 1.3 72.5 + - - +
343A LEU* 3.2 7.6 + - - +
344A GLU* 3.0 26.9 + - - +
356A VAL* 4.0 20.2 - - - +
359A VAL* 3.3 14.4 - - - +
368A PHE* 3.3 21.2 - - - -
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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 GLU* 3.0 41.4 + - - +
338A ALA* 4.1 3.8 - - - +
340A SER* 1.3 91.7 - - - +
342A LEU* 1.3 57.2 + - - +
344A GLU* 3.8 20.9 + - - +
345A ILE* 2.9 40.3 + - + +
356A VAL* 4.9 13.9 + - - +
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Residues in contact with LEU 342 (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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338A ALA 2.9 19.2 + - - +
339A MET* 3.8 8.5 - - + +
341A ARG* 1.3 75.9 - - - +
343A LEU* 1.3 59.7 + - - +
345A ILE* 4.7 5.2 - - + +
346A LYS* 3.0 59.2 + - + +
391A SER 4.7 7.9 - - - +
392A LEU* 3.6 25.5 - - + +
393A ALA 5.5 1.6 - - - +
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Residues in contact with LEU 343 (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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339A MET* 2.8 14.5 + - + +
340A SER 3.2 7.4 + - - +
342A LEU* 1.3 73.9 - - - +
344A GLU* 1.3 59.8 + - - +
346A LYS* 3.4 2.3 + - - +
347A LEU* 2.9 40.1 + - + +
354A VAL* 6.2 0.2 - - + -
356A VAL* 4.2 6.7 - - + -
368A PHE* 3.9 28.9 - - + -
370A ILE* 3.8 28.0 - - + -
388A LEU* 3.6 42.0 - - + -
392A LEU* 3.8 21.9 - - + +
411A ILE* 3.9 11.4 - - + -
413A ILE* 5.5 0.2 - - + -
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Residues in contact with GLU 344 (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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340A SER 3.0 14.7 + - - +
341A ARG* 3.3 24.8 + - - +
343A LEU* 1.3 77.6 - - - +
345A ILE* 1.3 62.9 + - + +
347A LEU* 3.4 2.6 + - - +
348A LYS* 2.9 29.4 + - + +
352A VAL 5.1 0.2 - - - +
354A VAL* 2.9 41.6 + - + +
355A SER* 4.1 12.9 - - - -
356A VAL* 4.6 9.9 + - + +
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Residues in contact with ILE 345 (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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341A ARG* 2.9 25.5 + - + +
342A LEU* 4.3 6.5 - - + +
344A GLU* 1.3 83.8 - - + +
346A LYS* 1.3 65.8 + - + +
348A LYS* 3.0 11.6 + - + +
349A GLU* 3.0 37.9 + - + +
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Residues in contact with LYS 346 (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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342A LEU* 3.0 42.6 + - + +
343A LEU* 4.1 2.0 - - - +
345A ILE* 1.3 80.3 - - + +
347A LEU* 1.3 60.5 + - - +
349A GLU* 3.6 34.6 + - - +
350A PHE* 3.1 28.0 - - + -
388A LEU* 4.5 4.0 - - + -
391A SER* 3.4 45.0 - - - +
371F GLN* 5.7 5.1 - - - +
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Residues in contact with LEU 347 (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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343A LEU* 2.9 30.5 + - + +
344A GLU 3.8 3.4 - - - +
346A LYS* 1.3 76.8 - - - +
348A LYS* 1.3 65.0 + - - +
349A GLU 3.1 0.2 - - - -
350A PHE* 3.0 15.9 + - - +
352A VAL* 3.3 28.8 + - + +
354A VAL* 3.6 22.7 - - + -
370A ILE* 4.1 20.4 - - + -
381A ILE* 3.7 25.4 - - + -
384A LEU* 3.8 16.6 - - + -
388A LEU* 3.6 35.2 - - + -
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Residues in contact with LYS 348 (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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344A GLU* 2.9 17.6 + - + +
345A ILE* 3.0 15.7 + - + +
347A LEU* 1.3 76.6 - - - +
349A GLU* 1.3 62.8 + - - +
351A GLY* 3.0 17.7 + - - -
352A VAL 3.7 6.9 + - - +
353A GLU* 3.9 44.3 + - + +
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Residues in contact with GLU 349 (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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345A ILE* 3.0 24.7 + - + +
346A LYS* 3.7 42.4 + - - +
347A LEU 3.1 0.4 - - - -
348A LYS* 1.3 78.0 - - - +
350A PHE* 1.3 63.0 + - + +
351A GLY 3.2 2.8 + - - -
373F ALA 4.8 1.4 - - - +
374F ALA* 3.8 35.2 - - + +
375F GLY* 4.0 20.9 + - - +
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Residues in contact with PHE 350 (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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346A LYS* 3.1 29.6 - - + -
347A LEU* 3.0 9.3 + - + +
349A GLU* 1.3 82.3 - - + +
351A GLY* 1.3 54.9 + - - +
352A VAL* 3.2 13.4 + - + +
380A ARG* 5.7 0.9 + - - -
384A LEU* 3.8 40.0 - - + +
387A ASP* 3.7 33.9 - - + -
388A LEU* 5.0 2.7 - - - -
390A ARG* 5.3 2.2 - - - -
391A SER* 5.5 3.1 - - - -
375F GLY* 3.3 37.5 - - - -
376F VAL 3.9 11.9 - - - -
377F LYS* 4.2 16.8 - - + -
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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