Contacts of the helix formed by residues 332 - 350 (chain D) in PDB entry 6T8G
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 D).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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330D SER* 3.1 10.8 + - - -
331D TYR* 1.3 73.9 - - - +
333D PRO* 1.3 63.4 - - - +
334D GLU* 3.3 13.0 + - - +
335D SER* 2.6 37.0 + - - -
336D LEU* 2.7 33.7 + - - +
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Residues in contact with PRO 333 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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330D SER* 5.7 2.2 - - - +
331D TYR 4.3 2.2 - - - +
332D SER* 1.3 83.0 - - - +
334D GLU* 1.3 59.6 + - - +
336D LEU* 4.2 10.7 - - + +
337D GLU* 2.9 31.2 + - - +
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Residues in contact with GLU 334 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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332D SER* 3.1 12.4 + - - +
333D PRO* 1.3 78.3 - - - +
335D SER* 1.3 58.9 + - - +
337D GLU* 3.3 6.0 + - - +
338D ALA* 2.9 33.8 + - + +
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Residues in contact with SER 335 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
331D TYR* 4.6 10.2 - - - +
332D SER* 2.6 29.5 + - - -
334D GLU* 1.3 75.3 - - - +
336D LEU* 1.3 60.1 + - - +
338D ALA* 3.3 7.0 + - - +
339D MET* 2.9 37.0 + - - +
416D GLU* 4.9 8.5 + - - -
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Residues in contact with LEU 336 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
331D TYR* 3.5 33.2 - - + +
332D SER 2.7 20.7 + - - +
333D PRO* 4.2 8.3 - - + +
335D SER* 1.3 73.9 - - - +
337D GLU* 1.3 57.7 + - - +
339D MET* 3.3 9.7 + - + +
340D SER* 2.9 28.1 + - - -
359D VAL* 3.9 39.0 - - + +
361D PRO* 4.2 22.0 - - + -
366D THR* 4.1 15.9 - - + +
368D PHE* 5.0 4.0 - - + -
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Residues in contact with GLU 337 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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333D PRO 2.9 21.0 + - - +
334D GLU* 3.7 7.4 - - - +
336D LEU* 1.3 74.0 - - - +
338D ALA* 1.3 61.0 + - - +
340D SER* 2.5 25.5 + - - -
341D ARG* 2.4 54.8 + - + +
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Residues in contact with ALA 338 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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334D GLU* 2.9 23.0 + - + +
335D SER* 3.5 9.0 - - - +
336D LEU 3.3 0.2 - - - -
337D GLU* 1.3 76.6 - - - +
339D MET* 1.3 64.4 + - + +
341D ARG* 3.4 5.2 + - - +
342D LEU* 2.9 29.9 + - - +
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Residues in contact with MET 339 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
335D SER* 2.9 27.0 + - - +
336D LEU* 3.7 11.0 - - + +
338D ALA* 1.3 81.7 - - + +
340D SER* 1.3 59.3 + - - +
342D LEU* 3.7 28.5 - - + +
343D LEU* 2.9 30.3 + - - +
368D PHE* 3.9 21.7 - - + -
392D LEU* 5.5 6.3 - - - +
413D ILE* 6.2 5.4 - - - -
416D GLU* 5.7 5.8 - - - +
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Residues in contact with SER 340 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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336D LEU 2.9 14.2 + - - -
337D GLU* 2.5 42.1 + - - -
339D MET* 1.3 77.0 - - - +
341D ARG* 1.3 64.9 + - - +
343D LEU* 3.3 4.7 + - - +
344D GLU* 2.9 27.5 + - - +
356D VAL* 3.7 36.6 - - - +
359D VAL* 4.7 7.0 - - - -
368D PHE* 4.6 4.0 - - - -
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Residues in contact with ARG 341 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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337D GLU* 2.4 53.5 + - + +
338D ALA* 4.0 5.2 - - - +
340D SER* 1.3 89.9 + - - +
342D LEU* 1.3 57.9 + - - +
344D GLU* 2.5 33.7 + - - +
345D ILE* 2.9 43.9 + - + +
355D SER* 5.6 1.2 + - - +
356D VAL* 4.2 31.1 + - - +
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Residues in contact with LEU 342 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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338D ALA 2.9 17.9 + - - +
339D MET* 3.7 30.1 - - + +
340D SER 3.3 0.2 - - - -
341D ARG* 1.3 73.9 - - - +
343D LEU* 1.3 58.4 + - - +
345D ILE* 3.4 7.8 + - + -
346D LYS* 2.9 56.1 + - + +
391D SER 5.4 1.3 - - - +
392D LEU* 3.9 24.7 - - + +
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Residues in contact with LEU 343 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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339D MET 2.9 17.7 + - - +
340D SER 3.6 4.0 - - - +
342D LEU* 1.3 76.0 - - - +
344D GLU* 1.3 63.4 + - - +
346D LYS* 4.0 2.6 - - - -
347D LEU* 3.0 47.3 + - + +
354D VAL* 4.7 2.5 - - + -
356D VAL* 3.9 13.9 - - + -
368D PHE* 3.9 23.6 - - + -
370D ILE* 3.8 22.2 - - + -
388D LEU* 3.9 23.8 - - + -
392D LEU* 3.8 30.0 - - + +
411D ILE* 4.6 3.6 - - + -
413D ILE* 4.3 4.9 - - + -
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Residues in contact with GLU 344 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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340D SER 2.9 12.9 + - - +
341D ARG* 2.5 52.6 + - - +
343D LEU* 1.3 79.2 - - - +
345D ILE* 1.3 64.0 + - + +
347D LEU 3.4 0.2 + - - -
348D LYS* 2.9 35.3 + - + +
354D VAL* 3.7 34.4 - - + +
355D SER* 5.4 3.3 - - - -
356D VAL* 5.0 4.0 - - + +
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Residues in contact with ILE 345 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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341D ARG* 2.9 30.0 + - + +
342D LEU* 4.1 8.1 - - + +
344D GLU* 1.3 82.5 - - + +
346D LYS* 1.3 61.4 + - + +
348D LYS* 3.1 11.7 + - + +
349D GLU* 2.9 43.7 + - + +
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Residues in contact with LYS 346 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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371C GLN* 5.6 5.9 - - - +
342D LEU* 2.9 41.4 + - + +
343D LEU* 4.1 3.1 - - - +
345D ILE* 1.3 78.5 - - + +
347D LEU* 1.3 61.9 + - - +
349D GLU* 3.4 32.8 + - - +
350D PHE* 3.3 24.8 + - + -
388D LEU* 4.7 7.4 - - + -
391D SER* 3.7 48.9 + - - +
392D LEU* 4.6 2.9 - - + -
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Residues in contact with LEU 347 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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343D LEU* 3.0 43.9 + - + +
346D LYS* 1.3 76.5 - - - +
348D LYS* 1.3 63.2 + - - +
350D PHE* 3.2 16.1 + - + +
352D VAL* 2.9 41.1 - - + +
354D VAL* 3.9 25.6 - - + -
370D ILE* 4.7 0.2 - - + -
381D ILE* 4.9 9.2 - - + -
384D LEU* 4.5 16.6 - - + -
388D LEU* 3.8 28.3 - - + -
411D ILE* 4.2 14.8 - - + -
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Residues in contact with LYS 348 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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344D GLU* 2.9 25.7 + - + +
345D ILE* 3.1 13.4 + - + +
347D LEU* 1.3 76.2 - - - +
349D GLU* 1.3 58.4 + - + +
350D PHE 3.0 11.6 - - - +
352D VAL 3.6 9.8 - - - +
353D GLU* 4.5 26.1 + - + +
354D VAL* 4.8 2.2 - - + +
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Residues in contact with GLU 349 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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374C ALA* 3.4 36.8 - - + +
375C GLY* 3.3 19.8 + - - +
345D ILE* 2.9 31.1 + - + +
346D LYS* 3.6 35.1 + - - +
347D LEU 3.2 0.6 - - - -
348D LYS* 1.3 78.7 - - + +
350D PHE* 1.3 62.4 + - + +
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Residues in contact with PHE 350 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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375C GLY* 4.0 14.8 - - - -
376C VAL 3.4 35.9 - - - -
377C LYS* 4.5 5.2 - - + -
346D LYS* 3.3 24.9 - - + -
347D LEU* 3.2 19.3 + - + +
348D LYS 3.0 16.9 - - - +
349D GLU* 1.3 81.8 - - + +
351D GLY* 1.3 60.4 + - - +
352D VAL 2.9 11.2 + - - +
384D LEU* 4.3 28.5 - - + -
387D ASP* 3.7 38.8 - - + -
388D LEU* 4.8 2.5 - - + -
390D ARG* 3.9 9.0 - - - -
391D SER* 4.6 12.3 - - - -
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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