Contacts of the helix formed by residues 335 - 347 (chain B) in PDB entry 6AHU
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 LEU 335 (chain B).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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304B MET* 3.8 18.6 - - + -
305B LEU 4.4 11.2 - - - +
306B GLY* 4.5 14.4 - - - -
307B PRO* 5.5 2.2 - - + -
331B LEU* 4.3 2.7 - - + -
332B HIS* 2.8 26.0 + - + +
334B THR* 1.3 91.8 + - - +
336B LYS* 1.3 55.5 + - - +
337B GLN 3.3 1.3 - - - -
338B ASP* 3.4 26.2 - - + +
339B ILE* 2.6 50.9 + - + +
659B VAL 5.1 7.4 - - - +
663B PHE* 5.1 4.5 - - + -
665B ASP* 4.8 2.9 - - - +
667B PRO* 4.8 1.3 - - + -
668B ALA* 3.8 19.3 - - + -
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Residues in contact with LYS 336 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
251B CYS* 4.3 19.5 - - + -
331B LEU* 3.8 15.7 - - + -
332B HIS 3.1 2.4 + - - -
333B PRO* 3.4 27.6 - - + +
334B THR 3.3 1.4 - - - -
335B LEU* 1.3 77.4 - - - +
337B GLN* 1.3 63.7 + - + +
338B ASP 3.6 0.2 + - - -
340B LEU* 3.3 40.0 + - + +
398B LYS* 5.9 2.8 - - - +
409B LEU* 5.7 8.7 - - + +
424B ASP* 5.4 1.3 - - - +
426B THR* 4.6 19.4 - - + +
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Residues in contact with GLN 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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333B PRO 4.4 2.7 + - - +
334B THR 4.3 6.1 + - - +
335B LEU 3.3 0.2 - - - -
336B LYS* 1.3 83.5 - - + +
338B ASP* 1.3 63.9 + - - +
341B GLU* 3.2 50.4 + - - +
671B LEU* 6.1 1.4 - - - +
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Residues in contact with ASP 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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304B MET* 4.0 10.6 - - + +
334B THR 3.3 19.6 - - - +
335B LEU* 3.0 25.3 + - + +
337B GLN* 1.3 86.7 - - - +
339B ILE* 1.3 64.7 + - - +
341B GLU* 4.1 1.8 - - - +
342B GLU* 3.3 23.0 + - - +
667B PRO* 3.3 41.7 - - + +
668B ALA* 4.3 0.7 + - - +
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Residues in contact with ILE 339 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
253B LEU* 3.9 11.2 - - + -
294B LEU* 4.0 28.0 - - + -
295B TYR 5.9 0.7 - - - +
304B MET* 3.8 24.0 - - + -
306B GLY* 5.5 3.6 - - - -
308B VAL* 5.4 3.4 - - + -
329B ILE* 4.1 11.0 - - + -
331B LEU* 3.8 31.2 - - + -
335B LEU* 2.6 38.8 + - + +
336B LYS 5.2 0.2 - - - +
338B ASP* 1.3 70.9 - - - +
340B LEU* 1.3 59.6 + - - +
342B GLU* 3.0 8.7 + - + +
343B ILE* 2.9 40.3 + - + +
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Residues in contact with LEU 340 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
253B LEU* 3.8 25.2 - - + +
331B LEU* 5.6 0.2 - - - +
336B LYS* 3.3 30.4 + - + +
338B ASP 3.5 0.2 - - - -
339B ILE* 1.3 78.3 - - - +
341B GLU* 1.3 63.5 + - + +
343B ILE* 4.5 2.1 - - + +
344B LYS* 3.3 25.3 + - + +
409B LEU* 4.6 15.3 - - + -
411B TYR* 4.4 11.7 - - + -
422B ILE* 4.4 16.6 - - + +
424B ASP* 3.3 41.3 - - + +
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Residues in contact with GLU 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 GLN* 3.2 45.2 + - - +
338B ASP 4.1 2.0 - - - +
339B ILE 3.3 0.4 - - - -
340B LEU* 1.3 79.9 - - + +
342B GLU* 1.3 58.0 + - - +
344B LYS* 4.1 10.6 - - + +
345B ALA* 3.4 21.7 + - - +
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Residues in contact with GLU 342 (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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269B MET* 3.3 30.3 - - - +
295B TYR 4.2 12.6 - - - +
296B ARG* 4.3 14.4 - - + -
297B VAL* 4.0 16.0 - - + +
304B MET* 5.4 8.3 - - + -
338B ASP 3.3 18.5 + - - +
339B ILE* 3.0 10.7 + - + +
341B GLU* 1.3 77.6 - - - +
343B ILE* 1.3 64.2 + - - +
344B LYS 3.2 1.6 - - - -
345B ALA* 3.0 5.9 + - + +
346B ALA* 2.7 55.3 + - - +
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Residues in contact with ILE 343 (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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253B LEU* 4.8 9.6 - - + -
255B LEU* 4.2 31.4 - - + -
266B LEU* 4.1 15.5 - - + -
269B MET* 4.0 19.3 - - + -
294B LEU* 5.5 1.6 - - + -
329B ILE* 5.7 5.6 - - + -
339B ILE* 2.9 34.3 + - + +
340B LEU* 4.5 4.0 - - + +
342B GLU* 1.3 91.0 - - - +
344B LYS* 1.3 63.8 + - - +
346B ALA* 4.3 3.8 - - + +
347B CYS* 3.3 37.9 + - - +
348B GLN 4.7 0.2 + - - -
422B ILE* 3.9 13.7 - - + +
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Residues in contact with LYS 344 (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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340B LEU* 3.3 19.3 + - + +
341B GLU* 4.2 10.8 - - + +
343B ILE* 1.3 79.9 - - - +
345B ALA* 1.3 58.2 + - - +
348B GLN 2.9 29.1 - - - +
349B CYS* 4.1 3.3 - - - -
350B VAL 5.0 10.8 - - - +
411B TYR* 3.4 49.6 - - + +
413B TRP* 4.5 13.1 - - - -
422B ILE* 4.1 10.6 - - + +
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Residues in contact with ALA 345 (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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297B VAL* 6.1 0.9 - - - -
341B GLU 3.4 18.0 + - - +
342B GLU* 3.0 7.9 + - + +
344B LYS* 1.3 79.7 - - - +
346B ALA* 1.3 61.6 + - - +
348B GLN* 5.0 1.1 + - - -
349B CYS* 4.1 21.5 - - - -
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Residues in contact with ALA 346 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
265B ALA* 4.3 21.0 - - - +
266B LEU* 5.5 0.4 - - + -
269B MET* 5.7 1.1 - - - -
297B VAL* 4.9 14.6 - - + -
342B GLU* 2.7 37.4 + - - +
343B ILE* 4.4 6.3 - - + +
344B LYS 3.5 0.4 - - - -
345B ALA* 1.3 74.9 - - - +
347B CYS* 1.3 69.8 + - - +
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Residues in contact with CYS 347 (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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255B LEU* 5.6 2.2 - - - -
262B ILE* 6.5 0.2 - - - -
265B ALA* 3.7 26.0 - - - +
266B LEU* 4.4 13.0 - - - -
343B ILE* 3.3 31.5 + - - +
346B ALA* 1.3 84.1 - - - +
348B GLN* 1.3 79.6 + - + +
418B THR* 4.6 3.3 - - - +
420B ILE* 3.8 35.4 - - + -
422B ILE* 5.2 4.3 - - + -
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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