Contacts of the helix formed by residues 336 - 349 (chain L) in PDB entry 6PSS
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 GLU 336 (chain L).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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286L LEU* 4.0 24.5 - - + +
290L LEU* 3.5 31.5 - - + +
332L ASP 4.9 2.9 - - - +
333L VAL* 3.6 19.4 + - + -
334L SER 3.3 0.4 - - - -
335L GLU* 1.3 91.0 - - - +
337L VAL* 1.3 61.2 + - + +
339L ARG* 3.2 25.3 + - - +
340L ALA* 3.6 3.3 + - - +
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Residues in contact with VAL 337 (chain L).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
286L LEU* 4.6 11.7 - - + +
287L ILE* 3.9 26.2 - - + +
290L LEU* 5.6 0.2 - - + -
291L CYS* 6.0 0.4 - - - -
315L TRP* 4.0 17.9 - - + -
316L PHE* 3.7 20.4 - - + -
333L VAL* 3.3 35.9 + - + +
334L SER 4.3 0.4 - - - -
336L GLU* 1.3 77.1 - - + +
338L HIS* 1.3 54.1 + - - +
339L ARG 3.2 1.3 - - - -
340L ALA* 3.1 21.8 - - + +
341L LEU* 2.5 37.4 + - + +
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Residues in contact with HIS 338 (chain L).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
313L ASP* 4.2 7.2 + - - -
317L ASN* 4.7 5.8 - - - -
334L SER 3.4 19.7 + - - +
335L GLU* 4.0 9.2 - - - +
336L GLU 3.2 1.0 - - - -
337L VAL* 1.3 77.6 - - - +
339L ARG* 1.3 61.8 + - - +
341L LEU* 3.4 31.1 + - + +
342L GLN* 3.5 36.7 + - + +
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Residues in contact with ARG 339 (chain L).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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286L LEU* 6.1 1.3 - - + -
335L GLU* 3.9 16.6 - - - +
336L GLU* 3.2 9.8 + - - +
337L VAL 3.2 0.2 - - - -
338L HIS* 1.3 80.0 - - - +
340L ALA* 1.3 56.3 + - - +
342L GLN* 3.8 2.8 + - - +
343L LYS* 3.2 51.3 + - - +
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Residues in contact with ALA 340 (chain L).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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283L GLN* 3.3 30.7 - - + +
286L LEU* 3.9 14.8 - - + +
287L ILE* 5.5 3.1 - - + -
315L TRP* 5.9 0.7 - - - -
336L GLU 3.6 1.0 + - - -
337L VAL* 3.0 28.4 + - + +
339L ARG* 1.3 76.4 - - - +
341L LEU* 1.3 59.7 + - - +
342L GLN 3.3 1.3 - - - -
343L LYS* 4.1 3.6 - - - +
344L LEU* 3.2 33.1 + - + +
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Residues in contact with LEU 341 (chain L).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
311L THR 5.4 1.6 - - - +
312L SER 3.6 15.7 - - - +
313L ASP* 3.3 36.1 - - + +
315L TRP* 4.0 23.8 - - + +
316L PHE* 5.1 2.2 - - + -
317L ASN* 3.2 36.8 - - - +
337L VAL* 2.5 22.6 + - + +
338L HIS* 3.6 21.5 - - + +
339L ARG 3.3 0.6 - - - -
340L ALA* 1.3 76.9 - - - +
342L GLN* 1.3 75.3 + - - +
344L LEU* 4.5 4.8 - - + +
345L GLN* 3.9 20.8 + - - +
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Residues in contact with GLN 342 (chain L).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
313L ASP* 3.8 11.5 + - - +
338L HIS* 3.5 31.0 + - + +
339L ARG* 3.8 3.1 + - - +
341L LEU* 1.3 95.1 + - - +
343L LYS* 1.3 72.5 + - - +
344L LEU 3.2 2.0 - - - -
345L GLN* 3.0 8.7 + - - +
346L GLN* 2.7 33.8 + - - +
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Residues in contact with LYS 343 (chain L).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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279L ARG* 3.0 42.0 + - - +
283L GLN* 5.5 8.1 - - - +
339L ARG* 3.2 37.7 + - + +
340L ALA* 4.7 2.9 - - - -
342L GLN* 1.3 96.1 - - - +
344L LEU* 1.3 63.6 + - - +
346L GLN* 3.7 27.2 + - - +
347L ILE* 3.3 15.7 + - - +
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Residues in contact with LEU 344 (chain L).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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280L VAL* 6.0 2.0 - - + -
283L GLN* 5.1 16.2 - - + +
287L ILE* 5.2 7.0 - - + -
306L PHE* 4.5 17.7 - - + -
310L GLU 3.3 27.8 - - - +
311L THR 3.6 14.6 - - - +
312L SER 5.7 0.4 - - - +
315L TRP* 5.3 5.6 - - + +
340L ALA* 3.2 22.1 + - - +
341L LEU* 4.6 7.4 - - + +
342L GLN 3.2 0.2 - - - -
343L LYS* 1.3 79.0 - - - +
345L GLN* 1.3 62.0 + - + +
347L ILE* 3.1 26.5 + - - +
348L GLU* 3.2 26.3 + - - +
355L ILE* 3.3 29.4 - - + +
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Residues in contact with GLN 345 (chain L).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
311L THR* 2.7 30.1 + - - +
312L SER* 3.6 14.1 - - - +
313L ASP* 3.9 11.1 + - - -
341L LEU 3.9 8.9 + - - +
342L GLN* 3.0 11.1 + - - +
344L LEU* 1.3 80.1 - - + +
346L GLN* 1.3 59.5 + - - +
347L ILE 3.3 0.2 - - - -
348L GLU* 3.2 29.3 + - - +
349L GLU* 2.9 28.1 + - - +
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Residues in contact with GLN 346 (chain L).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
279L ARG* 3.6 23.7 - - - +
342L GLN 2.7 18.8 + - - +
343L LYS* 3.6 33.4 + - + +
344L LEU 3.2 0.4 - - - -
345L GLN* 1.3 73.0 - - - +
347L ILE* 1.3 58.2 - - - +
349L GLU* 3.0 21.3 + - + +
350L GLU* 3.1 35.7 + - - +
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Residues in contact with ILE 347 (chain L).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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137L TYR* 5.5 3.8 - - - +
276L MET* 3.8 29.6 - - + +
279L ARG* 3.6 26.7 - - + +
280L VAL* 3.7 32.1 - - + +
283L GLN* 5.2 2.9 - - + -
343L LYS 3.3 19.5 + - - +
344L LEU* 3.1 13.2 + - - +
346L GLN* 1.3 74.6 - - - +
348L GLU* 1.3 56.3 + - - +
350L GLU* 2.8 24.5 + - + +
351L THR* 3.2 16.1 + - + +
355L ILE* 3.7 16.2 - - + -
358L VAL* 4.9 14.4 - - + -
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Residues in contact with GLU 348 (chain L).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
311L THR* 3.4 30.5 - - - +
344L LEU* 3.2 13.6 + - - +
345L GLN* 3.2 33.4 + - - +
347L ILE* 1.3 75.5 - - - +
349L GLU* 1.3 60.8 + - - +
350L GLU 3.1 1.0 + - - -
351L THR* 3.7 8.5 - - - -
352L GLY* 3.8 17.3 + - - -
353L LEU 3.7 16.4 - - - +
354L THR* 4.1 5.9 - - - +
355L ILE* 3.3 35.8 - - + +
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Residues in contact with GLU 349 (chain L).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
139L GLU* 4.5 1.7 - - - +
345L GLN 2.9 13.9 + - - +
346L GLN* 3.0 15.3 + - + +
348L GLU* 1.3 76.1 - - - +
350L GLU* 1.3 61.9 + - + +
351L THR 3.7 0.9 - - - -
352L GLY 5.1 1.1 - - - -
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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