Contacts of the helix formed by residues 334 - 343 (chain B) in PDB entry 6YB9
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 GLY 334 (chain B).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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302B ALA* 3.8 7.2 - - - -
303B HIS* 3.7 21.0 + - - -
329B ALA* 4.8 1.2 - - - +
332B SER* 3.2 8.5 + - - -
333B ASN* 1.3 72.3 - - - +
335B LEU* 1.3 58.9 + - - +
336B GLY 3.5 1.1 - - - -
337B PRO* 3.7 7.2 - - - +
338B VAL* 3.0 37.0 + - - +
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Residues in contact with LEU 335 (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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271B LEU* 3.3 38.4 - - + +
273B GLY* 4.1 10.3 - - - +
300B THR* 4.0 26.2 - - + +
302B ALA* 3.7 18.9 - - + +
309B THR* 3.7 28.9 - - + -
327B ALA* 4.1 5.8 - - + -
328B VAL 4.2 12.1 - - - +
329B ALA* 4.2 9.2 - - + -
333B ASN* 3.2 5.5 + - - +
334B GLY* 1.3 73.8 - - - +
336B GLY* 1.3 65.5 + - - +
338B VAL* 4.3 0.2 - - - +
339B MET* 3.1 36.2 + - + +
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Residues in contact with GLY 336 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
327B ALA* 3.5 20.4 - - - +
333B ASN* 3.0 10.3 + - - -
335B LEU* 1.3 77.8 - - - +
337B PRO* 1.3 61.7 - - - +
339B MET* 3.7 1.6 - - - +
340B SER* 2.8 31.4 + - - -
347B VAL* 4.0 2.7 - - - +
349B SER* 3.6 12.1 - - - -
374B CYS* 3.9 9.0 - - - -
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Residues in contact with PRO 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 ASN* 3.5 32.3 - - - +
334B GLY* 3.7 7.2 - - - +
336B GLY* 1.3 88.4 - - - +
338B VAL* 1.3 63.8 + - + +
340B SER* 3.2 5.4 + - - -
341B GLY* 2.9 20.6 + - - -
349B SER* 4.5 1.8 - - - +
364B SER 4.1 2.7 - - - +
365B SER* 5.6 0.9 - - - -
368B LEU* 3.9 24.2 - - + -
369B PRO* 6.1 1.1 - - + -
372B LEU* 3.9 24.1 - - + +
374B CYS* 4.8 4.5 - - + -
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Residues in contact with VAL 338 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
302B ALA* 4.1 20.9 - - + +
306B PRO* 5.5 8.1 - - + -
309B THR* 4.8 10.3 - - + -
310B LEU* 4.4 16.4 - - + -
334B GLY* 3.0 27.2 + - - +
335B LEU* 4.3 2.2 - - - +
337B PRO* 1.3 71.9 - - + +
339B MET* 1.3 63.3 + - - +
341B GLY* 3.2 4.2 + - - -
342B ASN* 2.6 37.6 + - - +
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Residues in contact with MET 339 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
271B LEU* 3.7 24.2 - - + -
309B THR* 3.9 23.1 - - + +
310B LEU* 5.8 1.6 - - - -
313B LYS* 3.8 36.7 - - + +
325B PHE* 3.6 44.6 - - + -
327B ALA* 5.6 1.1 - - + -
335B LEU* 3.1 26.8 + - + +
336B GLY 3.7 2.9 - - - +
338B VAL* 1.3 74.1 - - - +
340B SER* 1.3 64.1 + - - +
342B ASN* 3.0 15.5 + - - -
343B THR* 3.1 20.4 + - + +
347B VAL* 4.0 15.9 - - + -
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Residues in contact with SER 340 (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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385A GLN* 5.5 2.4 + - - -
389A GLN* 4.6 9.9 + - - +
406A ILE* 5.3 0.9 - - - +
336B GLY 2.8 18.4 + - - -
337B PRO* 3.5 5.8 - - - -
339B MET* 1.3 75.9 - - - +
341B GLY* 1.3 60.7 + - - +
342B ASN 3.4 0.7 + - - -
343B THR 3.4 15.2 - - - +
345B TYR 5.8 0.2 - - - -
347B VAL* 3.8 15.0 - - - +
372B LEU* 4.1 7.1 - - - +
373B GLY 3.6 9.0 + - - -
374B CYS* 3.1 42.6 + - - +
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Residues in contact with GLY 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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406A ILE* 4.0 21.1 - - - +
337B PRO 2.9 13.5 + - - -
338B VAL* 3.2 4.2 + - - -
339B MET 3.1 0.4 - - - -
340B SER* 1.3 74.8 - - - +
342B ASN* 1.3 67.8 + - - +
343B THR 3.8 0.7 - - - -
371B GLY 5.3 2.0 - - - -
372B LEU* 4.1 18.8 - - - +
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Residues in contact with ASN 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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406A ILE* 4.1 15.0 - - - +
410A TRP* 6.1 1.4 - - - -
310B LEU* 4.0 16.6 - - + +
313B LYS* 3.1 35.9 + - + -
317B GLU* 3.4 1.7 - - - +
338B VAL* 2.6 37.6 + - - +
339B MET 3.0 4.4 + - - +
341B GLY* 1.3 85.6 - - - +
343B THR* 1.3 58.5 + - - +
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Residues in contact with THR 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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389A GLN* 4.3 6.6 + - - -
406A ILE* 3.5 11.4 - - - +
313B LYS* 4.1 8.5 - - - -
317B GLU* 2.8 28.4 + - - +
325B PHE* 3.9 13.5 - - + -
339B MET* 3.1 17.5 + - + +
340B SER* 3.4 12.5 - - - +
341B GLY 3.8 0.6 - - - -
342B ASN* 1.3 76.2 - - - +
344B ALA* 1.3 60.4 + - - +
345B TYR* 3.2 32.4 + - - +
347B VAL* 3.8 15.7 - - + -
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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