Contacts of the strand formed by residues 291 - 296 (chain L) in PDB entry 6R90
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 VAL 291 (chain L).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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246L THR* 2.5 28.1 + - - +
261L ALA* 3.3 26.9 - - + -
262L SER 2.9 27.6 + - - +
263L VAL* 5.3 0.2 - - - +
266L THR 3.8 12.8 - - - +
267L VAL* 4.5 1.6 - - + -
287L HIS* 3.8 39.0 - - + +
289L HIS 4.3 0.4 - - - +
290L PRO* 1.3 83.0 - - - +
292L ASN* 1.3 56.1 + - - +
293L ALA 4.5 0.9 - - - +
305L THR* 3.9 11.0 - - - +
306L THR 3.3 15.5 - - - +
307L ASP* 4.4 1.3 - - + -
308L GLN* 5.0 0.4 - - - -
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Residues in contact with ASN 292 (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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96J G 5.0 0.8 + - - -
246L THR* 3.2 30.4 - - + +
247L HIS* 3.8 4.2 - - - +
291L VAL* 1.3 73.2 - - - +
293L ALA* 1.3 63.6 + - - +
306L THR* 2.9 5.8 + - + +
307L ASP 2.7 27.5 - - - +
308L GLN* 2.9 36.0 + - - +
333L HIS* 4.3 8.5 - - - +
339L PRO* 4.0 23.8 - - + +
340L ILE* 3.3 26.9 - - - +
341L LYS* 5.6 0.7 - - - +
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Residues in contact with ALA 293 (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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247L HIS* 3.6 19.5 - - + -
261L ALA* 4.3 4.0 - - - -
291L VAL* 3.5 1.1 - - - +
292L ASN* 1.3 84.0 - - - +
294L ALA* 1.3 61.6 + - - +
295L CYS* 4.2 2.0 - - + +
305L THR* 3.5 3.3 + - - -
306L THR* 2.9 43.8 + - + +
341L LYS* 3.8 28.9 - - + -
342L ALA 5.2 1.3 - - - +
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Residues in contact with ALA 294 (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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247L HIS* 3.3 18.6 - - - +
248L VAL* 4.8 1.9 + - - -
249L ALA* 3.9 10.7 + - - +
259L ALA* 4.5 7.7 - - + +
260L THR 4.9 1.8 - - - -
261L ALA* 3.9 9.3 - - + +
267L VAL* 3.6 31.4 - - + -
293L ALA* 1.3 76.1 - - - +
295L CYS* 1.3 59.6 + - - +
303L LEU* 4.1 12.2 - - + +
304L LEU 3.2 10.1 - - - +
305L THR* 3.8 8.1 - - - +
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Residues in contact with CYS 295 (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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163L LYS* 5.7 4.9 - - - -
247L HIS* 3.9 21.1 - - + +
249L ALA* 4.4 6.7 - - - -
293L ALA* 4.2 2.0 - - + -
294L ALA* 1.3 73.5 - - - +
296L PHE* 1.3 76.4 + - - +
303L LEU* 3.4 4.3 - - - -
304L LEU* 3.0 32.3 + - + +
341L LYS* 4.8 19.3 - - - -
342L ALA 5.1 5.2 - - - +
343L ALA* 5.9 2.5 - - - -
344L TRP* 3.2 11.6 + - + -
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Residues in contact with PHE 296 (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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249L ALA* 4.0 17.9 - - + +
250L LEU 3.3 28.0 - - - +
251L ASN* 3.5 24.2 - - + -
252L PRO* 4.6 3.1 - - + -
257L PHE* 3.7 34.3 - + - -
258L LEU 4.8 2.0 - - - -
259L ALA* 4.3 14.1 - - + -
269L ILE* 5.2 4.0 - - + -
294L ALA 4.3 0.4 + - - -
295L CYS* 1.3 85.1 - - - +
297L SER* 1.3 69.8 + - - +
298L PRO* 4.7 0.7 - - - +
300L GLY* 4.5 15.7 - - - -
302L ARG 4.4 1.8 - - - -
303L LEU* 3.7 35.3 - - + +
320L TRP* 4.9 8.7 - + - -
344L TRP* 3.0 15.8 - - - -
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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