Contacts of the strand formed by residues 245 - 249 (chain L) in PDB entry 6NR8
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 LYS 245 (chain L).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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244L ALA* 1.3 80.1 - - - +
246L ILE* 1.3 61.8 + - - +
293L THR* 2.5 49.3 + - - -
294L GLY* 2.7 13.7 + - - -
295L CYS* 3.3 11.1 - - + -
296L ASN* 2.9 22.7 + - - +
297L VAL* 3.6 6.5 + - - +
354L ASP* 5.4 6.7 - - - +
356L LEU* 5.7 6.5 - - + +
357L GLY 3.6 12.8 - - - +
358L SER* 4.4 10.5 - - - +
359L ALA* 3.7 12.8 - - - +
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Residues in contact with ILE 246 (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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229L LEU* 5.1 2.5 - - + -
245L LYS* 1.3 74.2 - - - +
247L GLY* 1.3 62.7 + - - +
248L LEU 4.3 0.7 - - - -
295L CYS* 3.6 2.9 - - - -
297L VAL* 3.8 31.4 - - + -
299L LEU* 5.5 0.9 - - + -
336L ILE* 3.7 29.2 - - + -
340L ILE* 3.7 22.2 - - + -
342L THR* 3.9 5.8 - - - +
356L LEU* 3.3 7.3 - - - +
357L GLY* 3.1 48.8 + - - +
359L ALA* 4.3 10.1 - - + -
374L LEU* 4.2 2.0 - - + -
376L ILE* 3.8 30.1 - - + -
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Residues in contact with GLY 247 (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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246L ILE* 1.3 80.2 - - - +
248L LEU* 1.3 60.5 + - - -
249L ILE* 3.8 2.5 - - - -
295L CYS* 3.4 7.4 - - - -
297L VAL* 2.9 22.2 + - - +
298L LEU* 3.4 4.9 - - - -
299L LEU* 3.0 28.3 + - - +
356L LEU* 3.7 15.7 - - - -
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Residues in contact with LEU 248 (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 GLY* 1.3 70.7 - - - -
249L ILE* 1.3 64.9 + - - +
250L GLN* 3.4 29.8 - - + +
299L LEU* 3.7 28.3 - - + +
333L ILE* 3.8 24.0 - - + -
336L ILE* 3.7 26.9 - - + -
337L CYS* 3.7 21.3 - - - -
342L THR* 3.4 26.7 - - + +
343L LYS 3.9 4.7 - - - +
344L PRO* 3.7 23.5 - - + +
356L LEU* 3.9 2.5 - - - +
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Residues in contact with ILE 249 (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 GLY 3.8 2.4 - - - -
248L LEU* 1.3 82.2 - - - +
250L GLN* 1.3 61.0 - - - +
251L PHE* 3.1 57.8 + - + +
252L CYS* 4.9 3.8 - - - -
253L LEU* 5.7 3.8 - - + +
298L LEU* 3.9 39.0 - - + -
299L LEU 2.9 32.5 + - - +
300L ILE* 3.7 19.2 - - + -
301L GLN* 3.8 11.3 + - - +
309L LEU* 5.7 2.7 - - + -
344L PRO* 5.1 0.2 - - - -
345L VAL* 4.8 6.7 - - + -
356L LEU* 4.9 3.6 - - + -
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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