Contacts of the strand formed by residues 236 - 240 (chain G) 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 236 (chain G).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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234G ASN* 3.1 23.6 + - + +
235G PRO* 1.3 70.1 - - - +
237G ILE* 1.3 55.7 + - - +
284G SER 5.2 0.6 + - - -
285G GLY* 3.3 36.1 + - - +
286G ALA* 3.6 6.1 - - - -
287G LYS* 2.7 41.0 + - - +
288G VAL* 2.7 14.8 + - - +
339G ALA* 4.9 11.7 - - - +
342G LEU* 4.5 16.0 - - + +
343G GLY 3.6 2.0 - - - -
344G ARG* 3.9 33.2 - - + +
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Residues in contact with ILE 237 (chain G).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
235G PRO* 3.3 28.3 - - + +
236G LYS* 1.3 72.9 - - - +
238G ALA* 1.3 62.4 + - - +
239G LEU* 3.7 17.9 - - + +
288G VAL* 3.8 10.8 - - + -
290G LEU* 3.7 28.9 - - + -
322G THR* 4.3 7.4 - - + -
326G CYS* 4.0 14.8 - - - -
342G LEU* 3.3 11.3 - - - +
343G GLY* 2.7 40.8 + - - +
344G ARG 4.2 0.7 - - - -
345G CYS* 3.7 30.1 - - - -
361G PHE* 4.7 9.9 - - + -
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Residues in contact with ALA 238 (chain G).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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237G ILE* 1.3 72.5 - - - +
239G LEU* 1.3 60.7 + - - +
240G LEU* 3.3 22.5 + - + +
281G ILE* 3.9 21.8 - - + -
286G ALA* 3.9 13.7 - - + -
288G VAL 2.7 17.8 + - - +
289G VAL* 4.8 3.8 - - + -
290G LEU* 2.9 30.6 + - - +
331G GLN* 4.3 1.8 - - - -
342G LEU* 4.0 3.8 - - + -
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Residues in contact with LEU 239 (chain G).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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237G ILE* 3.7 32.3 - - + +
238G ALA* 1.3 69.9 - - - +
240G LEU* 1.3 65.9 + - - +
241G ASN* 3.7 4.9 - - - +
290G LEU* 3.4 8.3 - - + -
319G LEU* 3.3 51.5 - - + +
322G THR* 3.8 15.7 - - + -
323G MET* 3.7 20.4 - - + +
328G GLY* 4.7 3.4 - - - -
329G SER 3.6 11.2 - - - +
330G ILE* 4.2 1.9 - - - -
331G GLN* 3.1 42.2 + - - +
343G GLY* 4.6 5.6 - - - +
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Residues in contact with LEU 240 (chain G).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
238G ALA* 3.7 25.4 - - + +
239G LEU* 1.3 76.6 - - - +
241G ASN* 1.3 61.7 + - - +
242G VAL* 3.7 6.7 - - + +
244G LEU* 5.1 11.9 - - + -
277G LYS 6.0 1.6 - - - +
278G LEU* 6.5 1.1 - - - -
281G ILE* 4.3 11.4 - - + -
289G VAL* 3.7 27.4 - - + -
290G LEU 2.5 17.8 + - - +
291G SER* 3.3 26.7 - - - +
292G LYS* 4.4 2.8 + - - +
303G PHE* 5.8 2.0 - - + -
319G LEU* 4.3 6.6 - - - +
331G GLN* 3.7 16.4 - - + -
332G THR* 3.7 29.8 - - + +
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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