Contacts of the strand formed by residues 258 - 265 (chain C) in PDB entry 2NRA
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 258 (chain C).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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192C ILE* 5.5 12.5 - - + +
193C ILE* 3.3 9.5 - - - +
194C SER* 3.9 22.8 - - - +
195C VAL 4.5 0.7 - - - +
248C VAL* 3.5 5.2 - - - +
249C HIS* 2.6 44.3 + - + +
250C GLU* 3.1 42.2 + - + +
256C ILE* 5.5 1.1 - - - +
257C SER* 1.3 87.9 + - - +
259C LEU* 1.3 61.1 + - - +
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Residues in contact with LEU 259 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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191C PHE 3.8 0.7 - - - +
192C ILE* 3.4 3.8 - - - +
193C ILE* 2.8 37.6 + - - +
195C VAL* 5.2 8.0 - - + +
198C LEU* 4.3 7.9 - - + -
220C PHE* 4.3 22.2 - - + -
223C PHE* 5.8 0.2 - - + -
228C LEU* 3.9 20.4 - - + -
246C PHE* 3.6 33.2 - - + -
247C THR 3.2 18.6 - - - +
248C VAL* 4.0 14.6 - - + +
249C HIS* 4.1 3.4 - - - -
256C ILE* 5.4 4.0 - - + -
257C SER 6.0 0.4 - - - -
258C LYS* 1.3 77.3 - - - +
260C LYS* 1.3 60.4 + - - +
261C PHE* 3.9 22.3 + - + -
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Residues in contact with LYS 260 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
190C TYR* 4.4 23.3 - - + -
191C PHE 3.5 10.3 - - - +
192C ILE* 4.2 14.1 - - + -
246C PHE* 2.9 5.2 - - - -
247C THR* 2.7 52.9 + - - +
249C HIS* 4.0 22.2 - - + +
259C LEU* 1.3 71.4 - - - +
261C PHE* 1.3 67.3 + - - +
262C GLU* 4.0 6.0 + - - -
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Residues in contact with PHE 261 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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174C LEU* 4.8 17.7 - - + -
177C LEU* 5.9 0.2 - - + -
178C ILE* 5.8 0.4 - - + -
190C TYR* 3.1 5.9 - - - +
191C PHE* 3.0 71.3 + + + -
193C ILE* 3.9 11.9 - - + -
198C LEU* 3.8 35.0 - - + -
228C LEU* 4.4 8.1 - - + -
232C ILE* 4.6 9.9 - - + -
244C VAL* 4.6 13.5 - - + -
245C GLY 3.3 8.7 - - - -
246C PHE* 3.5 29.2 - + + -
259C LEU* 3.9 22.9 - - + -
260C LYS* 1.3 76.7 - - - +
262C GLU* 1.3 62.1 + - - +
263C PHE* 5.0 0.7 - - + -
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Residues in contact with GLU 262 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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188C LYS* 3.2 28.6 - - - +
189C ASN 3.0 20.2 - - - +
190C TYR* 3.7 13.7 - - + +
244C VAL* 3.3 2.9 - - - +
245C GLY 2.8 35.4 + - - +
260C LYS* 4.0 8.2 + - + -
261C PHE* 1.3 74.6 - - - +
263C PHE* 1.3 70.1 + - - +
264C VAL* 4.9 4.9 - - - +
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Residues in contact with PHE 263 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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178C ILE* 3.4 37.9 - - + -
181C HIS 3.1 27.8 - - - -
182C TYR* 4.2 8.5 - - + -
189C ASN* 3.0 59.1 + - + +
190C TYR* 4.1 2.9 - - - -
191C PHE* 4.2 23.6 - + - -
241C ILE* 4.1 6.5 - - + -
243C PHE* 2.9 19.1 - - - +
244C VAL* 4.0 11.9 - - + -
261C PHE 5.0 0.2 - - - -
262C GLU* 1.3 81.4 - - - +
264C VAL* 1.3 61.8 + - - +
265C VAL* 3.8 25.1 - - + -
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Residues in contact with VAL 264 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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187C LYS* 3.8 24.2 - - + +
188C LYS* 4.2 13.5 - - + -
241C ILE* 3.7 3.6 - - - +
242C SER* 3.0 45.6 + - - +
243C PHE* 3.1 27.8 + - + +
262C GLU* 4.9 4.3 - - - +
263C PHE* 1.3 78.0 - - - +
265C VAL* 1.3 69.0 + - - +
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Residues in contact with VAL 265 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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179C ARG* 5.4 1.1 - - - +
182C TYR* 3.5 44.0 - - + +
186C LYS 5.8 1.6 - - - +
187C LYS 4.6 4.8 + - - +
189C ASN* 6.1 0.2 - - - +
240C GLU* 3.8 15.3 - - - +
241C ILE* 3.7 25.8 - - + -
242C SER* 4.2 1.8 - - - +
263C PHE* 3.8 21.1 - - + -
264C VAL* 1.3 84.6 - - - +
266C ASP* 1.3 62.5 + - - +
267C GLU* 3.4 14.4 + - - +
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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