Contacts of the strand formed by residues 258 - 263 (chain K) 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 ILE 258 (chain K).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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217K SER* 4.6 4.0 + - - -
218K MET* 3.0 23.7 - - + +
232K ILE* 4.2 23.4 - - + +
233K GLY 5.4 5.4 + - - +
234K GLN* 4.5 0.6 + - - -
237K ILE* 4.7 6.7 - - + -
253K ILE* 4.4 27.4 - - + -
256K SER 3.5 4.6 + - - +
257K THR* 1.3 85.7 - - - +
259K VAL* 1.3 61.2 + - - +
260K CYS 3.6 14.4 - - - +
273K LEU* 4.0 38.4 - - + -
274K GLY 3.5 12.8 - - - +
275K ASP* 3.9 9.6 - - + +
281K PHE* 4.8 9.4 - - + -
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Residues in contact with VAL 259 (chain K).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
218K MET* 3.6 17.3 - - - +
257K THR* 3.5 4.0 - - + +
258K ILE* 1.3 79.5 - - - +
260K CYS* 1.3 65.0 + - - +
274K GLY 2.9 10.3 + - - +
275K ASP 4.0 13.9 - - - -
276K MET* 3.4 44.0 - - + +
310K ILE* 5.5 2.0 - - + -
311K ALA 3.7 21.3 - - - +
312K GLU* 4.7 4.2 - - - +
80L ARG* 5.7 4.5 - - - +
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Residues in contact with CYS 260 (chain K).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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218K MET* 3.8 4.0 - - - +
258K ILE* 3.6 7.2 - - - +
259K VAL* 1.3 81.2 - - - +
261K HIS* 1.3 64.4 + - - +
273K LEU* 3.6 3.5 - - - -
274K GLY* 3.0 41.2 + - - +
311K ALA* 3.4 39.7 - - - -
312K GLU 3.5 19.5 - - - +
313K CYS* 4.1 5.6 - - - -
314K LEU* 4.1 11.2 - - - +
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Residues in contact with HIS 261 (chain K).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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168K LYS* 5.7 8.3 - - + -
218K MET* 4.2 27.0 - - + +
219K VAL 4.3 8.3 + - - -
220K ILE* 3.4 42.7 - - + +
232K ILE* 6.0 0.9 - - + -
260K CYS* 1.3 78.7 - - - +
262K ASN* 1.3 68.1 + - - +
271K TYR* 5.0 2.7 - - + -
272K LEU 3.3 8.1 - - - -
273K LEU* 3.5 20.2 - - + -
314K LEU* 4.2 9.3 + - - +
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Residues in contact with ASN 262 (chain K).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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20K THR* 5.4 2.6 + - - -
261K HIS* 1.3 80.7 + - - +
263K ARG* 1.3 80.7 + - - +
264K VAL* 4.3 0.5 - - - +
271K TYR* 3.1 11.1 - - - -
272K LEU* 2.8 38.0 + - + +
314K LEU* 3.2 34.7 + - + +
315K THR* 3.6 13.3 - - - +
316K TYR* 2.7 31.8 + - - +
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Residues in contact with ARG 263 (chain K).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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168K LYS* 5.8 2.2 - - - +
171K TYR* 2.6 38.5 + - - -
221K ALA 5.0 1.2 + - - -
223K PRO* 4.4 9.8 - - - +
261K HIS* 5.4 0.2 + - - -
262K ASN* 1.3 88.9 + - - +
264K VAL* 1.3 62.3 + - - +
265K ASP 3.2 24.5 + - - +
266K PRO* 4.3 17.4 + - - +
268K GLY* 4.2 2.2 - - - -
271K TYR* 3.4 37.6 + - + +
316K TYR* 4.3 4.0 - - - +
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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