Contacts of the helix formed by residues 290 - 296 (chain B) in PDB entry 2R8K
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 CYS 290 (chain B).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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222B PHE* 3.4 30.1 - - + +
223B ASN* 4.2 17.7 - - - -
224B PRO* 5.5 0.7 - - - -
227B ARG* 4.5 5.6 - - - -
286B VAL* 4.0 4.9 - - + -
287B LYS* 2.9 42.1 + - - +
289B ASP* 1.3 83.6 - - - +
291B LEU* 1.3 57.6 + - - +
292B LEU 3.3 2.5 - - - -
293B ASP* 3.2 13.2 + - + +
294B PHE* 2.7 36.2 + - - +
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Residues in contact with LEU 291 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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265B SER* 4.8 3.1 - - - -
266B SER* 4.6 1.1 - - - +
270B VAL* 3.7 30.1 - - + -
286B VAL* 3.7 17.9 - - + +
287B LYS 3.2 2.4 + - - +
288B ASN* 3.3 35.6 + - - +
289B ASP 3.7 0.2 - - - -
290B CYS* 1.3 77.9 - - - +
292B LEU* 1.3 59.7 + - + +
294B PHE* 3.4 0.5 + - - +
295B LEU* 2.8 36.8 + - + +
379B ARG 3.8 11.2 - - - +
380B GLY* 3.6 26.0 - - - +
381B ARG* 3.2 33.9 - - - +
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Residues in contact with LEU 292 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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288B ASN 6.0 0.7 - - - +
289B ASP 5.5 0.2 - - - -
290B CYS 3.3 0.4 - - - -
291B LEU* 1.3 72.3 - - + +
293B ASP* 1.3 72.9 + - - +
294B PHE 3.0 1.8 - - - -
295B LEU* 3.2 4.1 + - + +
296B ASP* 2.9 36.9 + - - +
332B ARG* 3.6 38.4 - - - +
379B ARG* 4.1 24.9 - - + -
381B ARG* 4.8 13.9 - - - +
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Residues in contact with ASP 293 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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222B PHE* 3.5 9.6 - - + -
224B PRO* 3.9 21.3 - - + +
225B GLU* 2.9 22.5 + - - +
227B ARG* 2.8 38.0 + - - -
289B ASP 4.1 1.6 - - - +
290B CYS* 3.2 18.7 + - + +
292B LEU* 1.3 80.7 + - - +
294B PHE* 1.3 57.5 + - - +
296B ASP* 3.8 3.3 - - - -
297B CYS* 3.1 23.0 + - - -
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Residues in contact with PHE 294 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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222B PHE* 3.2 33.8 - + + -
270B VAL* 3.9 20.9 - - + -
273B LEU* 4.0 8.1 - - + -
274B ALA* 3.7 23.8 - - - -
277B TYR* 4.1 18.8 - + + -
284B THR* 5.0 0.9 - - + -
286B VAL* 3.6 30.7 - - + -
290B CYS 2.7 18.3 + - - +
291B LEU 3.5 2.5 - - - +
293B ASP* 1.3 74.2 - - - +
295B LEU* 1.3 85.2 + - + +
296B ASP 3.1 2.2 - - - -
297B CYS* 3.2 24.6 + - - -
300B PHE* 3.5 34.2 - + - -
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Residues in contact with LEU 295 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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270B VAL* 4.4 13.7 - - + -
273B LEU* 4.6 9.9 - - + -
291B LEU* 2.8 28.9 + - + +
292B LEU* 3.9 4.0 - - + +
294B PHE* 1.3 93.2 - - + +
296B ASP* 1.3 62.7 + - - +
297B CYS 3.5 0.4 + - - -
298B GLY 4.9 1.0 + - - -
300B PHE* 4.0 27.7 - - + +
305B PHE* 4.9 9.9 - - + -
328B ILE* 4.2 16.4 - - + +
332B ARG* 4.1 11.7 - - - +
377B LEU 4.4 3.4 - - - +
378B SER* 3.9 23.1 - - - +
379B ARG* 4.1 2.5 - - - -
380B GLY* 3.6 27.8 - - - +
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Residues in contact with ASP 296 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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292B LEU* 2.9 17.9 + - - +
293B ASP* 3.8 4.5 - - - +
295B LEU* 1.3 78.5 - - - +
297B CYS* 1.3 58.3 + - - +
298B GLY* 2.8 15.1 + - - +
326B ASN* 4.8 12.2 + - - +
328B ILE* 4.4 1.7 - - - +
329B LYS* 3.3 36.8 + - + +
332B ARG* 2.6 43.5 + - - -
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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