Contacts of the helix formed by residues 250 - 264 (chain C) in PDB entry 1RR8
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 SER 250 (chain C).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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248C LYS 4.1 0.4 + - - -
249C LEU* 1.3 72.1 - - - +
251C PRO* 1.4 74.8 - - - +
252C LYS* 4.2 3.9 + - - +
253C ALA* 3.1 11.1 + - - +
254C GLU* 2.9 19.6 + - - +
285C GLU 4.3 2.9 + - - -
287C THR* 3.9 19.4 - - - +
290C GLU* 2.8 32.4 + - - -
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Residues in contact with PRO 251 (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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231C TYR* 4.1 13.0 - - + -
249C LEU 3.8 1.7 - - - +
250C SER* 1.4 84.0 - - - -
252C LYS* 1.3 55.2 + - - +
254C GLU* 3.8 8.6 - - + +
255C GLU* 3.0 31.4 + - - +
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Residues in contact with LYS 252 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
250C SER* 3.3 4.6 + - - +
251C PRO* 1.3 76.7 - - - +
253C ALA* 1.3 61.2 + - - +
255C GLU* 3.3 18.3 + - - +
256C VAL* 3.4 20.1 + - - +
284C LYS 5.5 0.7 - - - +
285C GLU* 3.5 45.0 + - + +
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Residues in contact with ALA 253 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
249C LEU* 4.4 8.3 - - + -
250C SER* 3.1 18.4 + - - +
252C LYS* 1.3 75.3 - - - +
254C GLU* 1.3 60.1 + - - +
256C VAL 3.3 1.0 + - - -
257C ALA* 3.0 16.9 + - - +
282C TRP* 2.9 36.5 + - - +
285C GLU* 3.3 14.0 + - - +
286C MET* 4.1 9.2 - - + -
290C GLU* 3.8 16.8 - - - +
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Residues in contact with GLU 254 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
231C TYR* 2.9 24.6 + - - +
233C PRO* 4.1 3.6 - - - +
234C LEU* 3.2 45.3 + - + +
249C LEU* 3.4 38.9 + - + +
250C SER 2.9 16.5 + - - +
251C PRO* 3.8 8.0 - - - +
253C ALA* 1.3 74.2 - - - +
255C GLU* 1.3 61.5 + - - +
257C ALA* 3.6 2.4 + - - +
258C THR* 3.0 30.5 + - - +
305C MET* 4.4 0.8 - - + +
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Residues in contact with GLU 255 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
231C TYR* 3.8 39.7 - - + +
251C PRO 3.0 18.3 + - - +
252C LYS* 3.6 11.0 - - - +
253C ALA 3.2 0.2 - - - -
254C GLU* 1.3 76.9 - - - +
256C VAL* 1.3 62.6 + - + +
258C THR* 2.6 22.7 + - - -
259C PHE* 3.6 22.0 - - + -
358C PRO* 3.8 9.9 - - - +
376C ARG* 2.7 38.8 + - - +
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Residues in contact with VAL 256 (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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252C LYS 3.4 15.0 - - - +
253C ALA 3.3 2.1 + - - +
255C GLU* 1.3 76.7 - - + +
257C ALA* 1.3 62.3 + - - +
259C PHE* 3.3 26.1 + - + +
260C PHE 3.7 0.2 + - - -
278C PHE* 3.6 30.6 - - + +
282C TRP* 3.7 28.3 - - + +
285C GLU* 3.9 15.0 - - + -
360C LEU* 4.7 0.9 - - + -
373C LEU* 3.9 41.7 - - + -
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Residues in contact with ALA 257 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
249C LEU* 4.0 11.4 - - + -
253C ALA 3.0 16.6 + - - +
254C GLU 3.8 6.5 - - - +
255C GLU 3.3 0.2 - - - -
256C VAL* 1.3 77.2 - - - +
258C THR* 1.3 55.0 + - - +
260C PHE* 3.4 5.2 + - - +
261C ALA* 3.1 26.0 + - - +
278C PHE* 4.5 4.5 - - - -
282C TRP* 3.9 20.8 - - + +
302C PHE* 3.9 18.1 - - + -
305C MET* 3.8 14.1 - - + -
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Residues in contact with THR 258 (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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231C TYR* 3.4 26.2 - - + +
234C LEU* 4.4 2.5 - - + -
254C GLU 3.0 17.0 - - - +
255C GLU* 2.6 20.3 + - - -
257C ALA* 1.3 76.0 - - - +
259C PHE* 1.3 73.1 + - - +
261C ALA* 3.3 4.4 + - - +
262C LYS* 3.1 34.3 + - - +
305C MET* 3.8 17.9 - - + -
309C PHE* 3.8 24.9 - - + -
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Residues in contact with PHE 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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231C TYR* 6.0 1.6 - + - -
255C GLU* 3.6 34.8 - - + -
256C VAL* 3.3 17.2 + - + +
258C THR* 1.3 83.7 + - - +
260C PHE* 1.3 61.6 + - - +
262C LYS* 3.6 16.7 + - + +
263C MET* 3.4 28.5 + - - +
358C PRO* 3.7 40.4 - - + -
359C GLY* 3.8 18.4 - - - -
360C LEU* 3.8 22.2 - - + +
373C LEU* 3.9 24.9 - - + -
376C ARG* 6.1 0.2 - - - -
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Residues in contact with PHE 260 (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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256C VAL 3.7 1.4 + - - -
257C ALA 3.4 6.7 + - - +
258C THR 3.3 0.2 - - - -
259C PHE* 1.3 77.1 - - - +
261C ALA* 1.3 63.4 + - - +
263C MET* 3.1 5.6 + - - +
264C LEU* 3.0 40.1 + - + -
269C THR* 3.8 26.0 - - + -
274C PHE* 3.7 33.2 - + - -
275C ARG* 4.2 8.5 - - + -
278C PHE* 3.6 46.9 - + + -
297C LEU* 4.1 18.8 - - + -
302C PHE* 3.7 33.9 - + + -
360C LEU* 4.3 4.0 - - - +
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Residues in contact with ALA 261 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
257C ALA 3.1 14.3 + - - +
258C THR* 3.5 11.4 - - - +
260C PHE* 1.3 76.7 - - - +
262C LYS* 1.3 60.2 + - - +
264C LEU* 3.3 14.7 - - - +
302C PHE* 4.3 15.7 - - + -
305C MET* 3.8 28.7 - - + -
306C SER* 3.3 32.0 + - - +
309C PHE* 4.5 3.8 - - + -
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Residues in contact with LYS 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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258C THR* 3.1 25.0 + - - +
259C PHE* 3.8 16.5 - - + +
260C PHE 3.2 0.4 - - - -
261C ALA* 1.3 76.1 - - - +
263C MET* 1.3 62.4 + - + +
265C ASP* 5.0 4.7 + - - +
266C HIS* 5.1 3.8 + - - -
309C PHE* 3.9 50.3 - - + -
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Residues in contact with MET 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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112B C 5.2 13.0 - - - +
259C PHE* 3.4 17.9 + - - +
260C PHE* 3.1 6.5 + - - +
262C LYS* 1.3 77.9 - - + +
264C LEU* 1.3 57.9 + - - +
265C ASP 3.2 3.6 - - - -
266C HIS* 3.0 32.5 + - + +
268C TYR* 3.3 39.5 - - + +
269C THR* 3.3 15.8 - - + +
274C PHE* 4.2 15.0 - - + -
360C LEU* 3.9 32.3 - - + +
362C ARG* 5.3 6.7 - - + -
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Residues in contact with LEU 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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260C PHE* 3.0 39.5 + - + +
261C ALA 3.3 15.5 + - - +
262C LYS 3.4 0.4 - - - -
263C MET* 1.3 75.1 - - - +
265C ASP* 1.3 62.6 + - - +
266C HIS 3.3 1.8 - - - +
269C THR* 3.5 17.8 + - - +
270C THR* 6.0 0.2 - - - +
302C PHE* 4.4 14.1 - - + +
303C THR* 4.4 25.1 - - + +
306C SER* 4.0 24.0 - - - +
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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