Contacts of the helix formed by residues 271 - 285 (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 LYS 271 (chain C).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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267C GLU* 4.1 11.0 - - - +
268C TYR* 3.2 30.4 + - + +
270C THR* 1.3 81.2 - - - +
272C GLU* 1.3 66.2 + - - +
273C ILE* 3.4 2.0 - - + +
274C PHE* 3.3 9.0 + - + +
275C ARG* 3.0 25.9 + - - +
362C ARG* 3.7 20.8 - - - +
366C ASN* 6.1 0.8 - - - +
370C MET* 4.5 18.4 - - + +
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Residues in contact with GLU 272 (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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270C THR 3.9 1.6 + - - -
271C LYS* 1.3 70.6 - - - +
273C ILE* 1.3 62.7 + - + +
275C ARG* 3.9 4.7 - - - +
276C LYS* 3.0 42.6 + - - +
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Residues in contact with ILE 273 (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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271C LYS* 3.4 1.9 - - + +
272C GLU* 1.3 79.1 - - + +
274C PHE* 1.3 62.7 + - - +
276C LYS* 3.4 19.3 + - - +
277C ASN* 2.9 33.9 + - - +
366C ASN* 4.7 17.7 - - - +
367C HIS 4.0 3.1 - - - +
368C PRO* 3.3 36.8 - - + +
370C MET* 3.9 18.4 - - + -
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Residues in contact with PHE 274 (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* 3.7 32.5 - + - -
263C MET* 4.2 7.9 - - - -
268C TYR* 3.2 58.1 - + - +
269C THR* 3.8 14.1 - - + -
271C LYS* 3.3 7.0 + - + +
273C ILE* 1.3 79.5 - - - +
275C ARG* 1.3 58.5 + - - +
278C PHE* 2.9 32.4 + - + +
360C LEU* 3.7 23.1 - - + -
361C SER 3.9 8.7 - - - -
362C ARG* 4.9 3.8 - - + -
370C MET* 3.4 31.5 - - + +
371C GLY* 3.7 25.6 - - - -
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Residues in contact with ARG 275 (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* 4.2 12.4 - - + -
269C THR 3.0 35.5 + - - +
270C THR* 3.9 18.5 - - - +
271C LYS 3.0 20.7 + - - +
272C GLU* 4.0 3.8 - - - +
274C PHE* 1.3 76.2 - - + +
276C LYS* 1.3 64.2 + - - +
278C PHE* 4.5 0.7 - - - -
279C PHE* 3.0 28.2 + - - +
297C LEU* 3.7 31.7 + - + +
298C SER* 3.2 39.0 + - - +
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Residues in contact with LYS 276 (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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272C GLU* 3.0 26.6 + - - +
273C ILE* 3.6 22.1 - - - +
275C ARG* 1.3 74.8 - - - +
277C ASN* 1.3 79.6 + - - +
279C PHE* 4.0 2.6 - - - +
280C LYS* 3.0 31.2 + - + +
368C PRO 5.7 0.6 + - - -
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Residues in contact with ASN 277 (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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273C ILE* 2.9 15.6 + - - +
276C LYS* 1.3 92.0 - - - +
278C PHE* 1.3 64.7 + - - +
280C LYS* 3.3 12.1 + - - +
281C ASP* 3.1 28.1 + - - +
368C PRO 2.8 27.1 + - - +
369C LYS* 3.6 4.0 - - - -
370C MET 3.0 26.4 - - - +
371C GLY 3.7 10.3 - - - -
372C MET* 3.9 18.1 - - + +
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Residues in contact with PHE 278 (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* 3.6 38.7 - - + +
257C ALA* 4.5 3.1 - - - -
260C PHE* 3.6 38.8 - + + -
274C PHE* 2.9 21.4 + - + +
275C ARG* 4.0 2.7 - - - +
277C ASN* 1.3 77.0 - - - +
279C PHE* 1.3 59.6 + - - +
281C ASP* 3.4 3.3 + - - +
282C TRP* 2.9 56.1 + + - +
297C LEU* 3.6 32.8 - - + -
302C PHE* 4.5 1.3 - + - -
360C LEU* 3.5 27.4 - - + -
371C GLY* 3.1 15.4 + - - +
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Residues in contact with PHE 279 (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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275C ARG 3.0 19.7 + - - +
276C LYS* 4.1 2.5 - - - +
278C PHE* 1.3 76.6 - - - +
280C LYS* 1.3 65.4 + - - +
282C TRP* 3.3 23.5 + + - +
283C ARG* 3.1 50.2 + - + +
286C MET* 4.4 2.9 - - + -
294C ILE* 3.6 28.5 - - + -
295C THR 3.3 36.6 - - - -
296C ASN* 3.6 14.6 - - - -
297C LEU* 3.8 25.8 - - + -
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Residues in contact with LYS 280 (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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276C LYS* 3.0 23.7 + - + +
277C ASN* 3.3 13.0 + - - +
279C PHE* 1.3 78.7 - - - +
281C ASP* 1.3 62.6 - - - +
283C ARG* 3.4 19.6 - - - +
284C LYS* 3.4 32.9 + - - +
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Residues in contact with ASP 281 (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* 5.3 0.7 - - + -
277C ASN 3.1 13.6 + - - +
278C PHE* 3.9 3.6 - - - +
280C LYS* 1.3 76.1 + - - +
282C TRP* 1.3 62.5 + - - +
284C LYS* 2.9 33.5 + - - +
285C GLU* 3.2 23.8 + - - +
371C GLY 5.2 0.2 - - - +
372C MET* 3.4 32.5 - - - +
373C LEU* 3.3 44.2 + - + +
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Residues in contact with TRP 282 (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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240C PHE* 3.8 8.3 - + - -
249C LEU* 4.2 16.8 - - + -
253C ALA* 2.9 31.4 + - + +
256C VAL* 3.7 29.6 - - + +
257C ALA* 3.9 20.5 - - + +
278C PHE* 2.9 37.6 + + + +
279C PHE* 3.3 24.6 + + - +
281C ASP* 1.3 74.7 - - - +
283C ARG* 1.3 63.9 + - - +
285C GLU* 3.3 8.6 + - - +
286C MET* 3.2 38.7 + - + +
294C ILE* 4.3 2.7 - - + -
297C LEU* 4.0 4.9 - - + -
300C CYS* 3.7 29.2 - - - -
302C PHE* 3.7 24.9 - + - -
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Residues in contact with ARG 283 (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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279C PHE* 3.1 51.5 + - + +
280C LYS* 3.4 12.3 - - - +
281C ASP 3.3 0.2 - - - -
282C TRP* 1.3 77.1 - - - +
284C LYS* 1.3 61.6 + - + +
286C MET* 3.2 23.9 + - - +
291C LYS* 2.6 73.9 + - - +
294C ILE 2.7 25.4 + - - -
295C THR* 4.3 6.9 - - - +
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Residues in contact with LYS 284 (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* 5.5 0.7 - - - +
280C LYS* 3.4 41.5 + - - +
281C ASP* 2.9 31.1 + - - +
282C TRP 3.3 0.4 - - - -
283C ARG* 1.3 77.3 - - + +
285C GLU* 1.3 75.7 + - - +
286C MET 3.2 9.8 + - - +
291C LYS* 5.0 6.2 - - - +
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Residues in contact with GLU 285 (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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250C SER* 4.3 1.4 + - - -
252C LYS* 3.5 42.0 + - + +
253C ALA* 3.3 22.2 + - - +
256C VAL* 3.9 27.8 - - + -
281C ASP 3.2 19.1 + - - +
282C TRP 3.3 10.2 + - - +
283C ARG 3.2 0.8 - - - -
284C LYS* 1.3 92.7 - - - +
286C MET* 1.3 58.6 + - - +
373C LEU* 3.5 15.1 - - + +
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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