Contacts of the helix formed by residues 275 - 293 (chain C) in PDB entry 3A0B
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 275 (chain C).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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271C TYR* 3.1 13.8 + - - +
272C LEU 3.8 0.9 - - - -
273C SER 3.1 0.4 - - - -
274C TYR* 1.3 76.3 - - - +
276C LEU* 1.3 62.6 + - - +
278C ALA* 3.7 10.4 - - - +
279C LEU* 4.0 4.7 - - - +
1031C CLA 2.9 49.5 + - - +
1033C CLA 3.1 49.5 + - - +
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Residues in contact with LEU 276 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
272C LEU* 2.8 23.8 + - + +
273C SER* 2.4 24.5 + - - +
275C SER* 1.3 65.2 - - - +
277C GLY* 1.3 68.8 + - - +
278C ALA 2.4 17.3 + - - -
279C LEU* 2.6 27.5 + - - +
280C SER 3.4 2.3 + - - -
437C PHE* 3.2 41.7 - - + +
440C GLY 3.8 19.5 - - - +
441C HIS* 3.5 10.8 - - + +
444C HIS* 4.0 17.7 - - + -
1032C CLA 4.1 30.1 - - + -
1033C CLA 4.8 2.9 - - - -
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Residues in contact with GLY 277 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
273C SER 3.0 9.3 + - - -
274C TYR 5.3 0.2 - - - -
276C LEU* 1.3 78.8 - - - +
278C ALA* 1.3 62.1 + - - +
280C SER* 3.9 11.6 - - - -
281C MET* 3.6 11.8 + - - +
438C LEU* 4.9 2.0 - - - +
441C HIS* 3.4 31.3 - - - +
1029C CLA 3.5 23.4 - - - +
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Residues in contact with ALA 278 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
274C TYR 4.4 1.0 + - - -
275C SER* 3.7 16.4 - - - +
276C LEU 2.4 6.1 + - - +
277C GLY* 1.3 75.0 - - - +
279C LEU* 1.3 54.7 + - - +
281C MET* 2.7 34.9 + - - +
282C MET* 3.0 24.5 + - + +
1025C CLA 3.6 25.1 - - + -
1029C CLA 4.2 4.6 - - - +
1031C CLA 4.1 17.0 - - + -
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Residues in contact with LEU 279 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
275C SER 4.0 9.0 - - - +
276C LEU* 2.6 15.0 + - - +
278C ALA* 1.3 73.3 - - - +
280C SER* 1.3 56.5 + - - +
282C MET* 2.7 27.6 + - + +
283C GLY 2.7 32.6 + - - -
437C PHE* 4.0 21.1 - - + -
1026C CLA 3.4 36.4 - - + +
1031C CLA 4.4 9.6 - - + +
1033C CLA 3.9 44.2 - - + +
1034C CLA 4.5 8.7 - - + -
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Residues in contact with SER 280 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
276C LEU 3.4 3.0 + - - -
277C GLY* 3.9 13.2 - - - -
278C ALA 3.1 0.8 + - - -
279C LEU* 1.3 78.9 - - - +
281C MET* 1.3 57.3 + - - +
283C GLY 3.2 6.4 + - - -
284C PHE* 2.8 29.6 - - - -
434C ALA* 2.3 35.8 + - - +
437C PHE* 3.7 10.8 - - - +
438C LEU* 2.8 41.1 + - - +
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Residues in contact with MET 281 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
223C TRP* 5.6 7.6 - - + -
277C GLY 3.6 8.4 + - - +
278C ALA* 2.7 18.9 + - - +
280C SER* 1.3 75.0 - - - +
282C MET* 1.3 48.3 + - - +
284C PHE* 3.6 8.9 + - - +
285C ILE* 2.7 42.5 + - + +
438C LEU* 5.6 0.8 - - - +
1025C CLA 4.1 31.4 - - + -
1029C CLA 4.5 16.4 - - + -
1030C CLA 3.4 50.7 - - + -
1054C BCR 4.7 6.3 - - + -
1055C DGD 5.6 0.2 - - - +
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Residues in contact with MET 282 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
278C ALA* 3.0 47.2 + - + +
279C LEU* 2.7 25.3 + - + +
281C MET* 1.3 74.4 - - - +
283C GLY* 1.3 52.1 + - - +
284C PHE 3.1 1.8 - - - -
285C ILE* 3.1 7.6 - - - +
286C ALA* 2.6 38.6 + - - +
1025C CLA 3.3 47.6 - - + -
1026C CLA 3.4 36.6 - - + +
1031C CLA 4.2 23.6 - - + +
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Residues in contact with GLY 283 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
279C LEU 2.7 14.5 + - - -
280C SER 3.2 0.4 + - - -
282C MET* 1.3 71.4 - - - +
284C PHE* 1.3 53.1 + - - +
286C ALA* 2.8 7.5 - - - +
287C THR* 2.5 41.1 + - - -
430C HIS* 4.2 4.2 - - - +
434C ALA* 3.2 23.1 - - - -
1026C CLA 3.5 16.1 - - - +
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Residues in contact with PHE 284 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
280C SER* 2.8 28.3 + - - -
281C MET* 3.7 8.5 - - - +
282C MET 3.1 0.6 - - - -
283C GLY* 1.3 73.0 - - - +
285C ILE* 1.3 55.6 + - - +
286C ALA 2.4 16.1 + - - -
287C THR* 3.0 11.7 + - - -
288C CYS* 3.1 16.0 + - - -
431C PHE* 3.5 44.0 - + - -
434C ALA* 3.3 20.1 - - + +
435C PHE* 3.5 30.1 - + + -
438C LEU* 4.5 14.6 - - + -
1055C DGD 3.4 52.3 - - + -
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Residues in contact with ILE 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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223C TRP* 5.2 6.7 - - + -
224C ILE* 3.2 39.0 - - + -
225C VAL* 4.9 0.4 - - + +
281C MET* 2.7 29.8 + - + +
282C MET* 3.1 20.9 - - - +
284C PHE* 1.3 73.7 - - - +
286C ALA* 1.3 57.6 + - - +
288C CYS* 4.3 2.5 - - - +
289C PHE* 3.3 22.3 + - + -
1025C CLA 3.2 44.8 - - + +
1055C DGD 3.9 25.4 - - + +
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Residues in contact with ALA 286 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
282C MET 2.6 17.0 + - - +
283C GLY* 2.8 13.0 - - - +
284C PHE 2.4 5.1 + - - -
285C ILE* 1.3 75.1 - - - +
287C THR* 1.3 51.1 + - - +
288C CYS 2.4 17.3 + - - -
289C PHE* 2.5 23.1 + - - +
290C VAL* 3.5 4.0 + - - +
297C TYR* 5.0 0.5 + - - -
430C HIS* 4.0 9.6 - - + -
1025C CLA 4.3 9.8 - - - +
1026C CLA 3.3 32.3 - - + +
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Residues in contact with THR 287 (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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295A PHE* 3.6 23.3 - - + -
283C GLY 2.5 16.1 + - - -
284C PHE* 3.0 6.0 + - - -
286C ALA* 1.3 69.7 - - - +
288C CYS* 1.3 60.4 + - - +
290C VAL* 3.0 26.3 - - - +
291C TRP* 3.3 8.8 + - - +
426C LEU 4.5 0.2 - - - -
427C ALA* 2.7 42.1 + - + +
430C HIS* 3.0 22.9 - - - +
431C PHE* 3.1 15.0 + - + -
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Residues in contact with CYS 288 (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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163A ILE* 4.9 11.7 - - - -
295A PHE* 5.7 5.4 - - - -
225C VAL* 3.9 9.0 - - + -
284C PHE* 3.4 14.4 - - - +
285C ILE 4.5 0.7 - - - -
286C ALA 2.4 5.7 + - - -
287C THR* 1.3 77.9 - - - +
289C PHE* 1.3 65.7 + - - +
291C TRP* 3.0 7.3 + - - +
292C PHE* 2.9 32.7 + - + +
1055C DGD 2.8 55.2 - - + -
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Residues in contact with PHE 289 (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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224C ILE* 3.0 50.3 - - + -
225C VAL* 3.6 15.9 - - + -
227C VAL* 4.1 0.9 - - + -
285C ILE* 3.3 20.0 - - + -
286C ALA 2.5 14.8 + - - +
288C CYS* 1.3 75.4 - - - +
290C VAL* 1.3 55.3 + - - +
293C ASN* 2.8 71.5 + - + +
296C VAL* 3.7 6.5 - - + -
297C TYR* 3.2 3.6 - - + -
1025C CLA 3.0 68.9 - + + +
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Residues in contact with VAL 290 (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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286C ALA 3.5 1.5 + - - +
287C THR* 3.0 30.5 - - - +
289C PHE* 1.3 76.0 - - - +
291C TRP* 1.3 59.9 + - - +
297C TYR* 3.4 26.6 - - + -
302C TYR* 5.8 1.6 - - + -
423C ARG* 3.0 60.8 + - + +
426C LEU* 3.6 26.2 - - + -
427C ALA* 3.7 19.1 - - - +
1026C CLA 4.3 4.5 - - - -
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Residues in contact with TRP 291 (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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163A ILE 4.1 0.9 - - - -
164A GLY 2.5 33.2 + - - -
165A GLN* 5.5 0.4 - - - -
294A ALA 4.1 0.2 - - - -
295A PHE* 2.9 65.4 - + + -
296A ASN* 3.9 8.1 - - - -
287C THR 3.4 14.8 - - - +
288C CYS* 3.0 6.0 + - - +
290C VAL* 1.3 83.0 - - - +
292C PHE* 1.3 82.2 + + + +
305C THR* 2.7 23.8 + - - -
306C GLY* 4.0 13.9 + - - -
307C PRO* 4.5 2.7 - - + +
400C PRO* 3.5 29.2 - - + -
423C ARG* 3.4 25.3 + - + -
424C SER* 3.7 9.4 - - - -
427C ALA* 3.8 6.3 - - + -
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Residues in contact with PHE 292 (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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91A LEU* 4.4 2.9 - - + -
163A ILE* 3.2 40.8 - - + -
164A GLY 4.8 1.3 - - - -
165A GLN 5.4 1.1 - - - -
295A PHE* 5.9 0.2 - + - -
225C VAL* 3.5 15.9 - - + -
288C CYS* 2.9 22.9 + - + -
291C TRP* 1.3 103.0 - + + +
293C ASN* 1.3 68.0 + - - +
305C THR* 3.2 11.9 + - - -
307C PRO* 4.3 24.0 - - + -
358C PHE* 5.6 2.5 - + - -
423C ARG* 4.5 0.2 - - - -
1055C DGD 2.9 80.0 + - - +
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Residues in contact with ASN 293 (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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225C VAL* 3.6 11.2 + - - +
227C VAL* 3.0 22.8 - - - +
289C PHE* 2.8 61.0 + - + +
292C PHE* 1.3 73.0 - - - +
294C ASN* 1.3 57.2 + - - +
295C THR* 2.5 38.9 + - - -
296C VAL* 3.1 14.5 + - - +
297C TYR* 3.5 8.8 - - + +
423C ARG* 2.6 31.5 + - - -
1055C DGD 4.1 6.6 - - - -
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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
------------------------------------------------------------
Atomic class I II III IV V VI VII VIII
------------------------------------------------------------
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