Contacts of the helix formed by residues 274 - 291 (chain A) in PDB entry 4CSC
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 HIS 274 (chain A).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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242A ASN* 3.7 4.7 + - + -
243A VAL* 3.6 21.5 - - + +
244A SER* 3.0 43.0 + - - -
268A GLY 3.5 14.6 - - - +
269A LEU* 3.6 29.2 - - + +
271A GLY* 2.8 7.7 + - - +
273A LEU* 1.3 79.0 - - + +
275A GLY* 1.3 67.1 + - - +
276A LEU 3.3 1.6 - - - -
277A ALA* 3.3 11.1 + - - +
375A ASP* 3.2 15.8 - - - +
401A ARG* 4.5 0.2 - - - -
700A ACO 2.9 26.2 + - + +
702A MLT 3.3 37.6 - - + +
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Residues in contact with GLY 275 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
269A LEU* 2.9 31.1 + - - -
274A HIS* 1.3 77.9 - - - +
276A LEU* 1.3 63.1 + - - +
277A ALA 2.8 6.8 + - - -
278A ASN* 2.9 25.5 + - - +
375A ASP* 4.1 1.2 - - - +
394A THR* 3.5 6.4 + - - +
397A PHE* 3.8 15.9 - - - -
700A ACO 4.3 0.2 - - - -
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Residues in contact with LEU 276 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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136A HIS* 3.8 19.5 - - + +
138A MET* 4.3 7.2 - - + -
269A LEU 3.0 5.7 + - - -
270A ALA* 3.3 30.1 - - + +
271A GLY 3.5 9.6 - - - +
272A PRO* 4.0 17.7 - - + -
274A HIS 3.3 1.4 - - - -
275A GLY* 1.3 74.6 - - - +
277A ALA* 1.4 50.9 + - - +
278A ASN 3.0 0.2 - - - -
279A GLN* 2.6 66.8 + - - +
280A GLU* 3.0 18.9 + - + +
394A THR* 3.5 18.3 - - - +
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Residues in contact with ALA 277 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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272A PRO 3.7 11.2 + - - +
274A HIS 3.3 8.8 + - - +
275A GLY 2.8 0.2 + - - -
276A LEU* 1.4 75.1 - - - +
278A ASN* 1.3 61.5 + - - +
280A GLU* 4.0 8.3 - - - -
281A VAL* 2.8 30.1 + - - +
316A PRO* 5.0 1.6 - - + -
317A GLY 4.4 4.3 - - - +
375A ASP* 3.2 28.3 - - + +
700A ACO 3.6 29.8 - - + +
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Residues in contact with ASN 278 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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231A TYR* 3.4 12.9 + - - -
235A HIS* 5.3 0.2 + - - -
275A GLY 2.9 16.5 + - - +
277A ALA* 1.3 76.8 - - - +
279A GLN* 1.3 63.0 - - - +
281A VAL* 3.9 7.6 + - - +
282A LEU* 3.9 7.8 + - - +
375A ASP* 3.3 21.6 - - - +
378A SER* 2.9 23.9 + - - -
379A GLY* 4.8 5.6 - - - -
382A LEU* 6.3 0.2 - - - -
393A TYR* 3.1 49.7 + - + -
394A THR* 3.3 16.0 - - - +
397A PHE* 3.8 11.9 - - - +
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Residues in contact with GLN 279 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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136A HIS* 2.9 31.9 + - - -
276A LEU* 2.6 30.9 + - - +
278A ASN* 1.3 75.6 - - + +
280A GLU* 1.3 84.3 + - - +
282A LEU* 3.3 6.8 + - - +
283A GLY* 3.2 18.4 + - - -
390A MET* 3.3 29.7 - - + +
391A ASN* 3.4 27.9 - - - +
393A TYR* 4.5 3.1 - - - -
394A THR* 4.0 11.1 + - - +
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Residues in contact with GLU 280 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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272A PRO* 4.7 17.6 - - + +
276A LEU* 3.0 29.3 + - + +
277A ALA* 3.7 9.9 - - - +
279A GLN* 1.3 103.5 + - - +
281A VAL* 1.3 64.3 + - - +
283A GLY* 3.6 2.3 + - - +
284A TRP* 3.0 26.3 + - - +
316A PRO* 3.7 18.0 - - + +
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Residues in contact with VAL 281 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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277A ALA 2.8 24.5 + - - +
278A ASN 4.0 3.8 - - - +
280A GLU* 1.3 76.2 - - - +
282A LEU* 1.3 69.3 + - + +
284A TRP* 3.0 8.2 + - + +
285A LEU* 2.8 41.4 + - + +
316A PRO* 3.6 36.1 - - - +
317A GLY* 3.7 8.1 - - - +
375A ASP 3.5 20.6 - - - +
376A ALA* 4.0 18.8 - - + +
379A GLY 6.4 0.4 - - - +
380A VAL* 5.9 0.4 - - + -
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Residues in contact with LEU 282 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
278A ASN 3.9 3.9 + - - +
279A GLN 3.3 9.2 + - - +
281A VAL* 1.3 80.0 - - + +
283A GLY* 1.3 52.2 + - - +
285A LEU* 3.1 19.9 + - + +
286A ALA* 2.5 40.0 + - + +
346A MET* 4.9 11.2 - - + +
379A GLY* 3.7 28.3 - - - +
380A VAL* 3.8 9.2 - - + +
383A GLN* 4.2 15.5 - - + -
388A THR* 5.1 3.6 - - - +
390A MET* 4.0 24.2 - - + -
393A TYR* 3.3 35.7 - - + +
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Residues in contact with GLY 283 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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279A GLN 3.2 9.5 + - - -
280A GLU* 3.9 4.0 - - - -
281A VAL 3.3 0.2 - - - -
282A LEU* 1.3 78.3 - - - +
284A TRP* 1.3 54.9 + - - +
286A ALA* 3.6 4.7 - - - -
287A GLN* 2.6 39.5 + - - -
390A MET* 4.0 18.4 - - - -
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Residues in contact with TRP 284 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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280A GLU 3.0 17.7 + - - +
281A VAL* 3.0 7.9 + - + +
283A GLY* 1.3 73.6 - - - +
285A LEU* 1.3 64.5 + - + +
287A GLN* 3.3 9.3 + - + +
288A LEU* 2.8 53.7 + - + +
304A TYR* 3.4 32.8 + + - -
305A ILE* 3.9 30.3 - - + -
308A THR* 3.3 29.7 + - + +
315A VAL* 4.3 19.7 - - + -
316A PRO* 3.8 30.5 - - + +
318A TYR* 6.3 1.6 - + - -
353A LEU* 4.1 20.6 - - + -
357A VAL* 4.7 1.3 - - + -
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Residues in contact with LEU 285 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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281A VAL* 2.8 33.8 + - + +
282A LEU* 3.4 13.5 - - + +
284A TRP* 1.3 84.0 - - + +
286A ALA* 1.3 61.2 + - - +
288A LEU* 3.8 6.1 - - + -
289A GLN* 2.7 36.1 + - - -
346A MET* 3.7 18.8 - - + -
349A LEU* 3.8 15.9 - - + -
350A VAL* 3.7 24.5 - - + -
353A LEU* 3.4 33.0 - - + -
380A VAL* 4.1 11.7 - - + -
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Residues in contact with ALA 286 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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282A LEU* 2.5 27.9 + - + +
283A GLY* 4.2 6.7 - - - +
285A LEU* 1.3 74.5 - - - +
287A GLN* 1.4 64.9 + - - +
289A GLN* 3.6 6.1 - - - +
290A LYS* 3.3 25.8 + - - +
346A MET* 4.6 6.9 - - + +
390A MET* 4.5 13.7 - - + -
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Residues in contact with GLN 287 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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283A GLY* 2.6 30.0 + - - +
284A TRP* 3.3 11.7 - - + +
286A ALA* 1.4 72.4 - - - +
288A LEU* 1.3 70.1 + - - +
290A LYS* 3.0 27.5 + - - +
291A ALA* 2.9 23.2 + - - +
304A TYR* 2.9 18.6 + - - +
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Residues in contact with LEU 288 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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284A TRP* 2.8 51.2 + - + +
285A LEU* 3.4 20.0 - - + +
287A GLN* 1.3 73.9 - - - +
289A GLN* 1.3 66.6 + - - +
290A LYS 2.8 1.6 + - - -
291A ALA* 3.0 16.6 + - - +
301A LEU* 4.4 24.7 - - + -
304A TYR* 3.3 44.8 - - + -
305A ILE* 5.9 0.7 - - + -
349A LEU* 4.5 8.1 - - + -
353A LEU* 4.4 9.4 - - + -
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Residues in contact with GLN 289 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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285A LEU 2.7 25.3 + - - +
286A ALA* 3.6 6.2 - - - +
288A LEU* 1.3 79.6 - - - +
290A LYS* 1.3 62.1 + - - +
291A ALA 4.6 1.9 - - - -
346A MET* 3.4 20.3 - - - +
349A LEU* 3.4 25.7 - - - +
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Residues in contact with LYS 290 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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286A ALA* 3.3 13.7 + - - +
287A GLN* 3.0 37.8 + - - +
288A LEU 2.8 0.6 + - - -
289A GLN* 1.3 83.8 - - - +
291A ALA* 1.3 65.0 + - + +
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Residues in contact with ALA 291 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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287A GLN 2.9 11.1 + - - +
288A LEU 3.0 11.9 + - - +
289A GLN 4.6 1.8 - - - -
290A LYS* 1.3 86.0 - - + +
304A TYR* 4.5 15.9 - - + -
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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
------------------------------------------------------------
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