Contacts of the helix formed by residues 283 - 305 (chain A) in PDB entry 4CBS
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 GLY 283 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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66A TYR* 3.4 10.3 - - - -
279A ILE 2.8 18.5 + - - -
280A ALA 4.0 5.6 - - - -
281A GLU 3.4 0.8 - - - -
282A GLN* 1.3 73.8 - - - +
284A LEU* 1.3 66.5 + - - -
285A GLU 3.4 2.7 - - - -
286A ASN* 3.2 8.4 + - - +
287A SER* 2.9 22.3 + - - -
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Residues in contact with LEU 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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66A TYR* 2.6 51.1 + - + +
67A VAL* 3.8 21.1 - - + +
69A GLN* 4.0 19.3 - - + +
188A LEU* 5.8 0.4 - - + -
189A GLY* 4.4 8.1 - - - +
193A LEU 5.0 0.7 - - - +
279A ILE* 4.2 20.8 + - + -
283A GLY* 1.3 72.0 - - - -
285A GLU* 1.3 60.8 + - + +
287A SER* 3.1 6.6 + - - -
288A TRP* 2.9 75.1 + - + +
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Residues in contact with GLU 285 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
283A GLY 3.4 0.4 - - - -
284A LEU* 1.3 77.6 - - + +
286A ASN* 1.3 68.3 - - - +
288A TRP* 3.0 32.9 + - + +
289A ARG* 3.0 30.1 + - + +
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Residues in contact with ASN 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 GLN* 3.0 33.8 + - + +
283A GLY* 3.2 10.3 + - - +
285A GLU* 1.3 78.8 - - - +
287A SER* 1.3 63.6 + - - +
289A ARG* 3.1 42.8 + - - +
290A GLN* 3.1 13.9 + - - +
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Residues in contact with SER 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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189A GLY 2.3 28.7 + - - -
279A ILE* 4.1 17.0 - - - +
282A GLN* 3.3 31.5 + - - +
283A GLY 2.9 11.1 + - - -
284A LEU* 3.4 8.7 - - - -
286A ASN* 1.3 76.0 - - - +
288A TRP* 1.3 59.6 + - - +
290A GLN* 3.4 0.9 + - - +
291A HIS* 2.7 43.4 + - - -
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Residues in contact with TRP 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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67A VAL 5.8 0.2 - - - -
69A GLN* 5.7 0.2 - - + -
189A GLY* 3.5 13.8 - - - +
190A GLY 4.2 6.6 - - - +
191A THR* 3.2 29.2 + - - +
192A PRO* 3.4 43.1 - - + -
193A LEU* 3.5 17.5 - - + -
194A TYR* 3.4 36.1 - + - -
284A LEU* 2.9 54.6 + - + +
285A GLU* 3.0 32.3 + - + +
287A SER* 1.3 73.9 - - - +
289A ARG* 1.3 64.3 + - - +
291A HIS* 3.5 2.3 + - - +
292A ARG* 3.0 34.5 + - - +
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Residues in contact with ARG 289 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
285A GLU* 3.0 22.1 + - + +
286A ASN* 3.1 35.2 + - - +
288A TRP* 1.3 74.9 - - - +
290A GLN* 1.3 55.4 + - - +
292A ARG* 3.0 28.6 + - - +
293A GLU* 2.7 68.3 + - + +
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Residues in contact with GLN 290 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
282A GLN* 3.1 22.6 + - - +
286A ASN 3.1 8.5 + - - +
287A SER 3.6 8.7 - - - +
289A ARG* 1.3 79.5 - - - +
291A HIS* 1.3 61.6 + - - +
293A GLU* 4.5 8.7 - - - +
294A ALA* 2.8 33.5 + - + +
365A GLY 3.2 23.0 + - - -
366A CYS* 4.7 3.6 - - - +
368A ALA* 2.6 29.4 + - - +
369A THR* 4.6 6.4 - - - +
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Residues in contact with HIS 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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189A GLY 3.6 6.1 - - - -
190A GLY* 3.2 27.0 - - - +
210A ALA* 3.9 6.9 - - + +
282A GLN* 5.7 0.9 - - - -
287A SER* 2.7 46.2 + - - +
288A TRP 4.0 0.2 - - - +
290A GLN* 1.3 79.8 - - - +
292A ARG* 1.3 58.7 + - - +
294A ALA* 3.9 4.6 - - - +
295A ALA* 2.9 31.5 + - - +
319A PRO* 3.7 10.2 - - + +
320A THR* 3.7 13.2 - - + -
363A LEU* 3.3 25.4 - - + +
365A GLY* 2.9 40.4 + - - -
368A ALA* 3.7 9.1 - - + +
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Residues in contact with ARG 292 (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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192A PRO* 4.9 15.0 - - - +
288A TRP* 3.0 28.1 + - - +
289A ARG* 3.3 39.7 + - - +
291A HIS* 1.3 77.6 - - - +
293A GLU* 1.3 59.7 + - + +
295A ALA* 3.5 5.8 + - - +
296A ALA* 2.8 28.4 + - + +
319A PRO* 4.4 12.0 - - + +
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Residues in contact with GLU 293 (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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289A ARG* 2.7 54.3 + - - +
290A GLN* 3.9 8.1 - - - +
292A ARG* 1.3 75.4 - - + +
294A ALA* 1.3 67.3 + - - +
296A ALA* 3.0 8.5 + - - +
297A TYR* 2.8 25.0 + - - +
370A ARG* 6.2 0.9 - - - -
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Residues in contact with ALA 294 (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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290A GLN* 2.8 23.5 + - + +
291A HIS 3.9 2.0 - - - +
293A GLU* 1.3 72.8 - - - +
295A ALA* 1.3 57.8 + - - +
297A TYR* 3.2 7.2 + - - +
298A LEU* 2.8 29.5 + - - +
363A LEU* 3.7 16.9 - - + +
368A ALA* 3.8 27.6 - - + +
369A THR 4.4 7.4 - - - +
370A ARG* 5.0 7.2 - - + +
373A VAL* 4.0 4.1 - - + +
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Residues in contact with ALA 295 (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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291A HIS 2.9 20.1 + - - +
292A ARG* 3.5 4.9 - - - +
294A ALA* 1.3 75.1 - - - +
296A ALA* 1.3 62.7 + - - +
298A LEU* 3.3 1.5 + - - -
299A HIS* 2.9 44.0 + - + +
319A PRO* 3.7 33.4 - - + +
363A LEU* 3.6 10.4 - - - +
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Residues in contact with ALA 296 (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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292A ARG* 2.8 17.5 + - + +
293A GLU* 3.0 13.2 + - - +
295A ALA* 1.3 78.8 - - - +
297A TYR* 1.3 65.5 + - - +
299A HIS* 3.4 11.9 + - - +
300A GLY* 3.4 9.0 + - - -
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Residues in contact with TYR 297 (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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293A GLU 2.8 15.2 + - - +
294A ALA* 3.4 8.7 - - - +
296A ALA* 1.3 74.3 - - - +
298A LEU* 1.3 61.5 + - - +
300A GLY* 3.3 2.3 + - - -
301A ARG* 3.3 47.5 + - + +
370A ARG* 3.7 67.5 + - + +
373A VAL* 3.6 22.4 - - + -
374A ASP* 2.4 34.9 + - - -
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Residues in contact with LEU 298 (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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294A ALA 2.8 19.5 + - - +
295A ALA* 3.8 3.1 - - - +
296A ALA 3.2 0.4 - - - -
297A TYR* 1.3 74.2 - - - +
299A HIS* 1.3 64.0 + - + +
301A ARG* 3.3 2.9 + - - +
302A LEU* 3.1 41.2 + - + +
322A THR* 3.5 32.1 - - + +
361A ILE* 4.1 18.6 - - + +
363A LEU* 3.8 20.0 - - + -
373A VAL* 3.4 28.5 - - + -
376A VAL* 4.1 21.5 - - + -
377A THR* 4.8 1.6 - - - +
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Residues in contact with HIS 299 (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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295A ALA* 2.9 36.1 + - + +
296A ALA* 3.9 6.1 - - - +
297A TYR 3.4 0.2 - - - -
298A LEU* 1.3 78.5 - - + +
300A GLY* 1.3 65.4 + - - +
302A LEU* 3.2 5.7 + - - +
303A GLN* 3.1 33.0 + - - +
309A LEU* 3.5 18.4 - - + -
317A ARG* 3.2 54.4 + - + +
318A LEU 5.1 3.0 + - - -
322A THR* 3.3 38.4 + - + +
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Residues in contact with GLY 300 (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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296A ALA 3.4 6.4 + - - -
297A TYR 3.3 6.7 + - - -
298A LEU 3.3 0.6 - - - -
299A HIS* 1.3 80.0 - - - +
301A ARG* 1.3 60.0 + - - +
303A GLN* 3.5 9.6 + - - +
304A ALA* 3.2 22.2 + - - +
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Residues in contact with ARG 301 (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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297A TYR* 3.3 46.2 + - + +
298A LEU 3.7 5.6 - - - +
300A GLY* 1.3 74.8 - - - +
302A LEU* 1.3 62.9 + - + +
304A ALA* 3.3 10.1 + - - +
305A LEU* 3.3 23.2 + - - +
373A VAL* 4.2 4.3 - - + -
374A ASP* 2.7 44.2 + - - +
377A THR* 3.4 37.7 - - + +
378A GLU* 5.1 7.3 + - - +
381A ARG* 3.8 24.4 - - - +
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Residues in contact with LEU 302 (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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298A LEU* 3.1 44.2 + - + +
299A HIS* 3.2 5.4 + - - +
301A ARG* 1.3 78.3 - - - +
303A GLN* 1.3 56.7 + - - +
305A LEU* 3.0 26.4 + - + +
307A LEU* 3.2 34.2 + - + +
309A LEU* 4.2 16.4 - - + -
322A THR* 4.4 6.3 - - + -
324A VAL* 3.6 28.7 - - + -
361A ILE* 4.3 7.4 - - + -
377A THR* 5.1 5.4 - - - +
380A LEU* 3.8 28.3 - - + -
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Residues in contact with GLN 303 (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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299A HIS* 3.1 20.8 + - - +
300A GLY* 4.0 7.8 - - - +
302A LEU* 1.3 76.3 - - - +
304A ALA* 1.3 57.1 + - - +
306A GLY* 2.9 20.6 + - - -
307A LEU 3.3 16.3 - - - +
308A GLN* 5.3 1.3 - - - +
309A LEU* 4.1 31.1 - - + +
317A ARG* 4.5 8.7 - - - +
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Residues in contact with ALA 304 (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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300A GLY 3.2 12.9 + - - +
301A ARG* 3.4 14.4 - - - +
302A LEU 3.2 0.4 - - - -
303A GLN* 1.3 76.5 - - - +
305A LEU* 1.3 61.3 + - + +
306A GLY 3.1 1.1 + - - -
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Residues in contact with LEU 305 (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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301A ARG 3.3 9.6 + - - +
302A LEU* 3.0 16.4 + - + +
304A ALA* 1.3 78.6 - - + +
306A GLY* 1.3 59.2 - - - +
307A LEU* 3.3 18.5 - - + +
377A THR* 3.5 37.7 - - + +
380A LEU* 4.3 10.3 - - + -
381A ARG* 3.7 44.4 - - + +
384A LEU* 4.6 14.0 - - + +
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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
------------------------------------------------------------
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