Contacts of the helix formed by residues 280 - 302 (chain A) in PDB entry 5I75
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 VAL 280 (chain A).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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265A VAL* 6.4 1.1 - - + -
268A PHE 4.8 2.0 - - - +
269A SER* 3.3 39.9 - - - +
276A THR* 2.6 28.8 + - + +
277A SER* 4.9 0.7 - - - -
279A LYS* 1.3 71.2 - - + +
281A VAL* 1.3 65.4 + - - +
283A VAL* 3.1 17.9 + - + +
284A THR* 3.3 16.5 + - + +
440A PHE* 3.6 21.3 - - + -
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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
----------------------------------------------------------
87A ASP 4.7 0.7 - - - +
90A LEU* 3.2 34.3 - - + +
91A SER* 3.6 20.6 - - - +
94A GLY* 4.9 3.4 - - - -
277A SER* 2.6 30.7 - - - +
278A GLY 4.6 6.1 - - - +
280A VAL* 1.3 75.5 - - - +
282A TRP* 1.3 65.0 + - - +
284A THR* 3.3 12.3 - - - +
285A ALA* 2.9 33.1 + - + +
437A ASP* 5.0 4.9 - - + +
440A PHE* 4.4 18.4 - - + -
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Residues in contact with TRP 282 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
84A LYS* 5.4 6.1 - - + -
86A VAL* 4.1 27.4 - - + -
87A ASP* 3.1 29.3 + - - +
90A LEU* 4.8 21.5 - - + +
278A GLY 3.1 22.6 + - - -
279A LYS* 3.3 23.8 + - + +
281A VAL* 1.3 77.8 - - - +
283A VAL* 1.3 53.7 + - + +
286A THR* 2.5 41.7 + - + +
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Residues in contact with VAL 283 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
279A LYS 4.9 2.9 - - - +
280A VAL* 3.1 10.4 + - + +
281A VAL 3.1 0.2 - - - -
282A TRP* 1.3 82.0 - - + +
284A THR* 1.3 68.9 + - + +
285A ALA 3.2 2.9 + - - -
286A THR* 3.4 2.8 + - - -
287A PHE* 3.2 31.5 + - + +
433A THR* 5.6 4.9 - - + -
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Residues in contact with THR 284 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
280A VAL* 3.4 18.4 - - + +
281A VAL* 3.2 16.8 + - - -
283A VAL* 1.3 78.6 - - + +
285A ALA* 1.3 58.0 + - - +
288A PRO* 3.3 14.7 - - - +
433A THR* 2.8 39.1 - - + +
436A LEU* 4.3 15.3 - - + -
437A ASP* 2.9 27.1 + - - +
440A PHE* 3.9 21.2 - - + -
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Residues in contact with ALA 285 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
90A LEU* 4.0 21.1 - - + +
93A ILE* 5.8 3.4 - - + -
94A GLY* 4.3 7.0 - - - +
281A VAL* 2.9 33.0 + - + +
284A THR* 1.3 79.4 + - - +
286A THR* 1.3 58.8 + - - +
287A PHE 3.7 0.4 - - - -
288A PRO* 3.8 4.0 - - - +
289A TYR* 3.3 28.2 - - - -
437A ASP* 3.5 10.1 - - - +
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Residues in contact with THR 286 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
90A LEU* 4.2 21.3 - - + -
282A TRP* 2.5 32.4 + - + +
283A VAL* 3.5 5.4 + - - -
285A ALA* 1.3 79.6 - - - +
287A PHE* 1.3 66.2 + - - +
288A PRO 3.4 0.7 - - - -
289A TYR* 3.4 16.1 + - - +
290A ILE* 3.5 20.3 + - - +
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Residues in contact with PHE 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 VAL* 3.2 21.0 + - + +
286A THR* 1.3 78.6 + - - +
288A PRO* 1.3 66.7 - - + +
290A ILE* 3.1 20.6 + - + +
291A ALA* 3.0 29.1 + - + -
426A ILE* 3.7 25.4 - - + -
429A LEU* 3.6 27.6 - - + -
430A MET* 3.3 31.0 - - + -
433A THR* 3.3 29.6 - - + +
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Residues in contact with PRO 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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97A VAL* 5.6 0.7 - - + -
284A THR 3.3 22.9 - - - +
285A ALA* 3.8 7.2 - - - +
286A THR 3.6 3.6 - - - -
287A PHE* 1.3 91.2 - - + +
289A TYR* 1.3 62.7 + - + +
291A ALA* 4.0 0.5 - - - +
292A LEU* 2.8 39.6 + - + +
430A MET* 3.9 14.7 - - + +
433A THR* 3.5 15.7 - - - +
434A LEU* 3.6 38.8 - - + +
437A ASP* 5.3 0.7 - - - +
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Residues in contact with TYR 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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93A ILE* 4.3 8.0 - - + +
97A VAL* 3.8 18.8 - - + +
285A ALA 3.3 26.5 - - - -
286A THR* 3.4 9.2 + - - +
287A PHE 3.2 1.2 - - - -
288A PRO* 1.3 78.8 - - + +
290A ILE* 1.3 63.6 + - + +
292A LEU* 3.5 9.0 + - + +
293A SER* 2.9 28.9 + - - -
367A VAL* 3.4 21.8 - - + +
371A THR* 2.7 45.8 + - + +
374A VAL* 5.9 4.3 - - + -
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Residues in contact with ILE 290 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
286A THR* 3.5 18.6 + - - +
287A PHE* 3.1 21.4 + - + +
289A TYR* 1.3 74.4 - - + +
291A ALA* 1.3 66.8 + - - +
293A SER* 3.0 8.9 + - - -
294A VAL* 2.9 36.1 + - + +
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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
----------------------------------------------------------
287A PHE* 3.0 24.6 + - + +
290A ILE* 1.3 76.8 - - - +
292A LEU* 1.3 58.7 + - - +
294A VAL* 3.3 7.8 + - - +
295A LEU* 2.9 37.5 + - + +
426A ILE* 3.9 19.3 - - + +
430A MET* 3.8 32.5 - - + -
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Residues in contact with LEU 292 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
102A VAL* 4.4 17.0 - - + -
288A PRO* 2.8 32.1 + - + +
289A TYR* 3.7 11.0 - - + +
291A ALA* 1.3 76.3 - - - +
293A SER* 1.3 57.2 + - - +
295A LEU* 3.7 2.0 - - - -
296A LEU* 2.8 29.9 + - - +
371A THR* 4.3 18.2 - - + +
374A VAL* 5.0 8.3 - - + -
375A SER* 3.5 25.1 - - - +
378A VAL* 3.4 39.2 - - + +
430A MET* 3.9 19.1 - - + -
434A LEU* 6.0 1.3 - - + -
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Residues in contact with SER 293 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
289A TYR 2.9 14.5 + - - -
290A ILE* 3.0 11.6 + - - -
292A LEU* 1.3 74.1 - - - +
294A VAL* 1.3 67.1 + - - +
296A LEU* 3.0 10.6 + - - +
297A VAL* 2.9 31.8 + - - +
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Residues in contact with VAL 294 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
290A ILE* 2.9 25.9 + - + +
291A ALA* 3.7 7.0 - - - +
293A SER* 1.3 77.2 - - - +
295A LEU* 1.3 57.6 + - - +
297A VAL* 3.4 3.2 + - - +
298A ARG* 2.9 29.6 + - - +
422A PHE* 4.0 20.6 - - + -
423A PHE* 3.7 24.5 - - + -
426A ILE* 4.0 9.0 - - + -
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Residues in contact with LEU 295 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
291A ALA* 2.9 22.4 + - + +
294A VAL* 1.3 77.0 - - - +
296A LEU* 1.3 57.0 + - - +
298A ARG* 3.6 5.9 - - + +
299A GLY* 2.9 25.3 + - - -
378A VAL* 3.6 16.6 - - + +
381A THR* 4.5 2.6 + - - -
382A VAL* 4.6 2.0 - - + +
410A TYR* 3.6 32.9 + - + +
414A ILE* 5.1 2.0 - - + -
417A MET* 5.8 2.0 - - + -
423A PHE* 3.8 35.7 - - + +
426A ILE* 4.4 8.7 - - + -
427A PHE* 3.7 27.4 - - + -
430A MET* 4.1 18.2 - - + -
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Residues in contact with LEU 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 LEU 2.8 20.4 + - - +
293A SER* 3.0 11.4 + - - +
295A LEU* 1.3 73.8 - - - +
297A VAL* 1.3 66.1 + - + +
298A ARG 3.1 1.6 - - - -
299A GLY 3.3 0.9 + - - -
300A ALA* 2.8 34.2 + - + +
374A VAL* 4.4 11.7 - - + +
377A PHE* 3.7 32.3 - - + +
378A VAL* 3.9 18.8 - - + +
381A THR* 4.6 6.1 + - + -
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Residues in contact with VAL 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 SER* 2.9 21.1 + - - +
294A VAL* 4.2 3.4 - - - +
296A LEU* 1.3 80.8 - - + +
298A ARG* 1.3 58.0 + - - +
300A ALA* 3.9 6.4 - - + +
301A THR* 2.9 37.7 + - + +
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Residues in contact with ARG 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 VAL 2.9 18.9 + - - +
295A LEU* 3.6 7.9 - - + +
296A LEU 3.1 0.2 - - - -
297A VAL* 1.3 75.1 - - - +
299A GLY* 1.3 66.5 + - - +
301A THR* 2.6 48.4 + - - -
302A LEU* 3.1 30.6 + - + +
303A PRO* 5.6 0.6 - - - +
382A VAL* 5.9 2.0 - - + -
417A MET* 4.0 26.2 - - + -
418A PRO* 4.1 24.3 - - - +
423A PHE* 3.6 40.1 - - + -
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Residues in contact with GLY 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 LEU 2.9 13.9 + - - -
298A ARG* 1.3 77.3 - - - +
300A ALA* 1.3 58.9 + - - +
302A LEU* 3.4 23.1 + - - +
305A ALA* 3.1 26.5 - - - +
381A THR* 3.3 23.6 - - - -
382A VAL* 4.1 5.8 - - - +
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Residues in contact with ALA 300 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
296A LEU* 2.8 22.4 + - + +
297A VAL* 3.9 8.7 - - + +
299A GLY* 1.3 76.9 - - - +
301A THR* 1.3 63.5 + - + +
302A LEU 3.6 4.7 + - - +
305A ALA* 4.9 3.6 - - - +
381A THR* 4.0 11.1 - - + -
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Residues in contact with THR 301 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
297A VAL* 2.9 28.7 + - + +
298A ARG* 2.6 45.8 + - - -
300A ALA* 1.3 79.0 - - + +
302A LEU* 1.3 61.2 + - - +
303A PRO* 3.6 4.2 - - - +
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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 ARG* 3.1 39.0 + - - +
299A GLY* 3.6 21.3 - - - +
300A ALA 3.3 3.8 - - - +
301A THR* 1.3 79.5 - - - +
303A PRO* 1.3 72.2 - - + +
304A GLY 3.6 0.2 + - - -
305A ALA* 3.4 17.2 + - - +
382A VAL* 4.2 12.8 - - + -
385A TYR* 3.6 46.2 - - + -
417A MET* 3.7 28.7 - - + -
418A PRO* 6.2 0.4 - - + -
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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