Contacts of the helix formed by residues 382 - 399 (chain B) in PDB entry 5A63
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 382 (chain B).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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380B LYS 3.4 5.7 + - - -
381B LEU* 1.3 75.5 - - - +
383B LEU* 1.3 65.7 + - - -
384B GLY 3.2 3.6 - - - -
385B ASP* 3.3 18.8 + - - -
386B PHE* 3.2 27.0 + - - -
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Residues in contact with LEU 383 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
226B LEU* 3.6 54.5 - - + +
229B ILE* 4.2 19.1 - - + -
230B SER* 4.5 2.7 - - - -
381B LEU 3.9 0.6 + - - -
382B GLY* 1.3 71.2 - - - -
384B GLY* 1.3 61.3 - - - +
386B PHE* 3.4 15.3 - - + +
387B ILE* 3.1 50.7 + - + +
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Residues in contact with GLY 384 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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382B GLY* 3.2 1.2 - - - -
383B LEU* 1.3 77.1 - - - +
385B ASP* 1.3 59.5 + - - +
387B ILE* 3.0 13.5 + - - +
388B PHE* 2.8 47.5 + - - -
435B LEU* 5.2 0.2 - - - -
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Residues in contact with ASP 385 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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381B LEU* 3.8 16.4 - - + +
382B GLY* 3.3 24.6 + - - +
384B GLY* 1.3 74.5 - - - +
386B PHE* 1.3 51.9 + - - +
388B PHE* 3.2 5.2 + - - +
389B TYR* 2.9 46.2 + - + -
434B ALA* 3.5 22.0 - - - +
435B LEU* 2.9 48.9 - - + +
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Residues in contact with PHE 386 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
85B LEU 5.5 0.4 - - - -
88B PRO* 3.8 21.8 - - + -
89B VAL* 3.3 48.4 - - + +
92B CYS* 4.5 10.3 - - + +
226B LEU* 5.5 8.1 - - + -
227B ILE* 4.2 10.3 - - + -
230B SER* 3.8 15.5 - - - +
381B LEU* 3.5 26.4 - - + +
382B GLY 3.2 21.7 + - - -
383B LEU* 3.4 22.4 - - + +
385B ASP* 1.3 78.4 - - - +
387B ILE* 1.3 58.1 - - - +
389B TYR* 3.2 12.3 + - - +
390B SER* 2.9 31.0 + - - -
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Residues in contact with ILE 387 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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230B SER* 3.5 28.3 - - - +
233B MET* 3.8 46.0 - - + +
234B ALA* 3.8 2.6 - - - +
237B PHE* 5.2 4.9 - - + -
383B LEU* 3.1 41.1 - - + +
384B GLY* 3.0 12.2 + - - +
386B PHE* 1.3 80.0 - - - +
388B PHE* 1.3 69.8 + - + +
390B SER* 3.2 4.3 + - - -
391B VAL* 2.9 43.7 + - + +
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Residues in contact with PHE 388 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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237B PHE* 4.4 23.6 - + - -
249B ILE* 4.8 7.0 - - + -
250B LEU* 4.1 20.3 - - + +
253B ILE* 3.3 40.2 - - + -
384B GLY* 2.8 35.8 + - - -
385B ASP 3.6 5.2 - - - +
387B ILE* 1.3 81.7 - - + +
389B TYR* 1.3 57.8 + - - +
391B VAL* 3.2 12.4 + - + +
392B LEU* 2.9 29.3 + - - +
435B LEU* 4.2 18.2 - - + -
439B ILE* 3.8 23.6 - - + -
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Residues in contact with TYR 389 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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89B VAL* 3.7 20.6 - - + -
93B MET* 3.2 29.4 - - - +
381B LEU* 4.0 24.5 - - + +
385B ASP* 2.9 32.7 + - + -
386B PHE* 3.4 9.0 - - - +
388B PHE* 1.3 76.4 - - - +
390B SER* 1.3 63.9 + - - +
392B LEU* 3.2 11.9 + - + +
393B VAL* 3.2 7.8 + - - +
414B ILE* 3.7 26.3 - - + +
418B LEU* 4.3 16.9 - - + +
434B ALA 3.8 5.7 + - - -
435B LEU* 3.7 18.3 - - + +
438B SER* 2.7 39.6 + - - -
439B ILE* 4.5 12.1 - - + -
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Residues in contact with SER 390 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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92B CYS* 2.6 40.2 + - - +
93B MET* 3.9 2.5 + - - +
96B VAL* 3.2 24.1 - - - +
230B SER 4.4 0.7 - - - -
234B ALA* 3.3 23.1 - - - -
386B PHE 2.9 10.3 + - - -
387B ILE* 3.4 6.7 - - - -
389B TYR* 1.3 77.1 - - - +
391B VAL* 1.3 56.5 + - - +
393B VAL* 3.3 7.3 - - - +
394B GLY 2.9 24.4 + - - -
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Residues in contact with VAL 391 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
234B ALA* 3.5 23.8 - - - +
237B PHE* 3.9 31.4 - - + -
238B ILE* 4.0 13.4 - - + +
241B LEU* 5.3 1.6 - - + -
246B ALA* 4.8 9.4 - - + -
250B LEU* 4.7 13.9 - - + -
387B ILE* 2.9 28.6 + - + +
388B PHE* 3.4 12.3 - - + +
390B SER* 1.3 75.8 - - - +
392B LEU* 1.3 58.5 + - - +
394B GLY* 3.2 0.5 + - - -
395B LYS* 2.8 42.1 + - + +
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Residues in contact with LEU 392 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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247B TRP* 4.4 7.0 - - + -
250B LEU* 3.1 33.0 - - + -
388B PHE 2.9 10.4 + - - +
389B TYR* 3.2 8.2 + - - +
391B VAL* 1.3 78.2 - - - +
393B VAL* 1.3 60.1 + - - +
395B LYS* 3.4 5.2 - - - +
396B ALA* 2.9 25.5 + - - +
410B CYS* 3.9 21.5 - - + -
414B ILE* 4.2 11.4 - - + -
439B ILE* 3.6 35.2 - - + +
442B GLY* 3.8 29.6 - - - +
443B LEU* 3.8 7.2 - - + +
446B TYR* 4.6 5.2 - - + -
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Residues in contact with VAL 393 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
93B MET* 3.4 51.1 - - + +
96B VAL* 4.8 0.4 - - + -
97B VAL* 3.7 22.7 - - + -
389B TYR 3.2 1.0 + - - -
390B SER 3.3 12.1 - - - +
392B LEU* 1.3 83.0 - - - +
394B GLY* 1.3 62.2 + - - +
396B ALA* 3.2 5.9 + - - +
397B SER* 2.9 14.6 + - - -
407B THR* 2.7 59.7 + - - +
410B CYS* 4.8 2.9 - - + -
411B PHE* 4.3 0.9 - - + +
414B ILE* 5.1 0.2 - - + -
1468B PC1 3.8 7.2 - - + -
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Residues in contact with GLY 394 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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96B VAL* 3.7 4.0 - - - -
97B VAL* 4.8 2.0 - - - -
100B ILE* 3.3 30.4 - - - +
238B ILE* 3.7 4.0 - - - -
390B SER 2.9 19.0 + - - -
391B VAL 3.6 0.9 - - - -
393B VAL* 1.3 76.9 - - - +
395B LYS* 1.3 57.1 + - - +
397B SER* 3.2 8.0 + - - -
398B ALA* 2.9 29.1 + - - +
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Residues in contact with LYS 395 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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107B THR* 5.5 5.1 + - - +
238B ILE* 4.0 37.1 + - + +
241B LEU 4.5 8.2 + - - -
243B GLU* 4.4 15.8 - - - +
246B ALA* 3.5 34.3 - - + -
247B TRP* 3.4 29.3 - - + +
250B LEU* 5.9 0.2 - - + -
391B VAL* 2.8 23.9 + - + +
392B LEU* 3.2 6.0 + - - +
394B GLY* 1.3 73.4 - - - +
396B ALA* 1.3 57.2 + - - +
398B ALA* 3.2 9.2 + - - +
399B THR* 2.9 55.8 + - - +
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Residues in contact with ALA 396 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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247B TRP* 4.2 0.6 - - - -
392B LEU 2.9 12.4 + - - +
393B VAL 3.2 10.3 + - - +
395B LYS* 1.3 77.8 - - - +
397B SER* 1.3 62.6 + - - +
400B ALA* 3.1 27.5 + - - +
403B ASP 4.5 2.6 - - - +
406B THR* 4.1 2.2 - - + +
407B THR* 3.8 13.0 - - - +
410B CYS* 3.7 17.5 - - - -
446B TYR* 3.6 33.4 - - + -
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Residues in contact with SER 397 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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97B VAL* 3.9 13.7 + - - -
100B ILE* 3.7 10.9 - - - +
101B LYS* 3.1 45.1 + - - +
393B VAL 2.9 6.8 + - - -
394B GLY* 3.3 13.5 - - - -
396B ALA* 1.3 77.6 - - - +
398B ALA* 1.3 63.4 + - - +
400B ALA 4.9 1.2 + - - +
403B ASP* 4.1 14.4 - - - +
407B THR* 3.4 22.6 + - - -
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Residues in contact with ALA 398 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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100B ILE* 4.0 10.5 - - + -
107B THR* 4.0 29.3 - - + +
238B ILE* 4.7 7.0 - - + -
394B GLY 2.9 14.5 + - - +
395B LYS* 3.5 17.0 - - - +
397B SER* 1.3 80.3 + - - +
399B THR* 1.3 68.5 + - - +
400B ALA 3.8 3.0 + - - +
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Residues in contact with THR 399 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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107B THR 5.7 0.3 + - - -
243B GLU* 3.9 31.0 + - + +
247B TRP* 4.6 5.0 - - - +
395B LYS* 2.9 40.7 + - - +
396B ALA 3.9 0.4 - - - -
398B ALA* 1.3 74.2 + - - +
400B ALA* 1.3 53.7 + - - +
446B TYR* 2.7 30.4 + - - +
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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
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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