Contacts of the helix formed by residues 384 - 399 (chain B) in PDB entry 6F0X
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 384 (chain B).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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181B PRO 4.3 4.9 - - - -
182B GLY 3.4 20.4 - - - -
321B PRO* 5.4 0.9 - - - -
322B PRO* 5.0 1.6 - - - -
383B LEU* 1.3 76.3 - - - +
385B GLY* 1.3 52.5 + - - +
386B ARG* 3.5 2.1 + - - +
387B VAL* 2.8 33.5 + - - +
388B LEU* 2.6 37.3 + - - +
425B ARG* 5.5 3.4 - - - +
311C ASP* 3.2 18.9 + - - -
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Residues in contact with GLY 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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182B GLY 4.1 4.2 + - - -
183B THR* 6.2 0.2 - - - +
322B PRO* 4.2 9.9 - - - +
330B ILE* 5.6 1.1 - - - -
384B SER* 1.3 70.9 - - - +
386B ARG* 1.3 56.2 + - - +
388B LEU* 3.3 20.6 - - - +
389B ARG* 2.8 35.2 + - - +
901B AGS 3.7 31.0 + - - -
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Residues in contact with ARG 386 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
182B GLY* 3.1 20.7 + - - +
384B SER* 3.0 8.2 - - - +
385B GLY* 1.3 75.3 - - - +
387B VAL* 1.3 63.2 + - - +
389B ARG* 3.4 2.5 + - - +
390B LYS* 3.0 30.9 + - - +
901B AGS 1.6 112.1 + - - +
170C THR 4.8 0.2 - - - +
172C ASN* 4.0 14.3 + - - +
285C ASP* 4.0 3.0 + - - -
288C LYS* 5.1 4.0 - - - +
311C ASP* 3.1 22.8 + - - +
312C ARG* 3.2 33.8 - - - +
313C ALA* 5.7 0.2 - - + -
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Residues in contact with VAL 387 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
383B LEU* 4.7 16.4 - - + -
384B SER* 2.8 34.9 + - - +
386B ARG* 1.3 71.4 - - - +
388B LEU* 1.3 65.7 + - - +
390B LYS* 3.0 11.6 + - + +
391B LEU* 2.9 25.6 + - + +
394B LEU* 6.5 0.7 - - + -
421B GLN* 3.6 30.5 - - + +
425B ARG* 4.7 12.6 - - - +
310C VAL 5.3 0.2 - - - +
311C ASP* 4.2 5.4 - - - +
313C ALA* 3.6 28.0 - - + -
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Residues in contact with LEU 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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322B PRO* 4.7 10.3 - - + -
327B ILE* 4.2 22.7 - - + -
330B ILE* 3.9 34.3 - - + -
331B TYR* 3.8 15.3 - - + +
380B SER 4.7 3.1 - - - +
383B LEU* 4.4 19.5 - - + -
384B SER 2.6 19.8 + - - +
385B GLY* 3.1 24.0 + - - +
387B VAL* 1.3 70.3 - - - +
389B ARG* 1.3 56.0 + - - +
391B LEU* 2.5 55.7 + - + +
392B PRO* 3.2 4.5 - - - +
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Residues in contact with ARG 389 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
138B SER* 3.2 33.2 + - - +
140B VAL* 5.1 0.8 - - - +
329B LYS 5.4 0.2 - - - -
330B ILE* 3.4 41.8 - - + +
333B SER* 3.5 23.6 + - - -
334B CYS* 4.0 9.2 - - - -
385B GLY 2.8 18.3 + - - +
386B ARG 3.7 1.8 - - - +
388B LEU* 1.3 71.6 - - - +
390B LYS* 1.3 54.6 + - - +
392B PRO* 4.1 6.1 - - - -
901B AGS 3.3 40.4 - - - +
167C ASN 4.6 4.0 - - - -
168C LEU* 2.8 36.6 + - - +
169C ILE* 3.7 11.1 - - - +
170C THR* 2.6 35.5 + - - +
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Residues in contact with LYS 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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386B ARG* 3.0 22.2 + - - +
387B VAL* 3.4 10.3 - - + +
388B LEU 2.9 1.4 + - - -
389B ARG* 1.3 79.0 - - - +
391B LEU* 1.3 64.3 + - - +
392B PRO* 3.4 1.1 - - - -
393B PHE* 3.0 7.3 + - - +
394B LEU* 3.0 41.0 + - + +
170C THR 3.5 13.2 - - - +
171C TRP* 3.5 11.4 - - + -
172C ASN* 2.8 44.9 + - - +
312C ARG 2.5 23.9 + - - -
313C ALA* 2.4 40.5 + - + +
314C ASP* 3.8 3.2 - - - +
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Residues in contact with LEU 391 (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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331B TYR* 3.2 28.7 - - + +
383B LEU* 4.6 7.0 - - + -
387B VAL* 2.9 19.5 + - + +
388B LEU* 2.5 39.7 + - + +
390B LYS* 1.3 69.9 - - - +
392B PRO* 1.3 54.9 - - + +
394B LEU* 5.1 4.3 - - + -
395B ALA* 2.7 39.6 + - - +
414B LEU* 3.9 11.7 - - + -
417B ALA* 4.8 6.8 - - + +
418B VAL* 3.6 29.2 - - + +
421B GLN* 4.0 25.4 - - + +
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Residues in contact with PRO 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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331B TYR* 5.2 6.1 - - + -
334B CYS* 3.6 32.5 - - + -
338B LEU* 4.7 3.6 - - + -
388B LEU 3.2 11.2 - - - +
389B ARG* 4.1 7.0 - - - +
390B LYS 3.6 2.5 - - - -
391B LEU* 1.3 91.3 - - + +
393B PHE* 1.3 55.6 + - - +
395B ALA* 3.2 5.1 - - + +
396B HIS* 2.9 31.7 + - - +
410B PHE* 4.4 20.2 - - + -
414B LEU* 4.2 10.5 - - + -
159C PHE* 5.0 1.8 - - - -
169C ILE* 4.0 20.4 - - + -
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Residues in contact with PHE 393 (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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390B LYS* 3.0 11.2 + - - +
392B PRO* 1.3 78.1 - - - +
394B LEU* 1.3 73.3 + - + +
395B ALA 3.0 1.2 + - - -
396B HIS* 3.3 2.6 + - - +
397B ALA* 2.9 22.1 + - + +
152C TYR* 4.1 13.7 - + - -
155C THR* 4.3 2.0 - - + +
156C THR* 3.4 41.1 - - - -
159C PHE* 3.9 34.8 - + + -
169C ILE* 4.2 19.0 - - + +
171C TRP* 3.3 68.2 - + + -
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Residues in contact with LEU 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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387B VAL* 6.5 0.4 - - + -
390B LYS* 3.0 38.2 + - + +
391B LEU* 4.5 4.3 - - + +
393B PHE* 1.3 84.9 - - + +
395B ALA* 1.3 57.2 + - - +
397B ALA* 3.1 7.4 - - + +
398B LEU* 2.9 38.1 + - + +
417B ALA* 5.1 5.8 - - + -
421B GLN* 4.4 17.9 - - - +
152C TYR* 3.6 20.0 - - + +
171C TRP* 5.6 1.6 - - + -
313C ALA 4.7 0.4 - - - +
314C ASP 4.3 15.9 - - - +
315C ILE* 3.6 37.7 - - + +
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Residues in contact with ALA 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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391B LEU 2.7 24.9 + - - +
392B PRO* 3.2 8.7 - - + +
393B PHE 3.0 0.2 - - - -
394B LEU* 1.3 75.8 - - - +
396B HIS* 1.3 65.3 + - - +
398B LEU* 2.9 13.6 + - - -
399B TYR* 3.0 16.4 + - - +
400B VAL* 3.9 2.9 + - - -
410B PHE* 5.3 5.4 - - + +
413B ALA* 4.6 4.3 - - + +
414B LEU* 4.3 26.2 - - + +
417B ALA* 4.2 15.6 - - + +
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Residues in contact with HIS 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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343B ILE* 4.5 11.1 + - + +
392B PRO 2.9 15.3 + - - +
395B ALA* 1.3 73.4 - - - +
397B ALA* 1.3 63.5 + - - +
400B VAL* 3.2 44.8 - - + +
401B GLN 4.1 1.7 + - - -
402B ALA 3.0 29.5 + - - -
403B PRO* 3.6 16.0 + - + -
404B THR* 5.1 0.6 - - - -
405B VAL* 4.8 6.3 - - + +
410B PHE* 4.5 16.2 - + + -
155C THR* 3.7 10.9 + - + +
158C LEU* 5.0 8.5 - - + -
159C PHE* 3.3 41.5 - + + -
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Residues in contact with ALA 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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393B PHE* 2.9 15.7 + - + +
394B LEU* 3.1 16.4 - - + +
395B ALA 2.9 1.4 + - - -
396B HIS* 1.3 81.0 - - - +
398B LEU* 1.3 70.6 + - + +
401B GLN* 4.2 6.4 + - - +
148C HIS 6.0 0.2 - - - +
151C ASP* 4.3 17.4 - - - +
152C TYR* 4.6 25.1 - - + +
155C THR* 3.9 24.1 + - + +
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Residues in contact with LEU 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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394B LEU* 2.9 21.5 + - + +
395B ALA 2.9 7.5 + - - -
397B ALA* 1.3 78.3 - - + +
399B TYR* 1.3 78.9 + - + +
400B VAL 3.3 1.1 - - - -
401B GLN* 3.2 36.6 + - - +
417B ALA* 5.1 4.5 - - + -
420B LYS* 2.9 42.0 - - + +
148C HIS* 3.6 45.8 - - + +
151C ASP* 5.5 0.7 - - - +
315C ILE* 5.3 12.1 - - + -
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Residues in contact with TYR 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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395B ALA 3.0 8.2 + - - +
398B LEU* 1.3 94.0 - - + +
400B VAL* 1.3 62.2 + - - +
401B GLN* 5.0 1.3 - - - -
409B GLY 5.2 0.3 - - - +
413B ALA* 3.3 31.9 - - + +
416B LEU* 3.5 45.1 + - + +
417B ALA* 3.2 34.8 - - + -
420B LYS* 4.0 15.8 - - + +
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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