Contacts of the helix formed by residues 384 - 398 (chain A) 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 A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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181A PRO 5.0 3.4 - - - -
182A GLY 4.2 6.7 - - - -
183A THR* 5.2 3.6 - - - -
322A PRO* 4.7 10.0 - - - +
383A LEU* 1.3 80.6 - - - +
385A GLY* 1.3 54.4 + - - +
386A ARG* 2.8 12.9 + - - +
387A VAL* 2.3 43.0 + - - +
388A LEU* 2.7 42.1 + - - +
311B ASP* 3.9 13.9 + - - -
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Residues in contact with GLY 385 (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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182A GLY 4.6 1.4 + - - -
183A THR* 5.0 3.6 - - - +
322A PRO* 4.0 16.1 - - - +
330A ILE* 5.9 0.7 - - - -
384A SER* 1.3 71.9 - - - +
386A ARG* 1.3 55.8 + - - +
388A LEU* 3.2 8.0 + - - +
389A ARG* 2.9 33.4 + - - +
901A AGS 3.6 39.7 + - - -
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Residues in contact with ARG 386 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
182A GLY* 3.4 23.3 + - - +
384A SER* 2.8 7.8 + - - +
385A GLY* 1.3 72.7 - - - +
387A VAL* 1.3 67.3 + - + +
389A ARG* 3.8 1.1 - - - +
390A LYS* 2.9 25.6 + - + +
901A AGS 2.7 52.4 + - - +
172B ASN* 5.1 6.2 - - - +
285B ASP* 4.2 2.4 + - - -
288B LYS* 4.1 17.2 - - - +
311B ASP* 3.6 11.2 - - - +
312B ARG* 2.6 75.6 - - - +
313B ALA 4.4 0.7 - - - +
314B ASP* 4.7 13.2 + - - +
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Residues in contact with VAL 387 (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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383A LEU* 3.7 25.1 - - + -
384A SER* 2.3 44.8 + - - +
386A ARG* 1.3 68.9 - - + +
388A LEU* 1.3 63.5 + - - +
390A LYS* 3.1 8.2 + - + +
391A LEU* 2.9 28.3 + - + +
421A GLN* 4.1 34.1 - - + +
425A ARG* 4.1 6.3 - - - +
311B ASP* 3.4 23.1 - - - +
313B ALA 6.1 0.4 - - - +
316B LYS* 6.6 0.4 - - - -
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Residues in contact with LEU 388 (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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322A PRO* 4.4 14.8 - - + +
327A ILE* 3.6 47.8 - - + -
330A ILE* 4.8 18.2 - - + -
331A TYR* 4.4 6.8 - - + +
334A CYS* 5.3 0.8 - - - -
380A SER 4.3 13.5 - - - +
383A LEU* 4.5 13.0 - - + +
384A SER 2.7 32.9 + - - +
385A GLY* 3.6 6.7 - - - +
387A VAL* 1.3 71.0 - - - +
389A ARG* 1.3 56.3 + - - +
391A LEU* 2.7 54.0 + - + +
392A PRO* 3.3 3.8 - - - +
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Residues in contact with ARG 389 (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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137A ASP 4.4 2.4 + - - -
138A SER* 2.5 43.1 + - - +
330A ILE* 3.6 25.4 - - + +
333A SER* 3.6 18.4 + - - -
334A CYS* 3.7 5.3 - - - -
385A GLY 2.9 15.6 + - - +
386A ARG 3.8 1.3 - - - +
388A LEU* 1.3 73.3 - - - +
390A LYS* 1.3 59.4 + - - +
392A PRO* 3.9 9.5 - - - +
901A AGS 3.1 36.0 + - + +
167B ASN 3.7 12.7 + - - -
168B LEU* 2.8 66.2 + - - +
169B ILE* 4.2 1.9 - - - +
170B THR* 2.8 31.4 + - - +
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Residues in contact with LYS 390 (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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386A ARG 2.9 20.0 + - - +
387A VAL* 3.3 9.6 - - + +
388A LEU 2.8 0.2 + - - -
389A ARG* 1.3 80.6 - - - +
391A LEU* 1.3 67.0 + - - +
392A PRO* 3.3 0.8 - - - +
393A PHE* 2.8 43.6 + - - +
394A LEU* 2.6 60.2 - - + +
421A GLN* 6.6 0.2 - - - -
152B TYR* 5.1 0.9 - - - -
170B THR 3.5 3.3 + - - +
171B TRP* 3.8 12.8 - - + -
314B ASP* 3.4 55.2 - - - +
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Residues in contact with LEU 391 (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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331A TYR* 3.6 31.4 - - + +
383A LEU* 5.0 3.4 - - + -
387A VAL* 2.9 24.5 + - + +
388A LEU* 2.7 40.3 + - + +
390A LYS* 1.3 70.2 - - - +
392A PRO* 1.3 66.7 - - + +
393A PHE 2.9 1.0 + - - -
394A LEU* 3.0 9.6 + - + +
395A ALA* 2.8 23.4 + - - +
414A LEU* 3.8 10.3 - - + -
417A ALA* 4.6 6.1 - - + +
418A VAL* 3.6 37.0 - - + +
421A GLN* 4.5 15.7 - - + -
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Residues in contact with PRO 392 (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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331A TYR* 6.1 3.8 - - + -
334A CYS* 3.7 31.2 - - + -
335A LEU* 6.2 0.7 - - + -
338A LEU* 4.7 7.3 - - + +
388A LEU 3.3 10.5 - - - +
389A ARG* 3.9 8.3 - - - +
390A LYS 3.3 6.5 - - - +
391A LEU* 1.3 89.6 - - + +
393A PHE* 1.3 56.2 + - - +
395A ALA* 3.4 8.8 - - + +
396A HIS* 2.9 30.8 + - - +
410A PHE* 4.0 19.3 - - + -
414A LEU* 4.6 4.7 - - + -
159B PHE* 4.7 2.1 - - - -
169B ILE* 4.2 19.3 - - + -
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Residues in contact with PHE 393 (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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390A LYS* 2.8 50.0 + - + +
392A PRO* 1.3 73.3 - - - +
394A LEU* 1.3 60.7 + - - -
396A HIS* 3.1 6.2 + - - +
397A ALA* 2.9 27.2 + - + +
152B TYR* 3.2 35.9 - + - -
156B THR* 3.2 41.3 - - + -
159B PHE* 3.4 44.3 - + - -
169B ILE* 4.7 7.2 - - + +
170B THR 5.2 0.4 - - - +
171B TRP* 4.0 30.7 - + + -
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Residues in contact with LEU 394 (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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390A LYS* 2.6 37.3 - - + +
391A LEU* 3.0 9.1 + - + +
393A PHE* 1.3 78.4 - - + +
395A ALA* 1.3 64.8 + - - +
397A ALA* 2.9 4.7 + - + +
398A LEU* 2.8 58.6 + - + +
399A TYR* 4.8 0.2 - - - -
417A ALA* 4.5 11.2 - - + +
420A LYS* 6.4 0.2 - - + -
421A GLN* 3.3 33.7 - - + +
152B TYR* 4.8 4.5 - - + -
314B ASP 3.6 12.3 - - - +
315B ILE* 4.0 27.6 - - + -
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Residues in contact with ALA 395 (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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391A LEU 2.8 11.8 + - - +
392A PRO* 3.4 15.0 - - + +
394A LEU* 1.3 77.4 - - - +
396A HIS* 1.3 62.3 + - - +
399A TYR* 4.0 2.1 + - - -
400A VAL* 3.3 25.7 + - - +
410A PHE* 4.0 14.8 - - + +
413A ALA* 3.6 8.7 - - - +
414A LEU* 3.8 31.0 - - + +
417A ALA* 4.2 10.4 - - + +
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Residues in contact with HIS 396 (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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338A LEU* 5.9 0.2 - - + -
343A ILE* 3.8 25.7 - - + +
392A PRO 2.9 16.5 + - - +
393A PHE 3.1 4.0 + - - +
395A ALA* 1.3 77.8 - - - +
397A ALA* 1.3 58.4 + - - +
400A VAL* 3.2 6.3 - - - +
401A GLN* 2.9 22.3 + - - -
402A ALA 3.1 28.5 + - - -
403A PRO 4.3 7.5 + - - -
405A VAL* 3.5 25.6 - - + +
410A PHE* 4.1 8.3 - + + -
155B THR* 3.3 27.6 - - + +
158B LEU* 4.2 15.5 - - + +
159B PHE* 3.9 16.2 - + + -
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Residues in contact with ALA 397 (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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393A PHE* 2.9 24.9 + - + +
394A LEU* 2.9 9.0 + - + +
396A HIS* 1.3 79.2 - - - +
398A LEU* 1.3 70.0 + - + +
401A GLN* 3.2 21.9 - - - +
148B HIS 5.9 0.7 - - - +
151B ASP* 3.7 14.2 - - - +
152B TYR* 4.5 24.9 - - + -
155B THR* 4.7 11.9 - - + -
159B PHE* 6.1 0.2 - - + -
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Residues in contact with LEU 398 (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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394A LEU* 2.8 47.9 + - + +
397A ALA* 1.3 80.0 - - + +
399A TYR* 1.3 82.1 + - + +
401A GLN* 3.8 16.6 + - - +
417A ALA* 5.3 1.8 - - + -
420A LYS* 3.1 48.5 - - + +
148B HIS* 3.6 46.0 + - + +
151B ASP* 5.3 1.3 - - - -
152B TYR* 6.5 0.2 - - + -
317B GLN* 5.3 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
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Atomic class I II III IV V VI VII VIII
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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