Contacts of the helix formed by residues 392 - 413 (chain B) in PDB entry 6HBU
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 PRO 392 (chain B).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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388B LEU* 3.3 18.6 - - - +
389B LEU* 4.3 9.0 - - + +
390B GLY 3.6 7.6 - - - +
391B ASN* 1.4 83.4 - - - +
393B GLN* 1.3 69.5 + - - +
394B ALA 3.5 1.6 - - - +
395B SER* 4.0 13.2 - - - +
396B ILE* 3.2 46.5 + - + +
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Residues in contact with GLN 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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536A VAL* 3.8 18.5 - - + +
390B GLY 5.3 0.4 + - - -
391B ASN* 3.1 42.9 + - - +
392B PRO* 1.3 82.2 - - - +
394B ALA* 1.3 59.1 + - - +
396B ILE* 4.3 1.2 - - - +
397B ALA* 3.1 32.2 + - - +
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Residues in contact with ALA 394 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
535A SER* 3.5 31.6 - - - +
536A VAL* 3.6 18.8 - - + +
539A LEU* 3.5 7.7 - - + +
391B ASN 4.7 1.8 + - - -
392B PRO* 4.6 0.2 - - - +
393B GLN* 1.3 78.7 - - - +
395B SER* 1.3 56.9 + - - +
397B ALA* 4.7 1.8 - - - -
398B GLN* 3.2 25.3 + - - +
481B MET* 3.6 12.7 - - + +
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Residues in contact with SER 395 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
388B LEU* 5.0 15.3 - - - -
392B PRO* 3.9 16.4 + - - -
393B GLN 3.2 0.6 - - - -
394B ALA* 1.3 79.1 - - - +
396B ILE* 1.3 64.0 + - - +
398B GLN* 3.5 2.0 - - - +
399B ILE* 3.3 32.5 + - - +
480B PRO* 3.9 20.1 + - - +
481B MET* 3.9 15.9 - - - -
484B LEU* 6.1 0.2 - - - +
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Residues in contact with ILE 396 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
392B PRO* 3.2 41.9 + - + +
393B GLN* 4.3 1.1 - - - +
395B SER* 1.3 76.3 - - - +
397B ALA* 1.3 60.2 + - - +
399B ILE* 3.2 8.8 + - + +
400B ILE* 3.0 46.7 + - + +
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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
----------------------------------------------------------
536A VAL* 4.0 11.0 - - + -
539A LEU* 4.6 2.7 - - + -
540A LEU* 3.9 23.9 - - + +
393B GLN 3.1 19.5 + - - +
394B ALA 4.6 1.8 - - - +
396B ILE* 1.3 75.9 - - - +
398B GLN* 1.3 61.8 + - - +
400B ILE* 4.0 9.2 - - - -
401B VAL* 3.2 29.0 + - + +
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Residues in contact with GLN 398 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
539A LEU* 3.2 30.5 - - + +
543A ILE* 4.3 5.9 - - - +
394B ALA 3.2 20.6 + - - +
395B SER* 3.5 8.3 - - - +
396B ILE 3.2 0.4 - - - -
397B ALA* 1.3 78.7 - - - +
399B ILE* 1.3 57.4 + - + +
401B VAL* 3.8 3.0 - - - +
402B THR* 2.6 53.2 + - - -
440B SER* 3.4 19.9 + - - +
443B SER* 4.6 1.0 + - - -
480B PRO 5.2 0.7 - - - +
481B MET* 3.5 29.4 + - + +
482B ARG* 5.3 0.9 + - - -
485B PRO* 3.6 29.3 - - + +
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Residues in contact with ILE 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 SER* 3.3 24.7 - - - +
396B ILE* 3.2 8.3 + - + +
398B GLN* 1.3 75.0 - - + +
400B ILE* 1.3 66.2 + - + +
402B THR* 3.4 5.3 + - - -
403B VAL* 3.1 32.3 + - + +
480B PRO 5.2 2.2 - - - +
484B LEU* 4.2 24.2 - - + -
485B PRO* 4.7 16.4 - - + -
488B ILE* 4.0 23.8 - - + -
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Residues in contact with ILE 400 (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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396B ILE* 3.0 39.1 + - + +
397B ALA* 4.3 7.2 - - - +
398B GLN 3.3 0.4 - - - -
399B ILE* 1.3 77.5 - - + +
401B VAL* 1.3 65.8 + - + +
402B THR 3.2 0.3 + - - -
403B VAL* 3.3 5.9 + - - +
404B VAL* 3.0 42.1 + - + +
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Residues in contact with VAL 401 (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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539A LEU* 5.1 1.8 - - + +
540A LEU* 4.3 26.9 - - + -
543A ILE* 3.6 41.7 - - + +
544A CYS* 6.0 5.2 - - - -
397B ALA* 3.2 19.9 + - + +
398B GLN* 3.8 3.6 - - - +
400B ILE* 1.3 82.1 - - + +
402B THR* 1.3 59.1 + - - +
404B VAL* 4.3 9.2 - - + -
405B LEU* 3.3 25.4 + - - +
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Residues in contact with THR 402 (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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543A ILE* 5.0 2.3 - - - +
398B GLN* 2.6 39.5 + - - -
399B ILE* 3.8 7.6 - - - -
400B ILE 3.2 0.4 - - - -
401B VAL* 1.3 79.8 - - - +
403B VAL* 1.3 60.1 + - - +
404B VAL 3.4 0.2 - - - -
405B LEU* 3.8 2.2 - - - -
406B GLY* 2.8 25.8 + - - -
436B ASN* 4.9 7.5 + - - +
437B GLN* 5.5 0.9 - - - +
485B PRO* 3.6 30.0 - - + +
488B ILE* 5.3 4.5 - - + -
489B PHE* 3.7 28.1 - - + +
492B ILE* 4.8 1.1 - - - +
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Residues in contact with VAL 403 (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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399B ILE* 3.1 23.5 + - + +
400B ILE* 3.7 4.9 - - - +
402B THR* 1.3 75.9 - - - +
404B VAL* 1.3 59.6 + - + +
406B GLY 3.2 0.9 + - - -
407B LEU* 2.9 46.2 + - + +
488B ILE* 3.9 16.8 - - + -
492B ILE* 3.8 27.2 - - + +
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Residues in contact with VAL 404 (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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547A PHE* 5.5 6.1 - - + -
400B ILE* 3.0 30.8 + - + +
401B VAL* 4.3 7.9 - - + -
403B VAL* 1.3 79.0 - - + +
405B LEU* 1.3 62.6 + - - +
407B LEU* 3.4 9.4 + - + +
408B VAL* 3.2 32.0 + - + +
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Residues in contact with LEU 405 (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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543A ILE* 3.7 17.3 - - + +
546A VAL* 3.8 11.7 - - + -
547A PHE* 4.0 39.5 - - + +
550A ILE* 4.2 4.9 - - + -
401B VAL 3.3 17.9 + - - +
402B THR* 4.1 2.5 - - - +
403B VAL 3.3 0.4 - - - -
404B VAL* 1.3 78.9 - - - +
406B GLY* 1.3 62.0 + - - +
408B VAL* 3.4 2.9 + - + +
409B ILE* 3.1 46.7 + - + +
432B PHE 5.6 0.2 - - - +
436B ASN* 3.4 39.3 - - + +
489B PHE* 4.6 0.4 - - + -
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Residues in contact with GLY 406 (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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402B THR 2.8 20.2 + - - -
403B VAL 3.7 1.3 - - - -
405B LEU* 1.3 76.9 - - - +
407B LEU* 1.3 57.3 + - - +
409B ILE* 4.8 0.2 - - - -
410B GLY* 3.2 19.2 + - - -
489B PHE* 3.6 20.3 - - - -
492B ILE* 3.4 16.8 - - - +
493B VAL* 3.4 17.5 - - - +
496B MET* 4.1 0.2 - - - +
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Residues in contact with LEU 407 (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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403B VAL* 2.9 36.7 + - + +
404B VAL* 3.9 9.2 - - + +
405B LEU 3.2 0.2 - - - -
406B GLY* 1.3 76.0 - - - +
408B VAL* 1.3 60.7 + - + +
410B GLY 3.6 0.4 + - - -
411B ALA* 3.0 28.1 + - - +
492B ILE* 4.1 11.0 - - + -
495B PHE* 5.8 4.5 - - + -
496B MET* 3.7 28.3 - - + +
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Residues in contact with VAL 408 (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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547A PHE* 3.6 38.6 - - + -
550A ILE* 4.9 5.4 - - + -
551A PHE* 4.3 8.7 - - + -
565A LEU* 5.0 8.3 - - + -
568A LEU* 4.9 7.2 - - + -
404B VAL* 3.2 23.8 + - + +
405B LEU 3.4 3.6 + - - +
407B LEU* 1.3 77.2 - - + +
409B ILE* 1.3 59.5 + - - +
411B ALA* 3.1 5.3 + - - +
412B ILE* 3.0 49.6 + - + +
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Residues in contact with ILE 409 (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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550A ILE* 3.7 21.1 - - + -
405B LEU* 3.1 37.3 + - + +
406B GLY 4.4 2.5 - - - +
408B VAL* 1.3 75.3 - - - +
410B GLY* 1.3 61.2 + - - +
412B ILE* 4.7 5.2 - - - +
413B TYR* 3.5 26.8 + - + -
429B VAL* 3.6 28.5 - - + +
432B PHE* 4.2 26.2 - - + +
433B LEU* 4.6 10.3 - - + -
489B PHE* 4.2 17.3 - - + -
493B VAL* 4.7 6.5 - - + -
497B LEU* 3.6 7.0 - - - +
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Residues in contact with GLY 410 (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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406B GLY 3.2 14.5 + - - -
407B LEU 3.6 0.2 + - - -
408B VAL 3.2 0.6 - - - -
409B ILE* 1.3 78.4 - - - +
411B ALA* 1.3 56.6 + - - +
414B PHE* 3.4 26.0 + - - +
493B VAL* 4.7 1.3 - - - +
496B MET* 3.5 36.2 - - - +
497B LEU* 3.7 15.8 - - - +
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Residues in contact with ALA 411 (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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564A TRP* 3.8 32.7 - - + -
565A LEU* 3.8 15.1 - - + +
407B LEU 3.0 18.5 + - - +
408B VAL* 3.1 6.5 + - - +
410B GLY* 1.3 75.9 - - - +
412B ILE* 1.3 64.7 + - - +
414B PHE* 3.7 15.8 - - - +
496B MET* 4.3 6.3 - - + -
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Residues in contact with ILE 412 (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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550A ILE* 3.7 22.2 - - + -
551A PHE* 3.6 32.1 - - + -
556A VAL* 4.0 29.6 - - + -
561A ILE* 4.6 14.6 - - + -
565A LEU* 3.8 19.1 - - + -
408B VAL* 3.0 28.1 + - + +
409B ILE* 4.4 1.3 - - - +
411B ALA* 1.3 79.6 - - - +
413B TYR* 1.3 73.8 + - + +
414B PHE 3.2 4.6 + - - +
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Residues in contact with TYR 413 (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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550A ILE* 5.3 5.2 - - + -
555A LEU* 4.4 2.2 - - - +
556A VAL* 3.4 35.6 + - + +
409B ILE* 3.5 19.1 + - + -
412B ILE* 1.3 87.5 - - + +
414B PHE* 1.3 62.2 + - - +
415B GLY 3.4 1.7 + - - -
416B LEU* 3.4 23.7 - - + +
424B GLN 4.8 1.5 + - - -
425B ASN* 3.5 55.0 - - + -
428B GLY* 3.9 13.8 + - - -
429B VAL* 3.7 27.8 - - + -
432B PHE* 4.1 15.3 - + - -
497B LEU* 3.3 27.1 - - + +
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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