Contacts of the helix formed by residues 459 - 480 (chain B) in PDB entry 6G1V
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 THR 459 (chain B).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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428B SER* 3.6 24.2 - - - +
451B PRO 5.2 0.2 - - - +
457B ASN 5.5 0.4 - - - +
458B TYR* 1.3 77.2 - - - +
460B ALA* 1.3 65.6 + - - +
461B GLU* 3.4 19.4 + - - +
462B GLU* 2.9 36.6 + - - +
463B GLU* 3.0 20.6 + - - +
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Residues in contact with ALA 460 (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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458B TYR 4.0 0.2 + - - -
459B THR* 1.3 73.5 - - - +
461B GLU* 1.3 75.3 + - - +
463B GLU* 3.3 12.9 + - - +
464B ALA* 3.0 22.0 + - - +
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Residues in contact with GLU 461 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
459B THR* 3.5 19.9 - - - +
460B ALA* 1.3 91.6 + - - +
462B GLU* 1.3 57.8 + - - +
464B ALA* 3.3 8.3 + - - +
465B LEU* 2.9 26.9 + - - +
507B THR* 3.7 27.4 - - + +
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Residues in contact with GLU 462 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
425B HIS* 2.7 34.8 + - + +
427B ALA* 3.3 2.9 - - - -
428B SER* 2.6 51.2 + - - -
446B PHE* 3.5 20.5 - - + -
451B PRO* 3.9 2.9 - - - -
458B TYR* 3.5 22.0 - - + -
459B THR* 2.9 29.2 + - - +
461B GLU* 1.3 76.7 - - - +
463B GLU* 1.3 59.7 + - - +
465B LEU* 4.2 2.5 - - - -
466B SER* 2.8 30.1 + - - -
507B THR* 4.5 1.1 - - + -
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Residues in contact with GLU 463 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
451B PRO* 3.8 22.5 - - - +
452B LEU* 4.1 19.9 - - + +
454B LYS* 5.1 11.1 - - - +
459B THR 3.0 11.4 + - - +
460B ALA* 3.3 13.5 + - - +
462B GLU* 1.3 77.2 - - - +
464B ALA* 1.3 62.3 + - - +
466B SER* 3.3 1.8 + - - -
467B ARG* 2.9 60.3 + - - +
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Residues in contact with ALA 464 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
460B ALA 3.0 14.4 + - - +
461B GLU* 3.5 10.8 - - - +
463B GLU* 1.3 77.7 - - - +
465B LEU* 1.3 56.9 + - - +
467B ARG* 3.3 9.2 + - - +
468B ARG* 2.9 35.1 + - + +
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Residues in contact with LEU 465 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
423B PHE* 4.4 7.0 - - + -
425B HIS* 4.0 14.4 - - + -
446B PHE* 3.9 19.7 - - + -
461B GLU 2.9 16.5 + - - +
462B GLU* 3.7 4.7 - - - +
463B GLU 3.3 0.2 - - - -
464B ALA* 1.3 76.8 - - - +
466B SER* 1.3 63.4 + - - +
468B ARG* 3.2 19.0 + - - +
469B ILE* 2.9 45.9 + - + +
505B LEU* 4.5 1.8 - - + -
506B ASN* 3.3 46.7 - - - +
507B THR* 3.9 14.1 - - + -
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Residues in contact with SER 466 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
446B PHE* 2.8 30.8 + - - +
449B GLY* 3.2 22.2 - - - -
451B PRO* 3.6 20.9 - - - +
452B LEU* 3.6 7.4 - - - +
462B GLU 2.8 19.9 + - - -
463B GLU 3.7 3.8 - - - -
465B LEU* 1.3 73.7 - - - +
467B ARG* 1.3 57.0 + - - +
469B ILE* 3.1 2.5 + - - +
470B MET* 2.8 32.0 + - - +
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Residues in contact with ARG 467 (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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23B LEU* 4.8 9.1 - - - +
138B THR* 3.9 20.1 + - + +
139B GLU* 4.4 2.5 - - - +
452B LEU* 3.7 36.2 + - + +
463B GLU* 2.9 51.5 + - - +
464B ALA* 3.7 6.7 - - - +
466B SER* 1.3 75.0 - - - +
468B ARG* 1.3 62.7 + - - +
470B MET* 3.6 9.5 + - + +
471B HIS* 3.0 26.0 + - - +
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Residues in contact with ARG 468 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
464B ALA* 2.9 18.0 + - + +
465B LEU* 3.2 22.8 + - + +
467B ARG* 1.3 76.6 - - - +
469B ILE* 1.3 56.7 + - + +
471B HIS* 3.3 6.0 + - - +
472B TYR* 2.9 76.0 + - + +
503B ILE* 4.7 1.8 - - - +
504B ASP 4.8 4.2 + - - -
505B LEU* 4.0 9.9 - - - +
506B ASN 3.1 27.1 + - - +
507B THR* 5.2 1.0 - - - +
508B GLU 4.3 9.0 + - - -
510B MET* 4.3 17.2 - - - +
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Residues in contact with ILE 469 (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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423B PHE* 3.9 29.2 - - + -
443B GLU* 5.6 0.7 - - + +
446B PHE* 4.0 11.7 - - + +
447B VAL* 3.8 37.0 - - + -
465B LEU* 2.9 41.9 + - + +
466B SER 3.7 3.6 - - - +
468B ARG* 1.3 72.8 - - + +
470B MET* 1.3 62.8 + - - +
472B TYR* 3.3 6.0 + - - -
473B TRP* 2.9 49.6 + - + +
505B LEU* 4.2 23.3 - - + -
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Residues in contact with MET 470 (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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134B TYR 4.3 1.6 - - - +
135B LEU* 3.7 39.1 - - + +
138B THR* 4.2 13.5 - - + +
139B GLU* 3.7 8.9 - - + +
446B PHE 3.8 4.5 - - - +
447B VAL 3.1 20.4 - - - +
449B GLY* 3.6 20.9 - - - -
452B LEU* 3.6 42.4 - - + -
466B SER* 2.8 18.5 + - - +
467B ARG* 3.9 9.2 - - - +
469B ILE* 1.3 76.2 - - - +
471B HIS* 1.3 57.6 + - - +
473B TRP* 3.4 4.5 + - - +
474B ALA* 2.9 32.6 + - - +
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Residues in contact with HIS 471 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
139B GLU* 2.7 33.3 + - - +
467B ARG 3.0 19.1 + - - +
468B ARG* 3.8 5.6 - - - +
470B MET* 1.3 74.3 - - - +
472B TYR* 1.3 58.7 + + + +
475B THR* 2.7 61.2 + - - -
478B LYS* 5.7 4.0 - - - -
482B PRO 5.3 3.6 - - - -
484B GLU* 2.6 35.4 + - + -
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Residues in contact with TYR 472 (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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320B LEU* 4.9 0.7 - - - -
468B ARG* 2.9 69.8 + - + -
469B ILE* 3.6 8.5 - - - +
471B HIS* 1.3 78.0 - + + +
473B TRP* 1.3 67.6 + + + +
476B PHE* 2.9 32.9 + - - +
482B PRO* 3.5 34.9 - - + +
483B ASN* 4.7 11.9 - - - -
489B GLU* 6.2 1.3 - - + +
490B SER 4.6 4.1 + - - -
492B TRP* 3.8 23.6 - + + -
503B ILE* 4.6 0.7 - - + -
505B LEU* 3.8 17.5 - - + -
510B MET* 3.3 20.4 - - + +
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Residues in contact with TRP 473 (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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112B MET* 3.9 13.0 - - + +
135B LEU* 5.5 2.7 - - + -
197B PHE* 4.0 8.3 - + - -
223B ILE* 3.6 25.8 - - + +
225B GLN* 2.9 26.2 + - + -
320B LEU* 3.8 21.3 - - + -
421B TYR* 3.6 41.3 - + - -
443B GLU* 5.8 0.9 - - + -
447B VAL* 3.6 36.2 - - + +
469B ILE* 2.9 46.9 + - + +
470B MET* 3.7 6.5 - - - +
472B TYR* 1.3 80.5 - + + +
474B ALA* 1.3 58.4 + - - +
476B PHE* 3.6 2.8 - - - +
477B ALA* 2.8 28.1 + - - +
492B TRP* 4.1 11.4 - + - -
505B LEU* 3.8 20.2 - - + -
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Residues in contact with ALA 474 (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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110B THR* 4.7 0.2 - - - +
112B MET* 4.1 8.7 - - - -
135B LEU* 4.9 1.3 - - + -
139B GLU* 3.5 34.1 - - + +
141B VAL* 4.2 12.8 - - + -
470B MET 2.9 17.7 + - - +
473B TRP* 1.3 74.1 - - - +
475B THR* 1.3 61.6 + - - +
477B ALA* 3.2 8.4 + - - +
478B LYS* 2.9 38.5 + - + +
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Residues in contact with THR 475 (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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471B HIS* 2.7 54.3 + - - -
474B ALA* 1.3 69.5 - - - +
476B PHE* 1.3 63.2 + - - +
478B LYS* 3.2 10.1 + - - +
479B THR* 2.8 40.0 + - + +
481B ASN 3.2 15.3 - - - +
482B PRO 3.6 14.8 - - - +
483B ASN 3.8 14.4 - - - +
484B GLU* 4.3 12.2 - - + +
485B PRO* 5.9 0.2 - - + -
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Residues in contact with PHE 476 (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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195B THR* 4.7 1.1 - - + -
221B ARG* 3.2 24.8 - - + -
222B ALA 3.6 15.3 - - - -
223B ILE* 3.8 25.1 - - + -
318B GLN* 3.6 36.1 - - + -
319B ILE* 3.6 29.2 - - - -
320B LEU* 3.8 21.3 - - + -
419B TYR* 4.1 3.8 - + - -
472B TYR 2.9 19.0 + - - +
473B TRP 3.6 2.0 - - - +
475B THR* 1.3 77.9 - - - +
477B ALA* 1.3 62.9 + - - +
480B GLY* 2.7 43.3 + - - -
481B ASN 3.4 9.3 + - - -
482B PRO* 3.9 9.9 - - + -
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Residues in contact with ALA 477 (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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110B THR* 3.6 18.8 - - + +
112B MET* 3.8 15.3 - - + -
193B THR* 3.7 9.9 - - - +
195B THR* 3.2 34.6 + - + +
221B ARG* 3.0 20.3 + - - +
473B TRP 2.8 18.8 + - - +
474B ALA 3.2 7.4 + - - +
476B PHE* 1.3 77.5 - - - +
478B LYS* 1.3 57.0 + - - +
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Residues in contact with LYS 478 (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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109B THR* 5.1 2.7 - - - -
110B THR* 2.9 27.3 + - - +
139B GLU* 2.8 38.6 + - - +
140B GLU* 4.4 7.6 + - - +
141B VAL* 3.9 14.6 - - - +
193B THR* 4.1 8.2 - - - +
221B ARG* 3.6 7.4 + - - -
471B HIS* 5.7 3.8 - - - -
474B ALA 2.9 25.7 + - - +
475B THR* 3.8 9.4 + - + +
476B PHE 3.2 0.2 - - - -
477B ALA* 1.3 77.3 - - - +
479B THR* 1.3 68.7 + - + +
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Residues in contact with THR 479 (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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221B ARG* 3.8 11.4 + - - -
318B GLN* 5.3 0.7 - - - -
475B THR* 2.8 28.7 + - + +
478B LYS* 1.3 89.4 - - + +
480B GLY* 1.3 60.2 + - - +
481B ASN* 2.9 24.0 + - - +
483B ASN 4.9 1.0 + - - -
485B PRO* 6.5 1.1 - - + -
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Residues in contact with GLY 480 (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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221B ARG* 3.4 22.1 - - - -
318B GLN* 3.6 23.1 - - - +
419B TYR* 3.4 18.2 + - - -
476B PHE* 2.7 31.2 + - - -
479B THR* 1.3 71.7 - - - +
481B ASN* 1.3 57.1 + - - +
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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
------------------------------------------------------------
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