Contacts of the helix formed by residues 473 - 490 (chain B) in PDB entry 6AHU
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 LYS 473 (chain B).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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469B GLU 3.6 13.4 + - - +
470B THR* 3.3 16.1 + - - +
471B CYS 3.3 1.0 - - - -
472B LYS* 1.3 76.9 - - + +
474B PRO* 1.3 70.2 - - + +
475B ASP* 3.3 7.0 + - + +
476B SER* 3.5 17.3 + - - +
477B VAL* 3.4 17.2 - - - +
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Residues in contact with PRO 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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472B LYS 3.4 8.5 - - - +
473B LYS* 1.3 81.8 - - + +
475B ASP* 1.3 71.4 + - - +
476B SER 3.4 0.4 - - - -
477B VAL* 3.6 11.0 + - + +
478B SER* 3.6 20.3 + - - -
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Residues in contact with ASP 475 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
473B LYS* 3.2 5.0 - - + -
474B PRO* 1.3 85.1 - - - +
476B SER* 1.3 61.1 + - - +
478B SER* 3.7 3.9 + - - -
479B LEU* 3.1 28.3 + - - +
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Residues in contact with SER 476 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
452B VAL* 5.6 1.4 - - - +
467B TRP* 5.6 2.6 - - - -
470B THR* 3.6 39.9 + - - +
473B LYS* 3.5 14.6 + - - +
474B PRO 3.4 0.4 - - - -
475B ASP* 1.3 76.0 - - - +
477B VAL* 1.3 59.4 + - - +
478B SER 3.5 0.2 - - - -
479B LEU* 3.7 12.6 - - - +
480B HIS* 3.1 28.1 + - - +
550B HIS* 5.9 1.7 + - - -
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Residues in contact with VAL 477 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
452B VAL* 4.3 18.1 - - + +
453B HIS* 3.6 32.1 + - + +
471B CYS* 3.4 40.8 - - - +
473B LYS 3.4 9.9 - - - +
474B PRO* 3.6 12.1 + - + +
475B ASP 3.2 0.8 - - - -
476B SER* 1.3 77.9 - - - +
478B SER* 1.3 61.9 + - - +
479B LEU 3.4 0.3 + - - -
480B HIS* 3.5 10.7 + - - +
481B CYS* 3.6 10.9 + - - +
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Residues in contact with SER 478 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
474B PRO 3.6 12.6 + - - -
475B ASP* 4.3 3.6 - - - -
477B VAL* 1.3 79.7 - - - +
479B LEU* 1.3 62.6 + - - +
480B HIS 3.4 0.2 - - - -
481B CYS* 3.6 8.6 + - - +
482B ARG* 3.5 36.6 + - - +
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Residues in contact with LEU 479 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
475B ASP 3.1 19.4 + - - +
476B SER* 3.9 11.9 - - - +
477B VAL 3.2 0.4 - - - -
478B SER* 1.3 76.5 - - - +
480B HIS* 1.3 59.3 + - - +
482B ARG* 3.2 17.3 + - + +
483B GLN* 3.0 39.8 + - - +
547B GLU* 3.3 52.5 - - + +
548B CYS* 4.4 2.0 - - - +
550B HIS* 5.0 13.5 - - + +
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Residues in contact with HIS 480 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
449B ALA* 4.1 9.7 - - + +
450B ALA* 2.5 30.9 + - + -
452B VAL* 4.0 24.7 - - + -
467B TRP* 4.3 9.9 - + + -
476B SER 3.1 17.9 + - - +
477B VAL 3.9 5.2 - - - +
478B SER 3.4 0.2 - - - -
479B LEU* 1.3 74.3 - - - +
481B CYS* 1.3 60.6 + - - +
483B GLN* 3.4 19.5 + - - +
484B GLU* 3.1 31.1 + - + +
507B LEU* 5.0 2.5 - - + -
508B THR* 3.3 47.2 + - + -
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Residues in contact with CYS 481 (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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453B HIS* 5.4 9.2 - - - +
477B VAL 3.6 9.5 + - - +
478B SER* 3.6 11.6 + - - +
479B LEU 3.2 0.4 - - - -
480B HIS* 1.3 79.9 - - - +
482B ARG* 1.3 58.4 + - + +
484B GLU* 3.4 8.5 + - - +
485B ALA* 3.0 29.9 + - - +
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Residues in contact with ARG 482 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
478B SER* 3.5 24.7 + - - +
479B LEU* 3.2 18.8 + - + +
481B CYS* 1.3 76.6 - - + +
483B GLN* 1.3 64.0 + - - +
485B ALA* 4.0 6.3 - - - +
486B ILE* 3.4 22.7 + - + +
547B GLU* 2.8 34.6 + - - -
548B CYS* 3.6 24.2 - - - -
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Residues in contact with GLN 483 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
479B LEU* 3.0 26.4 + - - +
480B HIS* 3.8 20.9 + - + +
481B CYS 3.3 0.2 - - - -
482B ARG* 1.3 78.5 - - - +
484B GLU* 1.3 59.0 + - - +
486B ILE* 4.5 1.1 - - - +
487B PHE* 3.3 21.5 + - - +
505B LEU* 4.5 5.1 - - + +
506B GLY 3.5 6.8 + - - +
507B LEU* 3.3 38.1 - - + +
508B THR* 4.2 1.7 + - - -
547B GLU 4.1 3.2 + - - -
548B CYS* 2.9 45.3 + - - +
550B HIS* 3.5 25.1 - - - +
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Residues in contact with GLU 484 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
449B ALA* 3.8 36.5 + - + +
450B ALA 5.1 1.6 - - - +
451B SER* 6.0 0.7 - - - -
480B HIS* 3.1 25.3 + - + +
481B CYS* 3.9 8.1 - - - +
483B GLN* 1.3 76.7 - - - +
485B ALA* 1.3 56.3 + - - +
487B PHE* 3.2 8.1 + - + -
488B GLU* 2.7 59.9 + - + +
507B LEU* 5.1 0.4 - - - -
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Residues in contact with ALA 485 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
481B CYS* 3.0 21.1 + - - +
482B ARG* 4.0 7.6 - - - +
483B GLN 3.4 0.2 - - - -
484B GLU* 1.3 77.4 - - - +
486B ILE* 1.3 59.2 - - + +
488B GLU* 3.5 10.1 + - - +
489B LEU* 2.9 25.9 + - - +
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Residues in contact with ILE 486 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
482B ARG* 3.4 9.0 + - + +
483B GLN* 4.5 2.9 - - - +
484B GLU 3.4 0.2 - - - -
485B ALA* 1.3 77.2 - - + +
487B PHE* 1.3 57.4 + - - +
489B LEU* 3.1 16.6 + - + +
490B LEU* 3.0 29.9 + - + +
505B LEU* 3.9 22.7 - - + -
539B LEU* 4.0 31.0 - - + -
545B PRO* 4.8 10.3 - - + -
548B CYS* 3.7 32.1 - - + -
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Residues in contact with PHE 487 (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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443B LEU* 3.2 44.2 - - + -
444B THR* 3.5 23.6 - - + +
447B ILE* 3.2 37.5 - - + -
448B LYS* 4.8 4.3 - - - -
449B ALA* 4.9 9.0 - - + -
483B GLN 3.3 19.4 + - - +
484B GLU* 3.2 8.7 + - + +
486B ILE* 1.3 79.5 - - - +
488B GLU* 1.3 66.2 + - + +
490B LEU* 3.4 36.3 + - + +
505B LEU* 5.2 2.6 - - + +
507B LEU* 3.8 26.9 - - + -
599B LEU* 3.9 11.2 - - + -
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Residues in contact with GLU 488 (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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444B THR* 4.8 5.5 - - + +
484B GLU* 2.7 49.9 + - + +
485B ALA* 4.0 7.7 - - - +
487B PHE* 1.3 75.4 - - + +
489B LEU* 1.3 62.2 + - - +
490B LEU 3.2 0.7 - - - -
491B GLY* 3.4 12.8 + - - +
492B GLY 4.2 1.9 + - - -
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Residues in contact with LEU 489 (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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485B ALA 2.9 18.1 + - - +
486B ILE* 3.1 24.4 + - + +
488B GLU* 1.3 74.5 - - - +
490B LEU* 1.3 59.0 + - - +
491B GLY 3.2 0.9 - - - -
492B GLY* 3.0 20.8 + - - +
493B ILE* 3.2 15.8 + - + +
532B ASP* 4.6 12.1 - - + +
535B LYS* 3.3 51.4 - - + +
536B VAL* 3.8 21.8 - - + +
539B LEU* 4.9 9.9 - - + -
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Residues in contact with LEU 490 (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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440B HIS* 2.9 49.7 + - + +
443B LEU* 4.8 7.6 - - + -
444B THR* 3.7 12.1 + - - +
486B ILE* 3.0 21.3 + - + +
487B PHE* 3.4 40.2 - - + +
488B GLU 3.2 0.6 - - - -
489B LEU* 1.3 75.4 - - - +
491B GLY* 1.3 58.6 + - - +
493B ILE* 2.9 33.8 + - + +
499B ILE* 6.2 1.6 - - + -
505B LEU* 5.5 9.0 - - + -
539B LEU* 4.5 9.2 - - + -
599B LEU* 5.0 3.6 - - + -
618B TRP* 4.8 13.2 - - + -
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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