Contacts of the helix formed by residues 473 - 485 (chain B) in PDB entry 6T8B
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 473 (chain B).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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548A ARG* 5.4 1.3 - - - -
472B LYS* 1.3 81.7 + - - +
474B VAL* 1.3 58.1 + - - +
475B GLY 3.0 4.5 - - - -
476B VAL* 3.2 5.9 + - - +
477B ASN* 2.9 36.8 + - - -
500B LYS* 5.9 0.2 - - - +
503B GLU* 3.4 30.7 + - - +
595B ASP* 4.2 10.5 + - - -
801B AGS 2.8 8.5 + - - -
802B MG 2.0 30.8 - - - -
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Residues in contact with VAL 474 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
548A ARG* 4.8 12.6 - - - +
471B GLY 3.6 2.6 + - - +
473B SER* 1.3 76.7 - - - +
475B GLY* 1.3 56.3 + - - +
477B ASN* 3.9 7.6 - - - +
478B ALA* 3.0 26.3 + - - +
694B ALA 3.5 12.0 - - - +
695B PHE* 3.8 8.7 - - + -
696B VAL* 3.3 37.4 - - - +
801B AGS 3.2 55.5 + - + +
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Residues in contact with GLY 475 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
464B VAL* 6.1 0.7 - - - -
471B GLY 3.2 16.1 + - - -
472B LYS 4.6 1.1 - - - -
473B SER 3.0 1.0 - - - -
474B VAL* 1.3 77.3 - - - +
476B VAL* 1.3 59.0 + - - +
478B ALA* 3.2 6.7 + - - +
479B MET* 2.9 40.0 + - - +
652B PHE* 4.4 15.5 - - - -
678B MET* 5.7 3.6 - - - -
694B ALA 5.4 1.3 - - - -
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Residues in contact with VAL 476 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
464B VAL* 4.7 14.8 - - + +
472B LYS 3.2 21.2 + - - +
473B SER* 3.2 9.8 + - - +
475B GLY* 1.3 76.0 - - - +
477B ASN* 1.3 58.4 + - - +
479B MET* 3.3 11.2 + - + +
480B LEU* 2.9 38.6 + - + +
504B LEU* 4.2 10.8 - - + -
593B VAL* 3.8 28.7 - - + -
595B ASP* 5.4 7.6 - - + +
627B ILE* 5.2 4.7 - - + -
628B LEU 4.9 2.5 - - - +
629B ALA* 4.5 16.6 - - + -
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Residues in contact with ASN 477 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
548A ARG* 3.3 37.5 + - - +
473B SER 2.9 23.7 + - - +
474B VAL* 4.0 8.0 - - - +
476B VAL* 1.3 74.6 - - - +
478B ALA* 1.3 60.4 + - - +
480B LEU* 4.4 0.2 - - - -
481B LEU* 2.9 36.4 + - - +
503B GLU* 4.7 4.9 + - - +
504B LEU* 4.3 8.4 - - - +
507B TYR* 2.8 37.6 + - - +
696B VAL* 4.8 9.2 + - + +
698B ASP* 4.9 0.8 + - - -
701B VAL* 4.4 15.5 - - + +
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Residues in contact with ALA 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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423B PHE* 3.2 27.5 - - + -
442B ALA 4.2 8.3 - - - +
443B LEU* 5.3 2.0 - - - +
474B VAL 3.0 20.0 + - - +
475B GLY* 3.2 7.6 + - - +
477B ASN* 1.3 76.2 - - - +
479B MET* 1.3 56.9 + - + +
482B SER* 2.8 33.4 + - - -
694B ALA* 4.1 10.3 - - + +
696B VAL* 3.9 12.9 - - + +
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Residues in contact with MET 479 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
441B LEU* 3.6 23.3 - - + +
442B ALA 5.2 1.8 - - - +
443B LEU* 3.8 17.7 - - + -
462B LEU* 3.6 20.2 - - + -
464B VAL* 3.7 23.1 - - + -
475B GLY* 2.9 23.2 + - - +
476B VAL* 3.5 12.6 - - + +
478B ALA* 1.3 77.7 - - + +
480B LEU* 1.3 58.4 + - + +
482B SER* 3.1 8.7 + - - -
483B ILE* 2.9 31.9 + - - +
627B ILE* 4.4 16.4 - - + -
650B ILE* 3.7 33.4 - - + -
652B PHE* 5.9 2.5 - - + -
678B MET* 5.9 0.7 - - + -
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Residues in contact with LEU 480 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
476B VAL* 2.9 27.5 + - + +
479B MET* 1.3 78.2 - - + +
481B LEU* 1.3 58.3 + - - +
483B ILE* 3.0 11.0 + - + +
484B LEU* 2.9 33.3 + - + +
494B LEU* 3.9 27.4 - - + -
496B MET* 3.5 21.8 - - + -
504B LEU* 3.7 16.6 - - + -
507B TYR* 3.5 34.1 - - + +
591B VAL* 5.6 0.4 - - + -
593B VAL* 3.7 27.6 - - + -
627B ILE* 5.8 1.6 - - + -
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Residues in contact with LEU 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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321B LEU* 3.8 28.3 - - + -
423B PHE* 3.7 20.5 - - + -
427B LEU* 4.7 0.2 - - - +
432B TYR* 4.1 0.3 + - - -
477B ASN 2.9 27.8 + - - +
478B ALA* 4.8 0.2 - - - -
480B LEU* 1.3 73.0 - - - +
482B SER* 1.3 64.5 + - - +
484B LEU* 3.8 6.7 - - + +
485B PHE* 3.4 31.2 + - + +
507B TYR* 3.3 28.3 - - + +
696B VAL* 3.9 18.2 - - + -
700B GLU 4.5 1.3 - - - +
701B VAL* 3.8 18.6 - - + -
704B VAL* 3.9 25.6 - - + -
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Residues in contact with SER 482 (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* 3.5 3.8 - - - -
432B TYR* 2.7 33.4 + - - -
440B PRO* 3.4 19.9 - - - +
441B LEU* 3.8 1.1 - - - -
442B ALA* 2.8 44.3 + - - +
478B ALA 2.8 18.8 + - - -
479B MET 3.1 11.0 + - - -
481B LEU* 1.3 75.9 - - - +
483B ILE* 1.3 64.6 + - - +
486B LYS* 3.9 0.7 - - - +
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Residues in contact with ILE 483 (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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438B THR 5.0 0.7 - - - +
439B VAL* 3.4 28.9 - - + -
440B PRO* 3.3 25.1 - - - +
441B LEU* 3.9 8.3 - - + -
456B LEU* 5.0 2.2 - - + -
479B MET 2.9 15.2 + - - +
480B LEU* 3.0 20.6 + - + +
482B SER* 1.3 78.2 - - - +
484B LEU* 1.3 64.9 + - + +
486B LYS* 4.2 0.5 - - - +
487B SER* 3.3 25.5 + - - +
492B ALA* 4.1 25.8 - - + +
494B LEU* 4.3 23.1 - - + -
512B HIS* 5.6 1.3 - - + -
591B VAL* 5.1 5.2 - - + -
627B ILE* 5.9 1.1 - - + -
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Residues in contact with LEU 484 (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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315B LEU* 4.1 1.4 - - - +
480B LEU* 2.9 20.3 + - + +
481B LEU* 3.6 6.9 + - + +
482B SER 3.2 0.2 - - - -
483B ILE* 1.3 75.3 - - + +
485B PHE* 1.3 62.9 + - + +
486B LYS 3.1 9.9 + - - -
487B SER 3.5 9.3 + - - +
494B LEU* 4.5 12.1 - - + -
507B TYR* 4.3 26.2 - - + -
510B ILE* 4.4 12.8 - - + -
512B HIS* 3.4 38.8 - - + +
704B VAL* 3.9 16.4 - - + -
705B VAL* 5.6 0.7 - - + -
708B TRP* 3.0 46.5 - - + +
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Residues in contact with PHE 485 (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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315B LEU* 4.2 14.2 - - - +
316B PRO* 3.8 38.5 - - + +
317B PRO 4.2 13.0 - - - -
318B LEU* 3.7 24.0 - - + +
320B LEU* 4.8 4.5 - - + -
321B LEU* 3.8 30.7 - - + -
427B LEU* 3.4 20.6 - - + -
432B TYR* 3.2 22.5 + - + +
481B LEU* 3.4 14.5 + - + +
483B ILE 3.5 0.4 - - - -
484B LEU* 1.3 80.0 - - + +
486B LYS* 1.3 57.2 + - - +
704B VAL* 3.4 41.3 - - + -
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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