Contacts of the helix formed by residues 472 - 485 (chain A) in PDB entry 6T8O
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 472 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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464A VAL* 3.9 26.2 - - + -
465A ALA 5.0 0.2 - - - -
466A GLY 4.2 14.8 - - - +
470A SER* 4.2 10.5 - - - +
471A GLY* 1.3 74.1 - - - +
473A SER* 1.3 60.3 + - - +
474A VAL 3.2 1.1 - - - -
475A GLY* 3.1 1.8 + - - -
476A VAL* 2.9 32.8 + - + +
500A LYS* 5.3 3.4 - - - +
595A ASP* 3.8 27.9 + - - -
596A GLU* 4.1 6.3 + - - -
629A ALA* 4.6 4.6 - - + +
630A THR 3.3 29.1 + - - +
631A GLN* 3.7 17.6 - - - +
652A PHE* 4.1 9.1 - - + -
801A ADP 2.5 35.9 + - - +
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Residues in contact with SER 473 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
472A LYS* 1.3 73.2 + - - +
474A VAL* 1.3 61.1 + - - -
476A VAL* 3.4 7.8 + - - +
477A ASN* 2.9 39.5 + - - -
503A GLU* 3.5 33.2 + - - +
504A LEU* 5.4 4.1 - - - +
595A ASP* 4.6 10.4 + - - -
801A ADP 2.6 34.0 + - - -
548F ARG* 6.1 0.9 - - - -
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Residues in contact with VAL 474 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
471A GLY 4.6 1.1 - - - -
472A LYS 3.2 0.2 - - - -
473A SER* 1.3 77.2 - - - +
475A GLY* 1.3 58.0 + - - +
477A ASN* 3.4 10.1 + - - +
478A ALA* 2.9 27.9 + - - +
694A ALA 3.8 9.0 - - - +
695A PHE* 4.0 9.0 - - + -
696A VAL* 3.8 33.5 - - + +
801A ADP 3.5 63.6 + - + +
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Residues in contact with GLY 475 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
471A GLY 3.7 11.2 + - - -
472A LYS 3.1 9.8 + - - -
474A VAL* 1.3 79.4 - - - +
476A VAL* 1.3 56.9 + - - +
478A ALA* 3.3 6.7 + - - +
479A MET* 3.0 39.9 + - - +
652A PHE* 4.6 11.7 - - - -
678A MET* 5.6 4.5 - - - -
694A ALA 5.7 0.7 - - - -
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Residues in contact with VAL 476 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
464A VAL* 5.1 7.6 - - + -
472A LYS* 2.9 19.0 + - + +
473A SER* 3.4 7.4 + - - +
475A GLY* 1.3 75.6 - - - +
477A ASN* 1.3 57.9 + - - +
479A MET* 3.3 8.3 + - + +
480A LEU* 2.9 46.8 + - + +
504A LEU* 4.3 21.8 - - + -
593A VAL* 4.8 12.8 - - + -
594A VAL 6.5 0.7 - - - -
595A ASP* 5.3 6.5 - - - +
627A ILE* 5.0 13.2 - - + -
629A ALA* 4.4 23.6 - - + -
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Residues in contact with ASN 477 (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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473A SER* 2.9 32.3 + - - +
474A VAL* 3.6 9.3 - - - +
476A VAL* 1.3 76.2 - - - +
478A ALA* 1.3 56.5 + - - +
480A LEU 3.4 0.2 + - - -
481A LEU* 2.9 35.5 + - - +
504A LEU* 3.7 13.5 - - - +
506A ILE* 5.2 2.7 - - - +
507A TYR* 2.5 36.8 + - - +
696A VAL* 4.0 17.4 + - + -
698A ASP* 5.1 7.7 + - - -
701A VAL* 4.7 14.8 - - + +
548F ARG* 5.1 7.7 - - - +
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Residues in contact with ALA 478 (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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423A PHE* 3.8 21.3 - - + -
442A ALA 4.3 7.9 - - - +
443A LEU* 5.6 1.3 - - - +
474A VAL 2.9 17.6 + - - +
475A GLY* 3.3 7.4 + - - +
477A ASN* 1.3 73.6 - - - +
479A MET* 1.3 57.5 + - + +
481A LEU* 3.5 1.7 + - - -
482A SER* 2.6 38.0 + - - -
694A ALA* 4.1 18.6 - - + +
696A VAL* 3.8 9.4 - - + +
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Residues in contact with MET 479 (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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441A LEU* 3.7 24.2 - - + +
442A ALA 5.3 1.3 - - - +
443A LEU* 3.8 28.3 - - + -
462A LEU* 3.8 32.3 - - + -
464A VAL* 4.4 9.4 - - + -
475A GLY* 3.0 27.0 + - - +
476A VAL* 3.7 7.6 - - + +
478A ALA* 1.3 76.9 - - + +
480A LEU* 1.3 61.2 + - + +
482A SER* 3.2 6.9 + - - -
483A ILE* 3.0 31.0 + - - +
627A ILE* 4.0 24.0 - - + -
650A ILE* 4.1 16.2 - - + -
652A PHE* 5.7 1.6 - - + -
678A MET* 5.3 2.7 - - + -
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Residues in contact with LEU 480 (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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476A VAL* 2.9 27.3 + - + +
477A ASN 4.1 1.3 - - - +
478A ALA 3.4 0.2 - - - -
479A MET* 1.3 80.1 - - + +
481A LEU* 1.3 59.0 + - - +
483A ILE* 3.2 10.4 + - + +
484A LEU* 2.9 33.1 + - + +
494A LEU* 3.8 32.1 - - + -
496A MET* 4.2 5.6 - - + -
504A LEU* 4.9 2.9 - - + -
507A TYR* 3.6 37.7 - - + +
591A VAL* 5.2 2.5 - - + -
593A VAL* 3.7 42.2 - - + -
627A ILE* 6.0 0.7 - - + -
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Residues in contact with LEU 481 (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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321A LEU* 4.5 5.2 - - + -
423A PHE* 4.4 7.6 - - + -
477A ASN* 2.9 25.2 + - + +
478A ALA* 4.1 4.0 - - - +
480A LEU* 1.3 74.5 - - - +
482A SER* 1.3 60.2 + - - +
484A LEU* 4.0 6.5 - - + +
485A PHE* 2.8 63.3 + - + -
507A TYR* 3.3 28.0 - - + +
696A VAL* 3.8 26.0 - - + -
700A GLU 4.8 3.8 - - - +
701A VAL* 4.4 9.9 - - + -
704A VAL* 4.0 28.7 - - + -
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Residues in contact with SER 482 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
423A PHE* 3.4 7.2 - - - -
427A LEU* 5.2 0.2 - - - -
432A TYR* 3.2 23.7 + - - -
440A PRO* 3.3 31.2 - - - +
441A LEU* 3.9 2.5 - - - -
442A ALA* 3.0 38.9 + - - +
478A ALA 2.6 23.1 + - - -
479A MET 3.2 5.8 + - - -
481A LEU* 1.3 75.4 - - - +
483A ILE* 1.3 62.2 + - - +
485A PHE* 4.1 0.8 + - - -
486A LYS 4.2 1.4 + - - -
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Residues in contact with ILE 483 (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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438A THR 5.1 0.4 - - - -
439A VAL* 3.7 39.0 - - + -
440A PRO 3.9 8.5 - - - +
441A LEU* 4.3 9.0 - - + -
456A LEU* 4.8 2.2 - - + -
479A MET 3.0 14.6 + - - +
480A LEU* 3.3 20.9 - - + +
481A LEU 3.2 0.2 - - - -
482A SER* 1.3 79.0 - - - +
484A LEU* 1.3 61.3 + - + +
487A SER* 3.1 32.2 + - - -
492A ALA* 4.2 24.2 - - + -
494A LEU* 4.3 23.1 - - + -
512A HIS* 5.7 0.9 - - + -
591A VAL* 4.8 8.1 - - + -
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Residues in contact with LEU 484 (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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316A PRO* 4.2 3.1 - - - +
480A LEU* 2.9 26.0 + - + +
481A LEU* 3.1 12.9 + - + +
483A ILE* 1.3 78.8 - - + +
485A PHE* 1.3 62.7 + - + +
486A LYS 3.2 1.6 + - - -
487A SER 4.0 3.6 - - - +
494A LEU* 4.6 10.8 - - + -
496A MET* 6.0 0.7 - - + -
507A TYR* 5.4 8.5 - - + -
510A ILE* 4.5 17.5 - - + -
512A HIS* 3.4 48.5 - - + +
704A VAL* 4.2 21.3 - - + -
705A VAL* 6.3 0.7 - - + -
708A TRP* 3.3 39.3 + - + +
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Residues in contact with PHE 485 (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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315A LEU* 4.6 9.6 - - - +
316A PRO* 4.4 23.1 - - + +
317A PRO 3.9 19.3 - - - -
318A LEU* 3.6 30.9 - - + +
320A LEU* 5.0 3.6 - - + -
321A LEU* 3.7 31.2 - - + -
423A PHE* 4.2 2.2 - + - -
427A LEU* 3.7 15.3 - - + -
432A TYR* 3.7 15.4 + - - +
481A LEU* 2.8 57.0 + - + +
482A SER 4.1 0.2 + - - -
483A ILE 3.4 0.2 - - - -
484A LEU* 1.3 73.2 - - + +
486A LYS* 1.3 59.3 - - - +
704A VAL* 3.6 24.9 - - + -
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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