Contacts of the helix formed by residues 468 - 479 (chain A) in PDB entry 1SLY
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 GLN 468 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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454A ASN* 2.7 34.4 + - - +
457A PHE* 3.9 14.9 - - + +
458A LYS* 3.3 37.1 - - - +
461A THR* 3.7 22.2 + - - +
466A ILE 3.5 1.8 + - - -
467A PRO* 1.3 71.4 - - - +
469A SER* 1.3 54.4 + - - +
471A ALA* 2.8 28.4 + - - +
472A MET* 3.0 23.7 + - - +
602A MET* 4.2 14.0 - - + +
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Residues in contact with SER 469 (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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467A PRO* 4.1 11.6 - - - +
468A GLN* 1.3 76.1 - - - +
470A TYR* 1.3 60.0 + - - +
472A MET* 4.0 2.7 - - - +
473A ALA* 2.8 29.6 + - - +
595A ASP* 2.9 19.3 + - - +
598A TYR* 3.9 20.7 - - - +
599A ARG* 3.6 22.3 + - - +
602A MET* 4.0 21.1 - - - +
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Residues in contact with TYR 470 (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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466A ILE* 4.4 14.6 - - + -
467A PRO* 3.4 20.8 + - + +
468A GLN 3.2 0.4 - - - -
469A SER* 1.3 80.9 + - - +
471A ALA* 1.3 63.6 + - - +
473A ALA* 3.4 1.2 - - - +
474A ILE* 3.1 34.1 + - + +
534A LEU* 3.4 31.9 - - + +
538A TYR* 4.1 13.9 - + - -
545A ARG* 3.8 21.1 - - + -
548A SER* 2.8 29.4 + - - -
549A SER* 3.1 34.0 + - - -
591A VAL* 3.8 16.2 - - + -
592A LEU* 6.1 0.9 - - + -
595A ASP* 3.4 24.9 - - - +
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Residues in contact with ALA 471 (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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457A PHE* 3.9 23.5 - - + -
461A THR* 3.9 18.2 - - + -
466A ILE* 4.7 6.3 - - + -
467A PRO 3.2 11.0 + - - +
468A GLN 2.8 17.9 + - - +
470A TYR* 1.3 71.1 - - - +
472A MET* 1.3 60.2 + - - +
474A ILE* 3.1 13.9 + - - +
475A ALA* 3.1 13.3 + - - +
495A MET* 4.7 3.3 - - + +
531A THR* 4.6 7.6 - - + -
534A LEU* 4.3 11.9 - - + -
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Residues in contact with MET 472 (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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451A LEU* 3.8 32.1 - - + -
452A ALA 3.3 25.8 - - - +
454A ASN* 4.2 8.3 - - - +
457A PHE* 3.6 23.8 - - + -
468A GLN* 3.0 30.9 + - - +
469A SER 4.0 5.2 - - - +
471A ALA* 1.3 72.6 - - - +
473A ALA* 1.3 52.3 + - - +
475A ALA* 4.4 0.7 - - - -
476A ARG* 2.8 36.4 + - - +
481A TRP* 3.7 16.1 - - + -
598A TYR* 4.1 15.0 - - + -
602A MET* 3.5 22.2 - - - -
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Residues in contact with ALA 473 (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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469A SER 2.8 23.2 + - - +
470A TYR* 3.4 7.2 - - - +
472A MET* 1.3 71.1 - - - +
474A ILE* 1.3 60.3 + - - +
476A ARG* 3.5 6.5 - - - +
477A GLN* 3.1 24.3 + - - +
591A VAL* 3.8 16.8 - - + +
594A TYR* 4.2 6.2 - - + -
595A ASP* 3.7 30.5 - - + +
598A TYR* 4.0 6.6 - - - -
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Residues in contact with ILE 474 (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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470A TYR* 3.1 32.4 + - + +
471A ALA 3.1 7.6 + - - +
473A ALA* 1.3 71.9 - - - +
475A ALA* 1.3 57.7 + - - +
477A GLN* 3.7 1.4 - - - +
478A GLU* 2.8 36.5 + - + +
495A MET* 4.4 10.5 - - + -
534A LEU* 3.6 23.3 - - + -
549A SER* 4.1 6.3 - - - +
552A TYR* 3.9 29.2 - - + +
587A TYR* 3.7 24.2 - - + +
591A VAL* 3.5 27.4 - - + -
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Residues in contact with ALA 475 (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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457A PHE* 3.9 11.2 - - + -
471A ALA 3.1 11.3 + - - +
472A MET 3.7 2.7 - - - +
474A ILE* 1.3 74.8 - - - +
476A ARG* 1.3 62.0 + - - +
478A GLU* 3.1 0.6 + - - -
479A SER* 3.0 31.4 + - - -
480A ALA 3.6 0.3 + - - -
481A TRP* 3.6 32.5 - - + -
494A LEU* 3.5 19.1 - - + +
495A MET* 4.0 11.6 - - + +
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Residues in contact with ARG 476 (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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433A VAL* 3.9 22.3 - - - +
437A ILE* 5.2 5.9 - - - +
448A ARG* 2.6 42.0 + - - +
449A PHE* 3.1 36.9 - - + -
472A MET 2.8 22.0 + - - +
473A ALA* 3.5 5.4 - - - +
475A ALA* 1.3 71.8 - - - +
477A GLN* 1.3 57.9 + - - +
480A ALA* 2.9 33.0 + - - +
481A TRP* 3.4 27.9 - - - +
594A TYR* 4.0 19.2 + - + -
598A TYR* 3.4 17.9 - - + +
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Residues in contact with GLN 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 ALA 3.1 14.9 + - - +
474A ILE 3.8 2.2 - - - +
476A ARG* 1.3 80.5 - - - +
478A GLU* 1.3 64.2 + - - +
479A SER 3.6 0.2 + - - -
480A ALA* 4.5 1.7 + - - +
587A TYR* 3.6 42.8 - - + -
590A ASN* 3.1 39.6 + - - +
591A VAL* 3.7 15.0 - - + -
594A TYR* 3.4 21.1 + - + -
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Residues in contact with GLU 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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474A ILE* 2.8 32.7 + - + +
475A ALA 3.1 2.9 + - - +
477A GLN* 1.3 75.6 - - - +
479A SER* 1.3 60.8 + - - +
485A VAL* 6.1 0.2 - - - +
494A LEU 4.1 7.0 - - - +
495A MET 4.0 11.7 - - - +
496A GLN* 3.5 38.2 - - + +
552A TYR* 3.7 3.8 - - - -
553A ASN* 5.3 0.2 + - - -
587A TYR* 2.6 34.8 + - - +
619A BLG 2.6 38.1 + - - -
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Residues in contact with SER 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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475A ALA 3.0 8.0 + - - -
478A GLU* 1.3 78.0 - - - +
480A ALA* 1.3 72.2 + - - +
481A TRP* 2.8 13.5 + - - -
482A ASN* 3.1 18.0 + - - +
485A VAL* 3.5 30.1 - - - +
493A GLY 3.7 6.7 - - - -
494A LEU* 2.9 29.8 + - - +
496A GLN* 4.5 0.2 - - - -
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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
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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