Contacts of the strand formed by residues 469 - 478 (chain G) in PDB entry 5IXM
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 TRP 469 (chain G).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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464G PRO* 3.7 5.7 - - - +
465G ILE* 2.7 61.6 + - + +
466G ALA* 3.9 12.8 - - + -
467G ASP 5.2 0.9 - - - -
468G ARG* 1.3 118.8 - - + +
470G ALA* 1.3 64.2 + - - +
491G LEU* 5.9 8.5 - - + -
492G GLN 3.6 4.9 - - - +
493G TYR* 4.0 13.2 - + + +
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Residues in contact with ALA 470 (chain G).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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463G TRP 3.6 11.2 - - - +
464G PRO* 4.6 4.5 - - + -
465G ILE* 3.7 4.2 - - - +
469G TRP* 1.3 79.3 - - - +
471G ILE* 1.3 61.2 + - - +
472G VAL* 5.7 0.4 - - - -
491G LEU* 3.3 5.2 - - - +
492G GLN* 2.6 58.4 + - + +
494G ASN* 5.2 4.7 - - - +
541G THR* 4.9 9.6 - - + -
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Residues in contact with ILE 471 (chain G).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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461G ALA* 4.1 0.7 - - - +
462G SER* 3.4 2.4 + - - -
463G TRP* 2.9 51.7 + - + +
465G ILE* 4.1 21.8 - - + -
470G ALA* 1.3 76.3 - - - +
472G VAL* 1.3 75.3 + - - +
489G VAL* 5.0 10.8 - - + -
490G GLY 3.3 12.8 - - - +
491G LEU* 3.8 16.6 - - + -
541G THR* 5.5 0.2 - - - +
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Residues in contact with VAL 472 (chain G).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
461G ALA 3.2 10.1 - - - +
462G SER* 3.8 10.5 - - - +
470G ALA 5.7 0.4 - - - -
471G ILE* 1.3 84.7 - - - +
473G GLY* 1.3 59.0 + - - +
488G LEU* 4.4 8.3 - - + -
489G VAL* 3.7 3.3 - - - +
490G GLY* 2.9 42.9 + - - +
492G GLN* 6.2 0.2 - - + -
541G THR* 3.5 35.4 - - + -
544G MET* 3.6 36.8 - - + -
545G LEU* 4.1 14.4 - - + -
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Residues in contact with GLY 473 (chain G).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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459G THR 4.5 0.2 - - - -
460G THR* 3.3 6.6 - - - +
461G ALA* 2.9 38.3 + - - +
472G VAL* 1.3 76.0 - - - +
474G ALA* 1.3 63.6 + - - +
488G LEU* 3.3 11.2 - - - -
489G VAL* 4.7 2.2 - - - -
545G LEU* 4.1 1.4 - - - +
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Residues in contact with ALA 474 (chain G).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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459G THR 3.3 9.6 - - - +
460G THR* 4.4 11.7 - - + +
473G GLY* 1.3 75.1 - - - +
475G TYR* 1.3 61.2 + - - +
476G TYR* 4.7 11.4 - - + -
486G SER* 4.0 1.1 + - - +
487G GLN* 3.3 5.7 + - - +
488G LEU* 2.8 56.4 + - + -
545G LEU* 5.2 2.7 - - + -
550G LEU 5.6 3.6 - - - +
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Residues in contact with TYR 475 (chain G).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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457G VAL 3.8 0.9 - - - +
458G GLY* 3.3 2.9 - - - -
459G THR* 2.9 42.6 + - - +
474G ALA* 1.3 73.1 - - - +
476G TYR* 1.3 64.6 + - - +
477G TYR* 3.5 37.3 - + + -
484G PRO* 3.4 30.2 - - + +
486G SER 3.8 1.6 - - - -
487G GLN* 3.8 41.7 - - + -
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Residues in contact with TYR 476 (chain G).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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427G GLN* 5.3 4.7 + - - -
429G ASN* 3.4 30.5 + - - -
456G GLN* 3.4 28.3 - - + -
457G VAL 3.4 2.9 - - - -
458G GLY* 3.5 13.2 - - - -
459G THR 4.5 2.5 - - - -
460G THR* 3.5 22.8 + - - -
474G ALA* 4.7 9.0 - - + -
475G TYR* 1.3 80.4 - - - +
477G TYR* 1.3 61.1 + - - +
484G PRO* 3.6 4.9 - - - +
485G ALA* 2.9 28.7 + - + -
486G SER* 2.9 25.3 + - - +
550G LEU* 3.5 48.7 + - + +
551G PRO 5.5 1.4 + - - -
552G TYR* 6.1 1.2 - - - -
67H VAL 5.1 2.0 - - - -
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Residues in contact with TYR 477 (chain G).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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456G GLN* 3.4 7.8 - - - +
457G VAL* 2.9 45.7 + - + +
475G TYR* 3.5 37.7 - + + -
476G TYR* 1.3 73.6 - - - +
478G ASP* 1.3 86.0 + - - +
479G THR* 3.6 15.5 + - + +
482G LYS* 3.0 27.4 + - + +
483G GLN* 3.5 23.3 - - - -
484G PRO* 3.9 4.7 - - + -
485G ALA* 5.2 0.4 - - - -
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Residues in contact with ASP 478 (chain G).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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455G SER 3.4 16.3 + - - +
456G GLN* 4.8 2.9 - - + +
477G TYR* 1.3 73.6 - - - +
479G THR* 1.3 62.2 + - - +
480G LYS* 3.2 15.4 + - - +
481G ALA* 3.1 30.1 + - + +
482G LYS* 2.9 22.3 + - - -
483G GLN* 2.9 29.3 + - + +
484G PRO 5.5 0.2 - - - -
485G ALA* 4.5 10.3 - - + +
508G ILE* 6.2 1.6 - - + -
70H PHE 5.9 0.5 - - - -
71H ARG* 4.2 13.5 + - - +
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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