Contacts of the strand formed by residues 483 - 495 (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 GLN 483 (chain G).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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477G TYR* 3.5 7.7 + - - -
478G ASP* 2.9 30.6 + - + +
481G ALA* 3.8 27.5 - - + +
482G LYS* 1.3 79.0 - - - +
484G PRO* 1.3 74.0 - - + +
508G ILE* 3.4 13.8 - - + +
511G TRP* 4.9 2.8 - - - -
517G THR* 5.1 2.8 - - - -
518G SER* 2.7 37.2 + - - -
520G TYR* 3.3 19.8 + - - +
71H ARG* 4.6 8.1 - - - +
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Residues in contact with PRO 484 (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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475G TYR* 3.4 31.4 - - + +
476G TYR 3.6 10.1 - - - +
477G TYR* 3.9 7.8 - - + -
483G GLN* 1.3 86.7 - - + +
485G ALA* 1.3 60.9 + - - +
486G SER 4.6 7.0 - - - +
487G GLN* 5.3 6.1 - - + +
506G ARG* 4.5 13.9 - - - +
508G ILE* 3.3 5.7 - - - +
520G TYR* 2.6 44.1 + - + +
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Residues in contact with ALA 485 (chain G).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
456G GLN* 4.8 7.9 - - + +
476G TYR* 2.9 21.6 + - + +
477G TYR 5.2 0.4 - - - -
478G ASP* 4.9 11.7 - - + +
483G GLN 3.6 2.4 + - - -
484G PRO* 1.3 73.7 - - - +
486G SER* 1.3 63.1 + - - +
506G ARG 4.9 0.4 - - - -
507G LYS* 4.6 0.2 - - - -
508G ILE* 2.9 38.7 + - + +
520G TYR* 5.2 0.2 - - - -
549G ILE* 3.9 0.7 - - - +
550G LEU* 5.0 1.3 - - + -
69H ILE* 3.6 30.8 - - + +
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Residues in contact with SER 486 (chain G).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
474G ALA 4.4 1.5 + - - -
475G TYR* 3.8 2.6 - - - -
476G TYR* 2.9 34.5 + - - +
484G PRO* 3.6 3.4 - - - +
485G ALA* 1.3 81.6 - - - +
487G GLN* 1.3 66.0 + - - +
488G LEU* 5.6 1.9 - - - +
505G GLU* 5.5 2.6 + - - +
506G ARG 3.5 8.3 - - - -
507G LYS* 4.2 5.7 - - - +
548G GLY* 5.3 2.9 - - - -
549G ILE* 3.8 29.8 + - - +
550G LEU* 4.3 18.0 + - - +
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Residues in contact with GLN 487 (chain G).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
474G ALA 3.3 5.6 - - - -
475G TYR* 3.8 30.5 - - + -
484G PRO* 5.3 6.2 - - + +
486G SER* 1.3 80.1 + - - +
488G LEU* 1.3 65.7 + - - +
489G VAL* 4.4 18.3 - - + +
504G TYR* 4.6 16.3 - - + -
505G GLU* 3.3 8.2 - - - +
506G ARG* 2.9 57.4 + - + +
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Residues in contact with LEU 488 (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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472G VAL* 4.4 21.8 - - + -
473G GLY* 3.3 7.2 - - - -
474G ALA* 2.8 56.8 + - + +
486G SER* 5.6 2.0 - - - +
487G GLN* 1.3 79.7 - - - +
489G VAL* 1.3 70.4 + - - +
490G GLY* 5.4 0.2 - - - -
503G GLY* 6.4 0.9 - - - -
504G TYR 3.3 9.4 - - - +
505G GLU* 4.4 17.9 - - + +
544G MET* 3.3 32.5 - - + +
545G LEU* 5.0 5.8 - - + +
547G SER* 3.6 9.6 - - - +
548G GLY* 4.5 11.9 - - - +
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Residues in contact with VAL 489 (chain G).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
471G ILE* 5.0 11.9 - - + -
472G VAL 3.7 7.0 - - - +
473G GLY* 5.6 1.3 - - - -
487G GLN* 4.4 21.5 - - + +
488G LEU* 1.3 83.9 - - - +
490G GLY* 1.3 65.1 + - - +
491G LEU* 6.0 2.5 - - + -
503G GLY* 3.3 2.6 - - - -
504G TYR* 2.9 45.5 + - + +
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Residues in contact with GLY 490 (chain G).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
471G ILE* 3.3 10.7 - - - +
472G VAL* 2.9 49.5 + - - +
488G LEU* 5.4 0.4 - - - -
489G VAL* 1.3 79.1 - - - +
491G LEU* 1.3 66.0 + - - -
502G LEU 3.1 11.0 - - - -
503G GLY* 4.3 1.8 - - - -
544G MET* 4.3 3.4 - - - -
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Residues in contact with LEU 491 (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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465G ILE* 4.6 12.1 - - + -
469G TRP* 5.9 9.0 - - + -
470G ALA 3.3 4.5 - - - +
471G ILE* 3.8 26.7 - - + -
489G VAL* 6.0 2.9 - - + -
490G GLY* 1.3 84.2 - - - +
492G GLN* 1.3 62.2 + - - +
500G VAL* 3.9 1.3 - - - +
501G ASN* 3.6 4.6 + - - -
502G LEU* 2.9 56.6 + - + +
544G MET* 4.1 1.4 - - - +
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Residues in contact with GLN 492 (chain G).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
469G TRP* 3.6 5.9 - - - +
470G ALA* 2.6 47.6 + - + +
472G VAL* 6.2 0.2 - - + -
491G LEU* 1.3 75.6 - - - +
493G TYR* 1.3 66.5 + - - +
494G ASN* 2.8 36.3 + - - +
499G ALA* 4.1 8.5 - - - +
500G VAL* 3.3 6.5 - - - +
501G ASN* 3.1 24.5 + - - +
541G THR* 2.5 47.9 + - + +
544G MET* 4.5 3.5 - - + +
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Residues in contact with TYR 493 (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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468G ARG* 3.1 67.5 + - - -
469G TRP* 4.0 11.2 - + + -
492G GLN* 1.3 76.4 - - - +
494G ASN* 1.3 75.1 + - - +
495G THR* 4.0 12.5 + - - -
498G TRP 4.2 0.2 - - - +
499G ALA* 3.4 2.3 - - - -
500G VAL* 2.8 59.2 + - + +
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Residues in contact with ASN 494 (chain G).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
468G ARG* 3.7 16.8 + - + +
470G ALA* 5.2 5.5 - - - +
492G GLN* 2.8 35.5 + - - +
493G TYR* 1.3 88.8 - - - +
495G THR* 1.3 69.4 + - - +
496G CYS 4.2 5.9 - - - +
498G TRP 3.6 4.0 - - - +
499G ALA* 3.2 24.6 - - - +
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Residues in contact with THR 495 (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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468G ARG* 5.2 2.1 - - - -
493G TYR* 4.0 16.7 + - - -
494G ASN* 1.3 79.8 + - - +
496G CYS* 1.3 73.6 + - + +
497G CYS 3.3 0.2 + - - -
498G TRP* 2.9 42.2 + - + +
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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