Contacts of the strand formed by residues 469 - 477 (chain A) in PDB entry 5IYB
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 MET 469 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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457A ILE* 3.7 35.6 - - + +
458A PHE 3.5 4.0 - - - -
459A ASN* 4.0 25.8 - - + +
463A THR* 4.2 3.6 - - + +
466A LYS 3.4 3.1 + - - +
467A MET 3.2 0.8 - - - -
468A SER* 1.3 78.6 - - - +
470A MET* 1.3 60.5 + - - +
504A HIS* 4.2 4.7 - - + +
1086B PHE* 3.5 26.5 - - + -
1090B GLU* 3.7 21.1 - - + +
1093B CYS* 4.2 17.9 - - + -
1094B GLN* 3.2 31.2 - - - +
1097B HIS* 3.5 23.4 - - - -
1102B PHE* 5.0 1.3 - - + -
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Residues in contact with MET 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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457A ILE* 3.8 7.2 - - - -
458A PHE 3.1 28.4 + - - +
467A MET* 3.2 32.5 - - - +
469A MET* 1.3 79.0 - - - +
471A GLY* 1.3 59.4 + - - +
472A HIS* 3.3 11.6 - - - +
488A VAL* 3.9 12.1 - - + -
491A PRO* 3.8 22.0 - - + -
492A TYR* 3.3 31.4 + - + +
519A ALA 3.7 9.6 - - - +
521A VAL* 4.3 21.5 - - + -
524A MET* 3.5 36.8 - - + -
535A MET* 5.1 1.8 - - + -
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Residues in contact with GLY 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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455A ILE* 4.7 0.2 - - - -
456A VAL 3.2 10.3 - - - -
457A ILE* 3.9 3.2 - - - +
470A MET* 1.3 72.1 - - - +
472A HIS* 1.3 59.8 + - - -
515A ILE* 4.0 22.0 - - - -
519A ALA 3.2 14.6 + - - -
520A MET* 3.2 14.0 - - - +
521A VAL* 3.1 27.7 + - - +
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Residues in contact with HIS 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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375A ILE 3.9 9.9 - - - -
376A ASP 3.2 10.8 - - - +
377A GLN 3.4 20.1 + - - -
378A VAL* 3.8 23.1 - - + +
455A ILE* 3.2 7.7 - - - +
456A VAL* 2.9 33.7 + - + +
458A PHE* 3.7 17.4 - + + -
470A MET* 3.3 26.0 - - - +
471A GLY* 1.3 75.9 - - - -
473A ARG* 1.3 65.4 + - - +
484A LEU* 5.2 5.4 - - + -
488A VAL* 4.3 17.6 - - + +
492A TYR* 3.4 23.2 + + - -
520A MET* 4.1 2.4 - - - -
521A VAL* 3.6 18.0 - - + +
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Residues in contact with ARG 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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374A SER* 4.2 13.3 + - - -
376A ASP* 2.7 48.6 + - - +
377A GLN* 3.3 18.2 - - + +
378A VAL* 2.7 33.1 + - - +
453A GLY* 4.7 15.0 - - - +
454A ASP 3.6 4.9 - - - +
455A ILE* 4.5 14.4 - - + -
472A HIS* 1.3 75.4 - - - +
474A VAL* 1.3 60.6 + - - +
520A MET* 4.7 7.9 - - + -
666A ARG* 6.0 0.6 - - - +
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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
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377A GLN* 5.2 1.4 + - - -
378A VAL* 3.1 7.2 - - + -
380A VAL* 3.6 26.5 - - + -
450A MET* 4.0 16.8 - - - -
451A CYS 3.5 24.0 - - - +
452A ASP* 3.5 14.2 - - - +
453A GLY* 3.6 5.4 + - - +
454A ASP 3.0 15.8 + - - +
456A VAL* 3.7 38.4 - - + -
473A ARG* 1.3 75.4 - - - +
475A ARG* 1.3 61.2 + - - +
476A ILE* 3.8 13.7 - - + -
503A LEU* 4.9 0.7 - - + -
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Residues in contact with ARG 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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373A LEU* 4.1 17.3 - - + +
377A GLN* 3.5 27.9 - - - +
378A VAL 2.5 15.3 + - - +
379A GLY* 3.0 10.3 - - - -
380A VAL 2.9 21.2 + - - -
452A ASP* 4.1 17.1 + - - +
473A ARG 5.0 0.2 - - - +
474A VAL* 1.3 74.6 - - - +
476A ILE* 1.3 85.4 + - - +
477A LEU* 3.5 13.4 + - - +
65K HIS* 6.1 4.9 - - - +
68K GLU* 2.8 36.0 + - - +
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Residues in contact with ILE 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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380A VAL* 3.4 11.9 - - + +
382A ARG* 3.5 35.7 - - + +
385A ALA* 3.5 19.7 - - + -
413A TYR* 3.4 31.9 - - + +
450A MET 4.5 0.7 - - - +
451A CYS* 3.8 2.2 - - - -
452A ASP* 3.7 27.5 - - + +
474A VAL* 3.8 22.7 - - + -
475A ARG* 1.3 92.1 + - - +
477A LEU* 1.3 61.4 + - - +
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Residues in contact with LEU 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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370A ASP* 4.5 1.6 - - - +
373A LEU* 5.5 3.1 - - + -
379A GLY* 4.8 9.9 - - - -
380A VAL 3.3 10.6 + - - +
381A PRO* 3.8 3.3 - - - +
382A ARG* 3.7 23.4 + - - +
475A ARG* 3.5 19.5 + - - +
476A ILE* 1.3 79.5 - - - +
478A PRO* 1.4 99.5 - - + +
479A TRP 4.4 3.1 - - - +
481A THR 5.3 2.0 - - - +
483A ARG* 3.4 36.1 - - + +
65K HIS* 3.7 35.7 - - + +
67K LEU* 3.8 7.6 - - + -
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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