Contacts of the strand formed by residues 484 - 492 (chain A) in PDB entry 4Y05
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 484 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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341A LYS* 4.5 15.0 - - - +
436A GLU* 4.6 1.3 - - - +
477A ILE* 3.0 35.9 - - + -
478A LEU 3.7 6.1 - - - +
479A ARG* 3.3 33.8 - - - +
480A ALA* 5.6 0.4 - - - -
483A ARG* 1.3 74.5 - - - +
485A HIS* 1.3 63.8 + - - +
486A GLY* 3.8 10.8 - - - +
487A LYS* 4.0 31.9 - - + +
550A ASP* 5.2 0.9 - - - +
703A SO4 3.8 23.3 + - - +
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Residues in contact with HIS 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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336A ILE 3.3 21.3 - - - -
337A PHE* 2.6 32.5 + - - -
338A GLU 4.4 1.8 - - - -
339A GLY* 3.0 41.6 + - - +
341A LYS* 5.1 2.3 + - - -
393A LEU* 5.9 4.0 - - + -
395A LEU* 4.0 35.3 - - + +
478A LEU* 2.7 23.7 + - + +
480A ALA* 4.3 12.3 - - + +
483A ARG 3.4 0.6 + - - -
484A MET* 1.3 75.9 - - - +
486A GLY* 1.3 55.6 + - - +
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Residues in contact with GLY 486 (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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336A ILE* 3.5 18.6 + - - -
339A GLY 4.6 0.2 - - - -
340A GLY 3.4 13.7 - - - -
341A LYS* 4.9 2.7 - - - -
477A ILE* 3.6 2.9 - - - +
478A LEU* 2.7 32.8 + - - +
484A MET* 3.8 5.2 - - - +
485A HIS* 1.3 81.0 - - - +
487A LYS* 1.3 60.2 + - - +
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Residues in contact with LYS 487 (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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336A ILE* 3.4 8.5 - - - +
340A GLY 3.4 6.5 + - - -
341A LYS* 3.5 14.6 - - + +
342A ALA 2.9 25.6 + - - +
475A GLN* 4.1 26.4 + - + +
476A ILE 3.3 11.4 - - - +
477A ILE* 3.8 21.9 - - + +
484A MET* 4.0 19.4 - - + +
486A GLY* 1.3 74.8 - - - +
488A PHE* 1.3 64.4 + - - +
489A SER* 4.1 11.2 - - - +
547A VAL 5.1 4.2 + - - -
548A LEU* 6.3 0.4 - - - +
550A ASP* 3.2 38.0 + - - -
551A SER* 4.7 2.8 + - - +
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Residues in contact with PHE 488 (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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329A ALA* 3.6 37.0 - - + -
332A LEU* 3.7 26.7 - - + -
333A VAL* 4.1 18.4 - - + -
336A ILE* 3.9 15.7 - - + +
342A ALA* 3.3 21.3 - - + -
343A THR 3.8 7.6 - - - -
344A CYS* 3.8 24.2 - - + -
377A ALA* 4.7 6.1 - - + -
381A VAL* 5.8 0.2 - - + -
474A PHE 3.9 0.7 - - - +
475A GLN* 3.2 4.2 - - - +
476A ILE* 2.7 51.2 + - + +
487A LYS* 1.3 74.1 - - - +
489A SER* 1.3 68.4 + - - +
490A LEU* 3.9 19.2 - - + +
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Residues in contact with SER 489 (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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342A ALA 2.9 8.9 + - - -
343A THR* 3.2 12.1 - - - -
344A CYS 2.9 25.5 + - - +
473A CYS* 4.0 7.4 - - - -
474A PHE 3.6 3.8 - - - -
475A GLN* 3.2 25.0 + - - +
487A LYS* 4.1 8.8 - - - +
488A PHE* 1.3 76.2 - - - +
490A LEU* 1.3 61.0 + - - +
491A VAL* 4.1 4.0 - - - +
548A LEU* 3.7 25.1 - - - +
551A SER* 4.5 5.2 + - - -
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Residues in contact with LEU 490 (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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344A CYS* 3.3 7.2 - - + -
358A MET* 3.7 6.7 - - + -
373A ILE* 3.4 38.4 - - + +
374A TYR* 3.6 25.9 - - + -
377A ALA* 4.3 5.4 - - + -
473A CYS* 3.5 1.7 - - - -
474A PHE* 2.7 64.8 + - + +
476A ILE* 4.3 8.5 - - + -
488A PHE* 3.9 40.8 - - + +
489A SER* 1.3 76.5 - - - +
491A VAL* 1.3 60.8 + - - +
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Residues in contact with VAL 491 (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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344A CYS 2.8 9.3 + - - +
345A PHE* 3.3 28.0 - - + -
346A ALA* 2.9 27.9 + - - +
358A MET* 4.1 7.1 - - - +
471A HIS* 4.5 3.6 - - + -
472A ALA 3.3 12.1 - - - +
473A CYS* 3.8 22.7 - - + -
489A SER 4.5 2.9 - - - +
490A LEU* 1.3 82.6 - - - +
492A ASP* 1.3 62.3 + - - +
493A LEU* 3.6 29.1 + - + -
544A LEU* 4.1 11.7 - - + -
548A LEU* 4.2 10.5 - - + -
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Residues in contact with ASP 492 (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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346A ALA* 4.3 2.5 - - - -
354A LYS* 3.4 22.3 - - - +
355A THR* 2.7 41.9 + - - +
358A MET* 4.1 11.5 - - + +
359A GLY 5.6 0.2 + - - -
374A TYR* 3.5 18.9 + - - +
470A SER 3.9 1.7 - - - +
471A HIS* 3.5 0.9 - - - -
472A ALA* 2.9 39.0 + - + +
491A VAL* 1.3 69.2 - - - +
493A LEU* 1.3 66.7 + - - +
701A MG 4.2 2.5 - - - -
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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