Contacts of the strand formed by residues 464 - 471 (chain F) in PDB entry 4OMD
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 ARG 464 (chain F).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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460F ASP 5.0 0.5 - - - +
461F ILE 3.2 12.5 + - - +
463F LYS* 1.3 85.6 - - + +
465F LEU* 1.3 64.0 + - - +
466F GLU* 2.5 40.8 + - - +
550F GLU* 3.8 32.8 + - - +
551F ILE 3.3 13.0 - - - +
552F GLU* 4.1 19.3 + - + +
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Residues in contact with LEU 465 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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459F LYS* 3.8 35.9 - - + -
460F ASP 3.8 15.9 - - - +
461F ILE* 4.0 20.0 - - + +
464F ARG* 1.3 79.6 + - - +
466F GLU* 1.3 75.8 + - - +
467F VAL* 4.1 7.6 - - + -
549F LEU 3.8 0.3 - - - +
550F GLU* 3.6 4.3 - - - -
551F ILE* 2.7 47.2 + - + +
563F LEU* 3.9 29.6 - - + -
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Residues in contact with GLU 466 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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459F LYS* 5.8 0.7 + - - -
464F ARG* 2.5 33.5 + - - +
465F LEU* 1.3 81.8 - - - +
467F VAL* 1.3 68.3 + - - +
468F ARG* 3.0 40.4 + - - +
548F VAL* 3.8 19.3 - - + -
549F LEU 3.4 3.6 - - - +
550F GLU* 4.5 5.8 - - + +
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Residues in contact with VAL 467 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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454F ILE* 3.9 27.6 - - + -
455F LEU* 4.1 16.6 - - + -
459F LYS* 4.7 12.8 - - + +
465F LEU* 4.1 24.7 - - + -
466F GLU* 1.3 79.1 - - - +
468F ARG* 1.3 67.5 + - - +
547F TRP 3.7 1.0 - - - +
548F VAL* 3.3 3.9 - - - -
549F LEU* 2.9 47.1 + - + +
563F LEU* 4.4 14.1 - - + -
566F PHE* 4.1 8.2 - - + -
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Residues in contact with ARG 468 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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454F ILE* 4.7 0.9 - - - +
466F GLU* 3.0 34.2 + - + +
467F VAL* 1.3 81.2 - - - +
469F LYS* 1.3 68.3 + - - +
546F GLU* 2.8 45.0 + - - +
547F TRP 3.5 4.0 - - - -
548F VAL* 3.4 23.0 - - + +
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Residues in contact with LYS 469 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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452F ILE* 4.9 7.2 - - - -
453F ASP 5.0 2.4 + - - -
454F ILE* 3.4 56.2 + - + +
467F VAL* 5.4 0.4 - - + +
468F ARG* 1.3 79.2 - - - +
470F THR* 1.3 75.8 + - - +
471F VAL* 3.7 12.6 + - + +
545F GLY 3.5 1.0 - - - +
546F GLU* 3.3 3.6 - - - +
547F TRP* 2.8 41.7 + - + +
566F PHE* 5.7 2.0 - - + -
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Residues in contact with THR 470 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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469F LYS* 1.3 89.1 + - - +
471F VAL* 1.3 69.3 + - - +
472F THR* 5.6 3.7 - - + +
545F GLY* 3.2 19.1 - - - +
546F GLU* 3.9 15.2 + - - +
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Residues in contact with VAL 471 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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452F ILE* 3.9 39.3 - - + -
454F ILE* 4.6 0.7 - - + -
469F LYS* 3.9 23.6 - - + +
470F THR* 1.3 83.0 - - - +
472F THR* 1.3 64.2 + - - +
473F ALA* 3.9 9.2 - - + +
543F PRO 3.5 23.8 - - - +
544F SER* 3.6 1.2 - - - -
545F GLY* 2.8 31.4 + - - +
547F TRP* 3.6 18.2 - - + +
568F LEU* 4.5 4.9 - - + -
570F LEU* 4.9 1.3 - - + -
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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