Contacts of the strand formed by residues 545 - 553 (chain F) in PDB entry 4OMC
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 GLY 545 (chain F).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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469F LYS 3.6 0.5 - - - +
470F THR* 3.4 10.5 - - - -
471F VAL* 2.8 41.5 + - - +
508F PRO* 3.5 7.4 - - - -
544F SER* 1.3 74.5 - - - +
546F GLU* 1.3 61.9 + - - -
547F TRP* 3.7 0.9 + - - -
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Residues in contact with GLU 546 (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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468F ARG* 2.6 46.2 + - - +
469F LYS 3.4 12.5 + - - +
470F THR* 3.9 15.9 + - - +
506F VAL 4.2 0.3 - - - +
507F SER 3.8 2.4 - - - +
508F PRO* 3.1 27.5 - - - +
545F GLY* 1.3 72.1 - - - -
547F TRP* 1.3 68.4 + - - +
548F VAL* 4.2 6.2 - - + +
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Residues in contact with TRP 547 (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* 5.7 2.2 - - + -
467F VAL 3.8 0.7 - - - +
468F ARG* 3.5 1.0 - - - -
469F LYS* 2.9 37.2 + - + +
471F VAL* 3.6 23.5 - - + +
484F LEU* 4.1 18.4 - - + -
487F ALA* 4.5 10.1 - - + -
505F LEU* 3.6 38.8 - - + -
506F VAL 3.3 17.5 - - - -
507F SER* 3.7 20.6 - - - -
508F PRO* 3.3 22.6 - - + +
535F THR* 5.8 2.2 - - + -
538F SER* 4.7 3.8 - - - -
543F PRO* 2.8 33.9 + - + +
545F GLY 3.8 0.4 - - - -
546F GLU* 1.3 74.5 - - - +
548F VAL* 1.3 64.8 + - - +
566F PHE* 5.7 5.3 - - + -
568F LEU* 3.8 24.0 - - + +
570F LEU* 4.0 15.5 - - + +
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Residues in contact with VAL 548 (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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466F GLU* 3.7 32.5 - - + -
467F VAL 3.3 4.9 - - - +
468F ARG* 3.2 36.8 - - + +
504F HIS 3.8 0.7 - - - +
505F LEU* 3.3 7.2 - - - +
506F VAL* 2.8 51.1 + - + +
546F GLU* 4.2 7.6 - - + +
547F TRP* 1.3 81.0 - - - +
549F LEU* 1.3 63.0 + - - +
550F GLU* 4.0 15.9 + - + +
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Residues in contact with LEU 549 (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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465F LEU 3.8 0.5 - - - +
466F GLU* 3.4 4.7 - - - -
467F VAL* 2.9 38.6 + - + +
491F LEU* 4.0 16.8 - - + -
503F ILE* 3.7 20.2 - - + -
504F HIS 3.4 13.2 - - - +
505F LEU* 4.3 8.1 - - + -
515F LEU* 4.2 13.7 - - + -
548F VAL* 1.3 73.7 - - - +
550F GLU* 1.3 61.3 + - - +
551F ILE* 4.0 15.3 - - + -
563F LEU* 4.0 19.3 - - + -
566F PHE* 3.6 45.5 - - + -
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Residues in contact with GLU 550 (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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464F ARG* 3.7 35.4 + - - +
465F LEU 3.5 4.7 - - - +
466F GLU* 4.6 1.9 - - + +
502F ALA 3.7 0.7 - - - +
503F ILE* 3.2 7.6 - - - +
504F HIS* 2.8 55.0 + - + +
506F VAL* 3.9 7.2 - - + +
512F ARG* 2.6 49.0 + - - -
548F VAL* 4.0 17.3 - - + +
549F LEU* 1.3 78.7 - - - +
551F ILE* 1.3 62.5 + - - +
552F GLU* 6.1 1.0 - - + -
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Residues in contact with ILE 551 (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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461F ILE* 3.8 17.6 - - + +
464F ARG* 3.3 3.6 - - - +
465F LEU* 2.8 50.8 + - + +
491F LEU* 4.9 0.9 - - + -
493F LEU* 4.3 11.4 - - + -
501F LEU* 3.6 28.7 - - + -
502F ALA 3.5 5.2 - - - +
503F ILE* 4.0 21.5 - - + -
549F LEU* 4.0 22.9 - - + -
550F GLU* 1.3 79.9 - - - +
552F GLU* 1.3 63.5 + - - +
563F LEU* 4.2 26.7 - - + -
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Residues in contact with GLU 552 (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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461F ILE* 5.7 1.3 - - - -
463F LYS 3.6 9.0 - - - +
464F ARG* 4.3 20.1 + - + +
501F LEU* 3.5 9.5 - - - +
502F ALA* 3.0 45.2 + - + +
504F HIS* 3.3 25.3 - - + +
550F GLU* 5.7 2.0 - - + -
551F ILE* 1.3 76.4 - - - +
553F ASN* 1.3 65.0 + - - +
554F THR* 3.4 12.0 + - + +
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Residues in contact with ASN 553 (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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461F ILE* 5.8 0.4 - - - +
462F GLY 4.0 5.6 + - - +
463F LYS* 2.9 46.9 + - + +
495F TYR* 3.4 20.1 + - - +
500F ASP* 3.7 7.6 - - - +
501F LEU* 5.0 0.9 - - - +
552F GLU* 1.3 74.8 - - - +
554F THR* 1.3 59.7 + - - +
555F SER* 2.9 22.8 + - - +
557F ALA 2.8 28.3 + - - -
558F ASN* 5.0 0.2 - - - +
559F ASN* 3.1 27.1 + - - +
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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