Contacts of the strand formed by residues 559 - 564 (chain C) in PDB entry 5W5G
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 ASN 559 (chain C).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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373C ARG* 5.1 2.0 - - - +
374C CYS* 3.4 28.4 - - - +
376C PHE* 3.5 17.3 - - + -
450C THR* 4.4 4.2 - - - +
451C ILE* 2.8 35.2 + - - +
452C ILE* 3.8 4.7 - - - -
453C ASP* 2.8 35.1 + - - +
454C HIS 3.2 8.0 + - - +
557C GLY 3.9 0.6 - - - -
558C ASN* 1.3 98.3 + - - +
560C ILE* 1.3 64.1 + - - +
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Residues in contact with ILE 560 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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373C ARG 6.2 1.8 - - - +
374C CYS 3.2 15.0 + - - +
375C LEU* 3.6 21.3 - - + +
376C PHE* 2.8 32.3 + - - +
454C HIS* 3.5 7.6 - - + +
456C TYR* 4.0 16.4 - - + -
549C ILE* 3.7 32.5 - - + +
550C ILE* 4.6 16.4 - - + +
553C CYS* 4.1 26.9 - - + -
554C LYS* 5.2 2.9 - - + +
557C GLY 6.0 1.8 - - - +
558C ASN 5.9 2.0 - - - +
559C ASN* 1.3 80.0 - - - +
561C LEU* 1.3 64.8 + - - +
562C ILE* 4.6 1.1 - - + -
611C TRP* 5.6 5.2 - - + -
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Residues in contact with LEU 561 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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376C PHE* 3.5 28.7 - - + +
378C CYS* 4.4 15.0 - - - -
445C LEU* 4.6 6.1 - - + -
452C ILE* 3.8 34.3 - - + +
454C HIS 2.9 10.4 + - - +
455C VAL* 3.3 13.0 - - + +
456C TYR* 2.9 27.2 + - - +
470C ILE* 3.9 29.6 - - + -
471C LEU* 5.6 0.9 - - + -
474C LEU* 5.3 1.1 - - + -
559C ASN 4.2 0.4 + - - -
560C ILE* 1.3 74.5 - - - +
562C ILE* 1.3 71.6 + - - +
563C VAL* 4.1 15.3 - - + -
599C PHE* 4.4 9.0 - - + -
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Residues in contact with ILE 562 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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375C LEU* 3.9 24.5 - - + -
376C PHE 2.7 13.7 + - - +
377C VAL* 3.4 19.5 - - + +
378C CYS 3.0 26.7 + - - +
456C TYR* 3.4 14.1 - - + -
488C LEU* 3.6 35.0 - - + -
546C THR* 4.8 14.1 - - + +
549C ILE* 4.2 20.6 - - + -
560C ILE* 4.6 4.9 - - + -
561C LEU* 1.3 79.5 - - - +
563C VAL* 1.3 62.3 + - - +
564C ALA* 4.1 13.9 - - + -
572C CYS* 5.2 5.2 - - + -
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Residues in contact with VAL 563 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
378C CYS* 3.6 11.9 - - - +
380C HIS* 4.7 4.9 - - - -
455C VAL* 4.6 2.0 - - + -
456C TYR 2.9 12.2 + - - +
457C CYS* 3.1 23.1 - - + +
458C SER 3.2 3.8 + - - -
463C CYS* 3.5 25.5 - - - +
466C THR* 3.7 25.1 - - + -
467C ALA* 3.7 27.8 - - + +
470C ILE* 3.9 15.5 - - + -
561C LEU* 4.1 15.7 - - + -
562C ILE* 1.3 74.3 - - - +
564C ALA* 1.3 60.3 + - - +
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Residues in contact with ALA 564 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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377C VAL* 5.4 1.6 - - + -
378C CYS 3.0 11.0 + - - +
379C ARG* 3.6 0.3 - - - -
380C HIS* 3.1 24.3 + - - -
458C SER* 4.3 3.1 - - - -
463C CYS* 3.6 15.3 - - - -
488C LEU* 4.0 15.7 - - + +
562C ILE* 3.9 16.1 - - + -
563C VAL* 1.3 76.3 - - - +
565C HIS* 1.3 67.7 + - - +
568C SER* 3.4 24.9 - - - +
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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