Contacts of the strand formed by residues 559 - 564 (chain B) in PDB entry 3MBK
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 B).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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374B CYS* 3.3 29.7 + - - +
376B PHE* 3.8 20.3 - - + -
450B THR* 3.9 18.6 - - - +
451B VAL* 2.9 31.4 + - - +
452B ILE* 4.4 2.9 - - + -
453B ASP* 3.0 34.8 + - - +
454B HIS 3.6 2.1 + - - +
557B GLY 3.5 0.2 - - - -
558B ASN* 1.3 84.8 - - - +
560B ILE* 1.3 64.4 + - - +
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Residues in contact with ILE 560 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
373B ARG* 6.2 3.4 - - - -
374B CYS 3.0 9.2 + - - +
375B LEU* 3.5 16.3 - - + +
376B PHE* 2.8 35.6 + - - +
452B ILE* 5.0 0.4 - - - -
454B HIS* 3.6 7.0 - - + +
456B TYR* 3.9 18.6 - - + -
549B ILE* 3.8 22.2 - - + +
550B ILE* 3.9 33.0 - - + +
553B CYS* 3.6 33.7 - - + -
557B GLY 4.9 4.7 - - - +
558B ASN 4.9 2.5 - - - +
559B ASN* 1.3 79.4 - - - +
561B LEU* 1.3 60.1 + - - +
562B ILE* 4.8 0.9 - - + -
611B TRP* 6.3 1.1 - - + -
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Residues in contact with LEU 561 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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376B PHE* 3.5 24.0 - - + +
378B CYS* 4.2 8.3 - - - -
445B LEU* 4.9 7.4 - - + -
452B ILE* 3.9 26.7 - - + +
454B HIS 3.0 8.2 + - - +
455B VAL* 3.3 13.7 - - + -
456B TYR* 2.8 32.6 + - - +
470B ILE* 3.9 27.8 - - + -
471B LEU* 6.2 0.7 - - + -
474B LEU* 5.4 0.9 - - + -
560B ILE* 1.3 74.6 - - - +
562B ILE* 1.3 68.1 + - - +
563B VAL* 3.8 21.1 - - + -
599B PHE* 4.1 18.2 - - + -
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Residues in contact with ILE 562 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
375B LEU* 3.8 29.6 - - + -
376B PHE 2.8 13.8 + - - +
377B VAL* 3.4 15.9 - - + -
378B CYS 2.9 26.3 + - - +
456B TYR* 3.4 15.7 - - + -
488B LEU* 3.9 35.2 - - + -
546B THR* 4.4 13.7 - - + +
549B ILE* 4.3 12.8 - - + -
560B ILE* 4.8 2.9 - - + -
561B LEU* 1.3 79.2 - - - +
563B VAL* 1.3 62.2 + - - +
564B ALA* 4.0 17.9 - - + -
572B CYS* 4.4 6.7 - - - -
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Residues in contact with VAL 563 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
378B CYS* 3.6 11.2 - - - +
380B HIS* 4.7 3.6 - - - -
455B VAL* 4.2 2.2 - - + -
456B TYR 2.9 12.8 + - - +
457B CYS* 3.1 24.7 - - + +
458B SER 3.2 4.0 + - - -
463B CYS* 3.6 23.5 - - - +
466B THR* 3.6 27.6 - - + -
467B ALA* 3.8 22.7 - - + +
470B ILE* 3.9 9.9 - - + -
561B LEU* 3.8 26.9 - - + -
562B ILE* 1.3 74.3 - - - +
564B ALA* 1.3 62.4 + - - +
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Residues in contact with ALA 564 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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378B CYS 2.9 13.5 + - - +
380B HIS* 3.0 24.3 + - - +
458B SER* 4.1 4.0 - - - -
463B CYS* 3.4 19.7 - - - -
488B LEU* 4.0 18.6 - - + +
562B ILE* 3.9 14.1 - - + -
563B VAL* 1.3 76.1 - - - +
565B HIS* 1.3 66.8 + - + +
568B SER* 3.2 21.5 - - - +
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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