Contacts of the strand formed by residues 559 - 564 (chain B) in PDB entry 5ULM
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 PHE 559 (chain B).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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554B VAL* 4.2 10.1 - - + -
556B VAL* 4.1 24.0 - - + -
557B VAL 5.3 1.3 - - - -
558B ARG* 1.3 76.7 - - - +
560B PRO* 1.3 67.1 - - + +
561B VAL* 3.6 18.6 + - + +
574B TYR* 3.3 9.1 - - - -
575B LEU* 2.8 56.6 + - + +
576B SER* 5.1 0.9 - - - -
577B ILE* 5.0 7.9 - - + -
637B PHE* 3.8 18.6 - + + -
642B HIS* 3.8 44.9 - + - -
645B LYS* 4.7 8.5 - - + -
646B PHE* 4.8 8.3 - + + -
649B MET* 4.9 16.6 - - - -
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Residues in contact with PRO 560 (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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541B PHE* 3.6 18.2 - - + -
544B ASP* 3.9 19.7 - - - +
545B PHE* 3.5 42.4 - - + +
548B GLU* 4.2 21.3 - - + -
558B ARG 4.0 6.5 - - - +
559B PHE* 1.3 83.5 - - + +
561B VAL* 1.3 62.1 + - - +
573B SER 3.6 5.8 - - - +
574B TYR* 3.6 14.8 - - + -
637B PHE* 4.6 0.9 - - - -
638B CYS* 4.5 10.3 + - - +
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Residues in contact with VAL 561 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
541B PHE* 3.3 8.6 - - - -
545B PHE* 4.3 1.1 - - - -
559B PHE* 3.7 22.4 - - + +
560B PRO* 1.3 81.0 - - - +
562B LEU* 1.3 63.7 + - - +
563B ILE* 4.6 4.9 - - + -
573B SER* 2.9 55.9 + - - +
575B LEU* 4.3 15.3 - - + -
588B ILE* 5.8 0.9 - - + -
635B ILE* 3.7 22.2 - - + -
636B TYR 3.3 11.0 - - - +
637B PHE* 3.8 24.9 - - + -
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Residues in contact with LEU 562 (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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502B PHE* 3.3 49.1 - - + -
541B PHE* 3.9 4.5 - - + -
542B TRP* 3.6 34.5 - - + -
545B PHE* 4.0 11.2 - - + -
561B VAL* 1.3 74.7 - - - +
563B ILE* 1.3 63.6 + - - +
564B LEU 3.5 1.7 + - - -
570B TYR* 3.9 26.7 - - + +
571B GLN 3.5 2.2 - - - -
572B PRO* 3.9 26.2 - - + -
636B TYR* 2.8 42.2 + - + +
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Residues in contact with ILE 563 (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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561B VAL* 4.6 7.0 - - + -
562B LEU* 1.3 71.9 - - - +
564B LEU* 1.3 67.9 + - - +
565B GLU* 3.2 21.7 + - - +
570B TYR* 4.5 0.7 - - - -
571B GLN* 2.9 34.4 + - + +
573B SER* 3.4 24.9 - - - +
588B ILE* 3.6 29.6 - - + -
590B HIS* 3.8 15.3 - - + -
602B TRP* 4.9 0.4 - - + -
633B PHE* 4.5 20.6 - - + -
634B GLN 3.5 17.3 - - - +
635B ILE* 4.7 10.5 - - + +
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Residues in contact with LEU 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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562B LEU 3.5 3.2 + - - -
563B ILE* 1.3 74.8 - - - +
565B GLU* 1.3 66.8 + - - +
566B PRO* 4.1 1.2 - - - +
568B LYS* 3.7 55.4 - - + +
569B ILE 3.8 4.7 - - - +
570B TYR* 3.9 27.8 - - + +
634B GLN* 3.0 36.8 + - + +
636B TYR* 3.8 35.9 - - + +
701B GOL 5.5 1.7 + - - -
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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