Contacts of the helix formed by residues 555 - 563 (chain B) in PDB entry 5TDE
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 555 (chain B).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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530B VAL* 4.5 1.8 - - - -
536B ASP* 4.6 0.8 + - - -
553B PHE* 3.6 10.4 - - - +
554B LYS* 1.3 100.5 - - - +
556B MET* 1.3 66.2 - - - +
557B ALA* 4.2 8.3 - - + +
558B ASP* 3.1 33.5 + - - +
559B ALA 3.4 7.6 + - - -
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Residues in contact with MET 556 (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 TRP* 3.6 29.6 - - + +
530B VAL* 4.0 24.5 - - + +
554B LYS 4.3 0.2 + - - -
555B ASN* 1.3 71.6 - - - +
557B ALA* 1.3 65.1 + - - +
559B ALA* 3.2 2.4 + - - +
560B MET* 3.0 43.0 + - + +
569B LEU* 4.1 7.0 - - + -
581B SER 3.9 4.7 - - - +
584B GLU* 3.5 38.9 + - - +
585B THR* 3.3 42.4 - - - +
588B TYR* 3.8 11.0 - - + -
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Residues in contact with ALA 557 (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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555B ASN* 3.2 6.5 - - + +
556B MET* 1.3 79.4 - - - +
558B ASP* 1.3 64.6 + - - +
560B MET* 3.6 1.2 + - - +
561B ARG* 3.1 25.7 + - - +
584B GLU* 4.8 1.6 + - - -
588B TYR* 3.2 29.4 + - + +
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Residues in contact with ASP 558 (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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536B ASP* 4.7 8.9 - - - +
553B PHE* 3.6 22.7 - - + -
555B ASN* 3.1 32.1 + - - +
557B ALA* 1.3 78.5 - - - +
559B ALA* 1.3 65.9 + - - +
561B ARG* 3.4 26.3 + - - +
562B LYS* 3.0 30.3 + - - +
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Residues in contact with ALA 559 (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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500B ILE* 3.9 15.3 - - + +
528B ALA* 4.5 3.6 - - + -
530B VAL* 3.7 24.9 - - + -
553B PHE* 3.5 32.8 - - + -
555B ASN 3.4 2.6 + - - +
556B MET 3.2 7.3 + - - +
558B ASP* 1.3 81.0 - - - +
560B MET* 1.3 61.7 + - - +
563B HIS* 3.1 29.6 + - - +
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Residues in contact with MET 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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500B ILE* 3.8 18.6 - - + -
556B MET* 3.0 46.7 + - + +
557B ALA 4.0 0.4 - - - +
559B ALA* 1.3 75.5 - - - +
561B ARG* 1.3 64.1 + - - +
563B HIS 3.2 17.7 + - - -
564B PRO* 3.6 2.8 - - - +
569B LEU* 4.0 12.6 - - + -
585B THR* 4.4 1.8 - - + -
588B TYR* 3.6 33.7 - - + -
590B GLN* 3.5 40.9 - - - +
591B ILE* 3.8 29.2 - - + -
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Residues in contact with ARG 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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557B ALA 3.1 18.3 + - - +
558B ASP* 3.6 28.0 + - - +
560B MET* 1.3 78.5 - - - +
562B LYS* 1.3 97.0 + - - +
563B HIS 3.5 0.2 + - - -
564B PRO* 3.7 10.6 - - - +
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Residues in contact with LYS 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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553B PHE* 3.6 28.0 - - + -
558B ASP 3.0 15.6 + - - +
561B ARG* 1.3 108.7 - - - +
563B HIS* 1.3 84.6 + - + +
564B PRO* 3.5 6.6 - - - +
565B GLU* 4.4 0.7 - - - +
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Residues in contact with HIS 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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500B ILE* 5.1 2.2 - - + -
527B ALA* 3.8 21.0 - - + +
528B ALA* 4.0 14.6 - - + -
551B PRO* 3.8 20.7 - - + +
553B PHE* 4.1 6.4 - + - -
559B ALA 3.1 19.0 + - - +
560B MET 3.2 4.6 + - - +
562B LYS* 1.3 103.3 + - + +
564B PRO* 1.3 62.1 - - - +
565B GLU* 2.9 34.2 + - - +
566B VAL* 3.1 20.1 + - + +
590B GLN* 2.8 18.0 + - - -
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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