Contacts of the helix formed by residues 558 - 565 (chain C) in PDB entry 3TAX
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 HIS 558 (chain C).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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554C ASP* 3.3 55.4 + - + +
556C GLY 2.9 4.2 + - - +
557C ASN* 1.3 76.5 - - - +
559C PRO* 1.4 88.4 - - + +
560C THR* 3.0 29.2 + - - -
561C SER* 3.0 12.6 + - - -
562C HIS* 3.2 20.8 + - - -
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Residues in contact with PRO 559 (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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558C HIS* 1.4 104.7 - - + +
560C THR* 1.4 61.9 + - - +
562C HIS* 3.1 20.9 + - + +
563C LEU* 3.0 34.0 + - + +
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Residues in contact with THR 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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552C SER* 4.1 11.0 - - - +
554C ASP* 3.6 17.6 + - + +
555C PHE* 5.7 0.2 - - + -
558C HIS* 3.0 21.2 + - - -
559C PRO* 1.4 74.5 - - - +
561C SER* 1.3 58.5 + - - +
563C LEU* 3.1 10.9 + - - +
564C MET* 3.0 36.2 + - + +
629C MET* 3.5 37.5 + - + +
653C LEU* 5.4 4.5 - - + -
654C GLY* 4.4 17.2 - - - +
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Residues in contact with SER 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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554C ASP 2.7 23.0 + - - -
555C PHE* 3.5 10.9 - - - -
556C GLY 3.1 31.0 + - - -
558C HIS 3.0 2.6 + - - -
560C THR* 1.3 71.9 - - - +
562C HIS* 1.4 59.9 + - - +
563C LEU 3.0 4.3 - - - -
564C MET* 4.1 8.4 - - - -
565C GLN* 2.9 40.6 + - - +
591C PHE* 3.9 16.1 - - - +
595C VAL* 5.0 2.6 - - - +
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Residues in contact with HIS 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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557C ASN* 3.0 28.2 + - - -
558C HIS* 3.4 24.9 + - - -
559C PRO* 3.1 21.7 + - + +
561C SER* 1.4 75.7 - - - +
563C LEU* 1.3 62.8 + - + +
591C PHE* 3.5 31.5 - + - -
696C GLY* 4.3 0.2 - - - -
697C ASP* 3.0 25.7 + - - +
698C HIS* 4.7 4.1 + - + -
701C MET* 3.9 23.2 - - + +
702C PHE* 6.3 0.7 - - + -
809C THR 4.8 3.1 + - - -
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Residues in contact with LEU 563 (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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559C PRO* 3.0 24.2 + - + +
560C THR* 3.1 9.2 + - - +
561C SER 3.0 0.2 - - - -
562C HIS* 1.3 84.5 - - + +
564C MET* 1.4 59.2 + - - +
565C GLN 3.8 1.3 - - - -
567C ILE* 5.0 0.3 - - - +
653C LEU* 4.1 24.5 - - + +
694C PHE* 3.6 35.9 - - + -
695C ILE* 3.3 27.5 - - - +
696C GLY* 3.4 18.1 + - - -
697C ASP* 3.3 18.3 + - - +
698C HIS* 4.8 9.0 - - + -
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Residues in contact with MET 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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550C TYR* 5.4 4.0 - - + -
555C PHE* 3.8 22.4 - - + -
560C THR* 3.0 25.9 + - - +
561C SER* 4.1 8.3 - - - -
563C LEU* 1.4 76.7 - - - +
565C GLN* 1.3 71.2 + - - +
566C SER 3.1 3.4 - - - -
567C ILE* 3.0 26.9 + - + +
568C PRO* 3.4 21.2 - - + +
595C VAL* 5.1 1.3 - - + -
629C MET* 3.8 34.3 - - + -
652C TRP* 3.7 26.2 - - + -
653C LEU* 3.8 15.5 - - + -
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Residues in contact with GLN 565 (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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561C SER* 2.9 23.4 + - - +
563C LEU 3.8 0.8 - - - -
564C MET* 1.3 78.5 - - - +
566C SER* 1.4 58.8 + - - +
568C PRO* 3.7 9.5 - - - +
569C GLY 5.1 0.2 + - - -
590C ASN 4.4 0.7 - - - +
591C PHE* 3.4 37.6 + - - +
594C LYS* 3.4 33.9 - - + +
595C VAL* 4.0 27.4 + - + +
598C GLU* 4.5 3.3 - - - +
697C ASP* 2.8 29.8 + - - +
700C ASN* 3.8 6.3 - - - +
701C MET* 3.5 23.4 - - - +
810C GLY 5.3 0.4 + - - -
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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