Contacts of the helix formed by residues 595 - 602 (chain B) in PDB entry 1TH1
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 THR 595 (chain B).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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537B VAL* 3.7 32.4 - - + +
540B LEU* 4.8 1.6 - - + -
590B ILE* 3.0 26.2 + - + -
591B ARG* 4.2 2.4 + - - -
593B LEU* 3.6 10.2 + - - +
594B ASN* 1.3 76.8 - - - +
596B ILE* 1.3 63.6 + - - +
597B PRO* 3.5 2.5 - - - -
598B LEU* 3.5 17.4 + - + +
599B PHE* 3.2 56.3 + - + -
621B LEU* 6.2 0.2 - - - -
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Residues in contact with ILE 596 (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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591B ARG* 4.1 33.2 - - + +
594B ASN* 4.5 0.2 - - - +
595B THR* 1.3 77.5 - - - +
597B PRO* 1.4 71.0 - - + +
599B PHE* 3.4 6.3 + - - +
600B VAL* 3.2 28.1 + - + +
618B LEU* 4.7 2.5 - - + -
621B LEU* 4.2 22.7 - - + -
627B ALA* 4.3 13.0 - - + +
630B ALA* 4.0 26.7 - - + +
631B ILE* 4.0 33.9 - - + -
634B GLU* 4.9 4.3 - - + +
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Residues in contact with PRO 597 (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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594B ASN* 3.7 35.7 - - - +
595B THR 3.6 2.2 - - - -
596B ILE* 1.4 91.2 - - + +
598B LEU* 1.3 61.8 + - - +
600B VAL* 3.4 5.4 + - - +
601B GLN* 3.3 25.7 + - - +
634B GLU* 4.0 37.3 - - + +
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Residues in contact with LEU 598 (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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537B VAL* 5.2 1.1 - - + +
540B LEU* 4.0 30.3 - - + -
541B VAL* 4.0 28.5 - - + -
544B HIS* 3.7 41.1 - - + +
594B ASN 5.3 2.5 - - - +
595B THR* 3.7 22.0 - - + +
596B ILE 3.3 0.2 - - - -
597B PRO* 1.3 79.5 - - + +
599B PHE* 1.3 62.2 + - + +
601B GLN* 3.2 17.9 + - + +
602B LEU* 3.3 25.3 + - + +
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Residues in contact with PHE 599 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
540B LEU* 3.7 23.8 - - + -
574B THR* 3.8 17.0 - - + -
577B LEU* 4.0 18.2 - - + -
590B ILE* 4.0 11.9 - - + -
595B THR* 3.2 39.1 + - + +
596B ILE* 3.7 6.1 - - - +
597B PRO 3.3 0.4 - - - -
598B LEU* 1.3 81.3 - - + +
600B VAL* 1.3 60.5 + - - +
602B LEU* 3.5 27.1 + - + +
603B LEU* 3.8 6.6 - - - +
614B ALA* 4.0 5.2 - - - +
617B VAL* 3.6 40.4 - - + -
618B LEU* 3.8 26.0 - - + +
621B LEU* 4.2 13.9 - - + -
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Residues in contact with VAL 600 (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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596B ILE* 3.2 24.1 + - + +
597B PRO 3.8 6.5 - - - +
598B LEU 3.3 0.6 - - - -
599B PHE* 1.3 76.3 - - - +
601B GLN* 1.3 64.3 + - + +
602B LEU 3.2 0.7 - - - -
603B LEU* 3.4 27.3 + - + +
604B TYR* 3.6 14.4 - - + -
618B LEU* 4.3 13.7 - - + -
631B ILE* 4.6 2.0 - - + +
634B GLU* 4.1 30.7 - - + +
635B GLY 4.3 3.8 - - - +
636B ALA* 4.0 32.8 - - + -
639B PRO* 4.9 3.1 - - + -
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Residues in contact with GLN 601 (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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544B HIS* 4.6 19.7 + - - +
548B GLN* 5.9 0.6 + - - -
597B PRO 3.3 14.4 + - - +
598B LEU* 3.2 14.5 + - - +
600B VAL* 1.3 77.7 - - + +
602B LEU* 1.3 56.7 + - - +
603B LEU 3.2 6.0 + - - -
604B TYR* 3.5 34.1 + - - +
605B SER* 4.2 3.1 + - - -
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Residues in contact with LEU 602 (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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540B LEU* 4.4 9.2 - - + -
544B HIS* 3.6 33.4 - - + +
570B VAL* 3.8 18.2 - - + -
574B THR* 3.6 28.5 - - + +
598B LEU* 3.3 19.7 + - + +
599B PHE* 3.7 25.1 - - + +
600B VAL 3.2 1.4 - - - -
601B GLN* 1.3 75.3 - - - +
603B LEU* 1.3 57.0 + - - +
604B TYR 3.3 1.6 - - - -
605B SER* 3.0 26.6 + - - +
610B ILE* 3.9 14.0 - - + +
611B GLN* 3.9 5.4 - - - -
614B ALA* 3.8 17.8 - - + +
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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