Contacts of the helix formed by residues 539 - 547 (chain A) in PDB entry 1U1H
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 539 (chain A).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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488A HIS* 5.3 0.9 - - - +
493A ARG* 3.3 31.4 + - - +
499A TYR* 4.2 4.7 - - - -
500A PHE* 3.6 20.4 - - - -
538A MSE 1.3 77.0 + - - +
540A VAL* 1.3 67.2 + - - +
541A PHE 3.2 3.4 + - - -
542A TRP* 3.3 8.3 + - + +
543A SER* 2.9 36.4 + - - +
557A MSE 4.2 9.4 - - - +
558A LEU* 3.7 6.9 - - + +
590A GLU* 3.0 13.4 + - - -
594A LEU* 4.1 7.6 - - + -
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Residues in contact with VAL 540 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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537A ALA* 4.2 17.3 - - + -
538A MSE 3.8 1.4 - - - +
539A THR* 1.3 76.5 - - - +
541A PHE* 1.3 58.6 + - - +
544A ALA* 2.8 42.5 + - + +
590A GLU* 4.1 6.1 - - - +
593A ASP* 3.6 46.2 - - + +
594A LEU* 3.9 17.5 - - + +
597A GLY* 4.9 10.5 - - - -
599A ILE* 5.4 1.3 - - + +
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Residues in contact with PHE 541 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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463A TYR* 3.4 46.2 - + - -
537A ALA* 5.5 2.0 - - - +
538A MSE 5.2 3.1 + - - +
539A THR 3.3 1.2 - - - +
540A VAL* 1.3 79.3 - - - +
542A TRP* 1.3 85.4 + + + +
544A ALA* 3.8 3.5 - - - +
545A MSE 3.1 55.2 + - + +
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Residues in contact with TRP 542 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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462A ASP* 5.1 3.6 - - - -
463A TYR* 3.3 41.9 - + - -
466A ALA* 3.6 27.6 - - + -
467A ILE 4.6 0.2 - - - -
470A GLU* 3.3 36.9 - - - +
488A HIS* 4.6 5.8 - - + +
492A GLU* 3.7 34.4 - - + +
493A ARG* 6.1 0.4 - - - +
499A TYR* 3.7 23.3 + - - -
538A MSE 4.5 8.9 + - - -
539A THR* 3.3 8.1 + - + +
541A PHE* 1.3 93.8 - + + +
543A SER* 1.3 57.1 + - - +
545A MSE 3.4 22.2 + - + +
546A ALA* 3.0 28.5 + - - +
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Residues in contact with SER 543 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
488A HIS* 4.8 8.5 - - - -
539A THR* 2.9 35.9 + - - +
540A VAL 4.2 0.4 - - - -
542A TRP* 1.3 73.4 - - - +
544A ALA* 1.3 60.6 + - - +
546A ALA* 3.3 6.5 + - - +
547A GLN* 2.8 31.7 + - - +
554A MSE 4.1 9.1 - - - +
555A LYS 4.9 0.3 + - - -
556A GLY* 4.3 9.8 - - - -
557A MSE 4.7 0.5 + - - -
594A LEU* 3.8 18.6 - - - +
599A ILE* 4.0 13.9 - - - +
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Residues in contact with ALA 544 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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540A VAL* 2.8 28.3 + - + +
541A PHE* 3.8 3.8 - - - +
543A SER* 1.3 76.6 - - - +
545A MSE 1.3 60.2 + - - +
547A GLN* 2.9 25.3 - - - +
548A SER* 3.6 5.0 - - - -
597A GLY* 5.0 8.7 - - - +
599A ILE* 4.0 13.6 - - + +
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Residues in contact with MSE 545 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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463A TYR* 5.4 1.3 - - + -
467A ILE* 3.6 50.5 - - + -
470A GLU* 3.8 19.5 - - - +
541A PHE* 3.1 55.4 + - + +
542A TRP* 3.5 12.1 - - + +
544A ALA* 1.3 74.9 - - - +
546A ALA* 1.3 61.9 + - - +
548A SER* 2.6 24.2 + - - +
549A MSE 3.3 15.4 - - + +
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Residues in contact with ALA 546 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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470A GLU* 4.5 5.8 - - + +
474A VAL* 4.6 8.4 - - + +
488A HIS* 3.7 17.7 - - + -
542A TRP 3.0 16.5 + - - +
543A SER 3.3 0.6 + - - +
545A MSE 1.3 76.9 - - - +
547A GLN* 1.3 58.4 + - - +
548A SER 2.9 7.4 + - - -
549A MSE 3.2 25.1 + - - +
550A THR* 4.0 5.9 - - - +
554A MSE 3.3 37.1 - - + +
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Residues in contact with GLN 547 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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543A SER 2.8 18.1 + - - +
544A ALA* 2.9 12.2 - - - +
546A ALA* 1.3 71.5 - - - +
548A SER* 1.3 60.1 + - - +
550A THR* 3.3 19.8 + - - +
551A SER 5.0 1.0 - - - -
552A ARG 3.1 19.8 + - - +
553A PRO* 3.7 3.3 - - - +
554A MSE 2.8 42.5 + - + +
598A GLY 5.2 9.9 - - - +
599A ILE* 4.3 17.0 - - + -
600A GLY 5.5 1.6 + - - -
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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