Contacts of the helix formed by residues 534 - 540 (chain A) in PDB entry 3U1K
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 LEU 534 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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309A ARG* 4.4 10.3 - - - +
359A CYS* 3.7 30.5 - - - -
360A ASP* 4.1 21.1 - - + +
362A ARG* 3.2 21.5 - - - +
368A ARG* 3.3 26.7 - - - +
480A ASN* 3.5 16.6 - - - +
481A GLY* 4.6 0.7 - - - -
532A ASP 3.8 0.2 + - - -
533A ILE* 1.3 77.1 - - - +
535A GLY* 1.3 66.5 + - - +
536A ILE* 3.9 15.9 - - + -
537A GLU* 2.9 31.3 + - - +
538A ASP* 3.1 11.7 + - - +
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Residues in contact with GLY 535 (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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1A CIT 6.0 1.6 - - - -
306A LYS* 6.1 2.9 - - - -
480A ASN* 3.1 27.1 + - - -
481A GLY* 4.7 4.3 - - - -
534A LEU* 1.3 70.6 - - - +
536A ILE* 1.3 58.6 + - - +
538A ASP* 2.9 24.6 + - - +
539A TYR* 3.0 22.8 + - - -
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Residues in contact with ILE 536 (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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299A PHE* 3.9 22.2 - - + -
309A ARG* 4.1 18.2 - - + +
310A ASP* 4.5 7.4 - - - +
313A VAL* 5.4 2.9 - - + -
348A PHE* 3.9 26.6 - - + -
359A CYS* 4.0 12.1 - - - -
480A ASN* 5.3 0.4 + - - -
534A LEU* 3.9 16.8 - - + +
535A GLY* 1.3 75.7 - - - +
537A GLU* 1.3 59.5 + - - +
539A TYR* 3.5 31.0 - - + +
540A ASN* 3.0 47.0 + - - +
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Residues in contact with GLU 537 (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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348A PHE* 3.6 28.3 - - + -
352A VAL* 5.4 1.2 - - - +
358A ARG* 2.7 62.3 + - - +
359A CYS* 4.9 0.7 + - - -
362A ARG* 3.7 1.2 + - - -
513A LEU 5.2 2.3 + - - +
514A VAL* 5.6 0.5 - - - +
530A LEU* 4.2 14.3 - - + +
533A ILE* 3.2 18.8 - - + +
534A LEU* 2.9 39.2 + - + +
536A ILE* 1.3 76.4 - - + +
538A ASP* 1.3 60.6 + - - +
541A GLY* 3.0 25.4 + - - -
543A MET 5.2 0.9 - - - +
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Residues in contact with ASP 538 (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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1A CIT 4.1 15.2 - - - +
533A ILE* 4.0 12.9 - - + +
534A LEU 3.1 9.4 + - - +
535A GLY* 2.9 13.7 + - - +
537A GLU* 1.3 77.9 - - - +
539A TYR* 1.3 65.9 + - + +
541A GLY* 3.0 13.9 + - - -
543A MET 4.1 5.3 - - - +
544A ASP* 3.2 30.0 - - - +
560A ASP* 5.7 0.3 - - - +
562A LYS* 3.1 21.1 + - - +
670A CIT 3.1 20.8 - - - +
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Residues in contact with TYR 539 (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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310A ASP* 3.5 25.9 + - - -
345A LYS* 4.6 7.4 + - - +
535A GLY* 3.0 25.6 + - - -
536A ILE* 3.5 39.9 - - + +
538A ASP* 1.3 76.8 - - - +
540A ASN* 1.3 75.4 + - - +
541A GLY 3.2 1.0 - - - +
562A LYS* 3.5 17.6 + - - +
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Residues in contact with ASN 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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299A PHE* 5.1 2.4 - - - -
341A ASN 5.0 0.5 - - - +
344A ALA* 4.6 4.1 + - - +
345A LYS* 3.6 37.9 + - + +
348A PHE* 3.7 33.5 - - + +
349A ARG* 2.9 32.2 + - - +
514A VAL* 5.0 0.4 - - - +
536A ILE* 3.0 39.5 + - - +
537A GLU* 4.0 0.7 - - - -
539A TYR* 1.3 91.9 - - - +
541A GLY* 1.3 57.6 + - - +
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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