Contacts of the strand formed by residues 526 - 531 (chain D) 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 ASP 526 (chain D).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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353D LEU* 4.3 6.6 - - + +
356D TYR* 4.5 1.1 + - - -
516D LYS* 3.0 37.4 + - + -
524D ILE* 3.4 5.9 - - - +
525D GLU* 1.3 81.8 - - + +
527D TYR* 1.3 74.4 + - - +
528D ARG* 2.7 47.2 + - - -
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Residues in contact with TYR 527 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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353D LEU* 4.5 1.8 - - - -
513D LEU* 4.0 16.2 - - + -
514D VAL 3.2 13.0 - - - +
515D THR* 3.8 15.0 - - + -
524D ILE* 4.3 7.4 - - + -
525D GLU 5.3 2.0 - - - -
526D ASP* 1.3 87.1 + - - +
528D ARG* 1.3 81.0 + - - +
529D LEU* 4.4 13.2 - - + -
569D LYS* 3.3 33.4 + - + +
570D ILE* 3.9 28.5 - - + -
573D GLU* 2.6 29.5 + - - -
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Residues in contact with ARG 528 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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352D VAL* 3.2 37.9 + - + +
353D LEU* 2.1 51.1 + - + -
356D TYR* 3.0 38.7 + - - -
364D LEU* 3.7 28.5 - - + -
513D LEU* 3.4 6.6 - - - +
514D VAL* 2.9 33.0 + - + +
526D ASP* 2.7 43.2 + - - -
527D TYR* 1.3 81.6 + - - +
529D LEU* 1.3 62.4 + - - +
530D LEU* 3.9 3.4 + - + +
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Residues in contact with LEU 529 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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364D LEU* 3.3 21.3 - - - +
511D ILE* 4.0 6.3 - - + -
512D GLY 3.5 15.0 - - - +
513D LEU* 3.8 15.3 - - + -
527D TYR* 4.3 11.5 + - + -
528D ARG* 1.3 74.0 - - - +
530D LEU* 1.3 59.8 + - - +
543D MET* 3.6 21.8 - - + -
570D ILE* 4.0 10.1 - - + +
573D GLU* 3.7 38.1 - - + +
574D ALA* 3.8 13.0 - - + +
577D GLN* 3.2 34.8 + - - +
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Residues in contact with LEU 530 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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348D PHE* 6.0 0.7 - - + -
352D VAL* 4.0 17.7 - - + -
358D ARG* 4.0 18.6 - - + +
364D LEU* 3.4 33.2 - - + -
511D ILE* 3.1 7.7 - - - +
512D GLY 2.7 36.5 + - - +
513D LEU 4.5 6.3 - - - +
514D VAL* 4.1 22.2 - - + -
528D ARG* 4.1 8.5 - - + +
529D LEU* 1.3 76.8 - - - +
531D THR* 1.3 62.3 + - - +
533D ILE* 3.7 18.2 - - + +
537D GLU* 4.0 29.2 - - + +
577D GLN* 3.9 1.1 - - - -
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Residues in contact with THR 531 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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358D ARG* 3.0 13.2 + - - +
362D ARG* 3.2 5.7 + - - -
364D LEU 3.1 5.1 + - - -
365D THR* 3.0 34.6 + - - +
366D SER 3.4 8.7 + - - -
367D LEU* 4.1 1.2 + - - +
511D ILE* 3.7 13.5 - - + -
530D LEU* 1.3 72.6 - - - +
532D ASP* 1.3 74.1 + - - +
577D GLN* 2.8 42.2 - - + +
581D ALA* 4.2 16.1 - - + +
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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