Contacts of the strand formed by residues 526 - 530 (chain D) in PDB entry 5HIE
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 ALA 526 (chain D).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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482D VAL* 3.6 28.7 - - + -
483D LYS 3.2 11.9 - - - +
484D MET* 3.9 10.8 - - - -
485D LEU* 4.3 2.0 - - - +
519D TYR* 3.4 9.6 - - - +
520D SER* 2.8 42.0 + - - +
522D LYS 5.8 0.9 - - - +
524D GLN 4.1 4.0 - - - +
525D LEU* 1.3 81.9 - - - +
527D ILE* 1.3 62.4 + - - +
528D VAL 4.0 0.2 - - - -
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Residues in contact with ILE 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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468D PHE* 4.6 3.8 - - + -
481D ALA 3.6 1.9 - - - +
482D VAL* 3.7 0.7 - - - -
483D LYS* 2.8 40.1 + - + +
485D LEU* 3.7 27.1 - - + -
495D LEU* 3.9 22.4 - - + -
498D PHE* 4.2 20.4 - - + -
516D PHE* 3.6 25.4 - - + -
518D GLY 3.9 3.4 - - - -
519D TYR* 4.2 8.7 - - + -
526D ALA* 1.3 72.8 - - - +
528D VAL* 1.3 62.2 + - - +
529D THR* 3.9 7.0 + - + +
801D P06 3.2 35.2 - - + -
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Residues in contact with VAL 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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452D ILE* 3.7 20.0 - - + -
457D ILE* 3.8 16.8 - - + -
476D TRP* 4.1 17.0 - - + -
480D VAL* 3.8 35.4 - - + -
481D ALA 3.3 3.6 - - - +
482D VAL* 4.4 11.2 - - + -
516D PHE* 3.9 2.4 - - - -
517D MET* 2.8 32.9 + - + -
518D GLY 2.8 20.6 + - - +
520D SER* 4.2 15.0 - - - +
526D ALA 4.7 0.2 - - - +
527D ILE* 1.3 73.7 - - - +
529D THR* 1.3 60.2 + - - +
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Residues in contact with THR 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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480D VAL* 3.4 8.7 - - - +
481D ALA* 2.8 44.1 + - - +
514D LEU* 3.5 16.9 - - + +
515D LEU 3.3 13.2 - - - +
516D PHE* 4.3 0.7 - - - -
517D MET* 4.0 7.0 - - - +
527D ILE* 3.9 6.3 - - + +
528D VAL* 1.3 79.3 - - - +
530D GLN* 1.3 66.6 + - - +
801D P06 3.5 54.7 - - + -
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Residues in contact with GLN 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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479D ASP 5.0 0.7 - - - -
480D VAL* 4.8 0.9 - - - +
481D ALA* 3.8 0.5 - - - +
514D LEU* 3.8 10.7 - - + -
515D LEU* 3.0 55.9 + - + +
517D MET* 3.8 17.5 - - - -
529D THR* 1.3 85.1 + - - +
531D TRP* 1.3 71.8 + - - +
532D CYS* 4.6 3.8 - - - -
585D HIS* 4.6 10.1 + - - -
591D LYS* 3.4 39.9 + - - +
801D P06 3.3 12.5 - - - -
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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