Contacts of the strand formed by residues 534 - 541 (chain D) in PDB entry 3A8P
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 LYS 534 (chain D).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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512D PHE* 3.8 4.9 - - - -
513D PHE* 2.7 39.9 + - + +
532D LYS* 4.0 28.3 - - + +
533D TRP* 1.3 84.3 - - - +
535D GLN* 1.3 61.8 + - - +
536D TYR* 2.9 44.9 + - + -
563D ARG* 4.5 13.9 - - - +
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Residues in contact with GLN 535 (chain D).
Click here for Legend to table.
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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510D TRP* 3.7 41.8 - - + +
511D LEU 3.5 10.7 - - - +
512D PHE* 3.4 44.0 - - + -
534D LYS* 1.3 74.0 + - - +
536D TYR* 1.3 78.7 + - - +
549D GLU* 5.5 1.7 - - - -
563D ARG* 4.9 3.1 + - - -
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Residues in contact with TYR 536 (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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510D TRP* 3.1 14.2 - - - -
511D LEU 2.9 29.5 + - - +
513D PHE* 4.0 23.4 - + + -
534D LYS* 2.9 54.2 + - + -
535D GLN* 1.3 87.2 - - - +
537D TRP* 1.3 63.6 + - - +
538D VAL* 3.5 8.0 + - + +
547D PHE* 3.8 40.2 - + + -
548D TYR 3.5 17.9 - - - +
549D GLU 5.3 0.2 - - - -
563D ARG* 3.3 39.6 + - + +
564D CYS* 5.2 6.1 - - - -
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Residues in contact with TRP 537 (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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508D ALA* 3.8 23.3 - - + +
509D GLY* 3.6 27.6 - - - -
510D TRP* 3.5 57.7 - + + -
536D TYR* 1.3 71.2 - - - +
538D VAL* 1.3 57.9 + - - +
539D THR* 3.8 20.6 + - - -
546D LEU 3.5 2.6 - - - +
548D TYR* 2.9 60.3 + + + +
549D GLU 5.0 1.1 - - - +
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Residues in contact with VAL 538 (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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508D ALA* 3.1 4.5 - - - -
509D GLY 2.8 37.1 + - - +
511D LEU* 3.8 36.8 - - + +
513D PHE* 5.9 0.4 - - + -
536D TYR* 3.9 18.2 - - + +
537D TRP* 1.3 76.6 - - - +
539D THR* 1.3 63.5 + - - +
545D LEU* 3.9 32.5 - - + -
546D LEU 3.2 9.6 - - - +
547D PHE* 4.1 20.0 - - + -
598D PHE* 5.0 2.5 - - + -
609D TRP* 3.4 9.6 - - + -
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Residues in contact with THR 539 (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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505D VAL* 3.5 34.3 - - + -
507D LYS 3.4 4.9 - - - +
508D ALA* 3.6 13.1 - - + +
537D TRP* 3.8 13.9 + - - -
538D VAL* 1.3 78.0 + - - +
540D LEU* 1.3 65.6 + - - +
541D LYS* 3.7 1.9 + - + +
544D THR 3.4 1.9 - - - +
545D LEU* 3.4 5.5 - - - -
546D LEU* 2.6 58.6 + - + +
548D TYR* 4.0 10.9 - - + -
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Residues in contact with LEU 540 (chain D).
Click here for Legend to table.
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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504D VAL 3.7 0.2 - - - +
505D VAL* 3.4 3.8 - - - +
506D ARG* 2.9 36.3 + - + -
507D LYS* 2.9 17.0 + - + +
538D VAL 4.3 0.2 - - - -
539D THR* 1.3 71.9 - - - +
541D LYS* 1.3 58.4 + - - +
542D GLY 3.4 20.4 - - - +
543D CYS* 4.4 3.8 - - - -
544D THR 3.4 16.8 - - - +
545D LEU* 3.8 24.4 - - + +
568D ALA* 5.4 4.0 - - + -
609D TRP* 4.4 6.7 - - + -
612D ALA* 3.5 43.5 - - + +
613D ILE* 3.9 13.2 - - + +
616D ALA* 4.1 9.9 - - + -
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Residues in contact with LYS 541 (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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502D GLN* 4.3 12.6 - - - +
503D GLY* 2.6 43.3 + - - +
504D VAL 3.5 3.1 - - - -
505D VAL* 4.1 23.8 - - + +
539D THR* 3.7 1.1 + - + -
540D LEU* 1.3 72.5 - - - +
542D GLY* 1.3 66.8 + - - +
543D CYS 3.2 0.5 + - - -
544D THR* 2.8 31.1 + - - +
546D LEU* 4.2 26.2 - - + -
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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