Contacts of the strand formed by residues 534 - 541 (chain B) 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 B).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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512B PHE* 3.6 5.6 - - - -
513B PHE* 2.9 34.8 + - + +
532B LYS* 4.9 8.1 - - + +
533B TRP* 1.3 75.8 - - - +
535B GLN* 1.3 63.0 + - - +
536B TYR* 2.8 47.9 + - + +
549B GLU* 3.8 21.6 + - - -
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Residues in contact with GLN 535 (chain B).
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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510B TRP* 3.8 39.8 - - + +
511B LEU 3.4 13.1 - - - +
512B PHE* 3.7 39.1 - - + -
534B LYS* 1.3 74.8 - - - +
536B TYR* 1.3 72.1 + - - +
549B GLU* 4.1 13.3 - - - +
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Residues in contact with TYR 536 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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510B TRP* 3.3 12.3 - - - -
511B LEU 3.0 31.2 + - - +
513B PHE* 3.8 23.2 - + + -
534B LYS* 2.8 61.5 + - + +
535B GLN* 1.3 72.6 - - - +
537B TRP* 1.3 61.4 + - - +
538B VAL* 3.6 5.4 + - + +
547B PHE* 3.7 43.1 - + + -
548B TYR 3.5 15.0 - - - +
549B GLU* 3.4 28.3 - - - -
563B ARG* 4.3 12.9 - - + +
564B CYS* 4.6 9.6 - - - -
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Residues in contact with TRP 537 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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508B ALA* 3.8 22.4 - - + -
509B GLY* 3.5 31.6 - - - -
510B TRP* 3.4 51.5 - + + -
536B TYR* 1.3 72.0 - - - +
538B VAL* 1.3 58.2 + - - +
539B THR* 3.6 23.1 - - + +
546B LEU 3.4 2.6 - - - +
547B PHE* 3.7 0.3 - - - -
548B TYR* 2.9 51.7 + + + +
550B THR 3.9 10.1 - - - +
551B TYR* 3.4 44.4 - + - -
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Residues in contact with VAL 538 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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508B ALA* 3.0 6.2 - - - +
509B GLY 2.9 36.9 + - - +
511B LEU* 3.9 30.7 - - + +
536B TYR* 3.9 12.8 - - + +
537B TRP* 1.3 75.8 + - - +
539B THR* 1.3 68.2 + - - +
545B LEU* 3.9 33.2 - - + -
546B LEU 3.2 10.5 - - - +
547B PHE* 3.8 30.1 - - + -
598B PHE* 5.4 0.2 - - + -
609B TRP* 3.7 7.7 - - + -
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Residues in contact with THR 539 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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505B VAL* 4.3 15.7 - - + -
507B LYS 3.4 5.8 - - - -
508B ALA* 3.8 9.9 - - + -
537B TRP* 3.6 25.4 - - + +
538B VAL* 1.3 83.6 - - - +
540B LEU* 1.3 61.8 + - - +
541B LYS* 4.0 3.4 + - - +
544B THR 3.5 1.6 - - - +
545B LEU* 3.3 6.4 - - - +
546B LEU* 2.9 52.9 + - - +
548B TYR* 3.8 11.7 + - + +
609B TRP* 4.8 0.2 - - - -
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Residues in contact with LEU 540 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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505B VAL* 3.6 4.6 - - - -
506B ARG* 2.8 44.4 + - + +
507B LYS* 2.7 20.4 + - + +
539B THR* 1.3 73.1 - - - +
541B LYS* 1.3 56.8 + - - +
542B GLY 3.6 20.6 - - - +
543B CYS 4.4 2.7 - - - -
544B THR 3.6 14.4 - - - +
545B LEU* 3.9 20.4 - - + -
568B ALA* 5.8 1.6 - - + -
609B TRP* 4.2 5.6 - - + -
612B ALA* 3.5 46.2 - - + +
613B ILE* 3.8 15.0 - - + +
616B ALA* 4.3 4.5 - - + -
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Residues in contact with LYS 541 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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504B VAL* 3.1 45.1 - - - +
505B VAL* 4.6 13.4 - - + +
506B ARG 4.7 0.2 - - - +
539B THR* 4.0 4.6 - - - +
540B LEU* 1.3 73.8 - - - +
542B GLY* 1.3 69.0 + - - +
544B THR* 3.0 29.0 + - - +
546B LEU* 5.8 7.6 - - + -
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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