Contacts of the strand formed by residues 540 - 545 (chain A) in PDB entry 3K5M
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 540 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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408A ARG* 2.9 38.3 + - - +
535A GLU* 5.1 1.7 - - - +
538A GLY 5.3 0.7 - - - +
539A TYR* 1.3 78.9 - - - +
541A VAL* 1.3 59.9 + - - +
542A ILE 3.6 0.5 + - - -
551A VAL* 3.4 5.5 - - - +
552A TRP* 2.9 48.4 + - + +
554A LYS* 2.5 42.9 + - - +
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Residues in contact with VAL 541 (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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405A MET* 3.2 29.1 - - - +
408A ARG* 4.0 12.0 + - - +
531A LYS* 3.7 48.8 + - + +
534A ILE* 3.7 31.0 - - + -
535A GLU* 4.1 9.4 + - + +
539A TYR 3.9 0.4 + - - -
540A ASP* 1.3 73.1 - - - +
542A ILE* 1.3 55.8 + - - +
543A TYR 4.0 5.6 - - - +
544A GLY* 5.6 0.4 - - - -
549A THR* 3.8 20.2 - - + -
550A PHE 3.4 11.9 - - - +
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Residues in contact with ILE 542 (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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405A MET* 3.3 8.3 - - - +
407A SER* 3.3 0.5 - - - -
408A ARG* 3.0 56.5 + - + +
412A TYR* 3.7 39.3 - - + +
415A VAL* 4.1 14.1 - - + -
540A ASP 3.6 0.4 + - - +
541A VAL* 1.3 73.8 - - - +
543A TYR* 1.3 64.1 + - + +
550A PHE* 3.1 18.8 + - + +
552A TRP* 3.6 24.5 - - + -
601A PHE* 3.6 34.1 - - + -
603A MET* 5.0 2.0 - - + -
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Residues in contact with TYR 543 (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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404A VAL* 4.1 7.1 - - + +
405A MET* 3.6 24.4 - - - +
407A SER* 3.5 23.8 - - - -
541A VAL* 3.5 3.9 - - - +
542A ILE* 1.3 85.2 - - + +
544A GLY* 1.3 74.5 + - - +
545A ASP* 3.5 24.8 + - + +
549A THR* 3.8 0.9 - - - -
550A PHE* 2.8 71.7 + + + +
603A MET* 4.0 19.5 - - + -
613A SER 4.5 1.1 - - - -
614A LYS* 4.1 13.9 - - + +
615A LYS* 3.0 30.0 + - - +
616A ARG 5.6 0.2 - - - -
617A TYR* 4.2 16.6 - + - -
913P G 5.2 0.8 + - - -
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Residues in contact with GLY 544 (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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403A TYR* 4.3 11.7 - - - -
404A VAL* 3.4 22.3 - - - +
405A MET* 3.4 18.2 + - - +
527A MET* 4.9 1.3 - - - -
541A VAL* 5.6 0.9 - - - -
543A TYR* 1.3 86.1 - - - +
545A ASP* 1.3 62.9 + - - +
548A SER 3.2 11.9 - - - -
549A THR* 4.6 1.8 - - - -
550A PHE* 4.2 1.3 - - - -
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Residues in contact with ASP 545 (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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403A TYR 3.5 6.5 - - - +
404A VAL* 3.7 11.1 - - + +
527A MET* 4.6 1.0 - - - +
543A TYR* 3.5 19.4 + - + +
544A GLY* 1.3 75.5 - - - +
546A THR* 1.3 81.9 + - - +
547A ASP 2.7 16.5 + - - -
548A SER* 3.0 26.6 + - - +
550A PHE* 4.8 0.2 - - - -
615A LYS* 2.8 40.9 + - - +
913P G 3.1 30.1 - - - +
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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