Contacts of the strand formed by residues 547 - 553 (chain A) in PDB entry 2WKP
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 ILE 547 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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545A GLU 3.8 10.8 - - - +
546A LEU* 1.3 74.0 - - - +
548A LYS* 1.3 63.9 + - - +
549A CYS 3.7 0.2 + - - -
594A VAL* 3.4 27.1 - - + -
595A ASN 3.0 12.4 + - - +
596A LEU* 3.8 18.0 - - + +
597A GLY* 2.8 32.2 + - - +
619A ASP* 3.5 20.6 - - + +
620A VAL* 4.6 3.6 - - + -
716A ILE* 3.8 23.3 - - + -
719A VAL* 4.0 21.8 - - + -
720A LEU* 4.1 19.7 - - + -
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Residues in contact with LYS 548 (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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419A ASP* 4.2 13.9 + - - -
421A ARG* 5.3 6.1 - - - +
507A GLN* 4.8 4.9 - - - +
508A TYR* 4.2 11.7 + - - +
546A LEU 3.5 2.8 + - - +
547A ILE* 1.3 72.2 - - - +
549A CYS* 1.3 59.2 + - - +
550A VAL* 3.9 4.0 - - + -
597A GLY 3.9 1.3 - - - -
599A TRP* 3.5 46.6 - - + -
613A LEU 5.1 0.8 + - - -
614A SER 3.0 28.9 + - - -
616A PRO* 2.9 22.0 + - - +
617A GLN* 3.7 20.6 - - - +
618A THR* 3.7 12.6 - - - +
619A ASP* 2.8 43.7 + - - +
620A VAL* 3.2 7.3 + - - +
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Residues in contact with CYS 549 (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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548A LYS* 1.3 75.4 - - - +
550A VAL* 1.3 63.6 + - - +
551A VAL* 4.2 2.0 + - - -
596A LEU* 3.9 10.5 - - + -
597A GLY 2.9 14.7 + - - +
598A LEU* 3.4 25.5 - - + +
599A TRP* 2.9 26.3 + - - -
620A VAL* 3.2 26.5 - - + -
622A LEU* 3.7 32.5 - - - -
715A ALA* 4.5 6.1 - - - -
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Residues in contact with VAL 550 (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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548A LYS* 3.9 7.9 - - - -
549A CYS* 1.3 76.8 - - - +
551A VAL* 1.3 63.0 + - - +
552A VAL* 4.0 14.4 - - + -
599A TRP* 3.7 16.8 - - + +
601A THR* 4.0 8.5 - - + -
614A SER* 3.6 32.8 - - - +
615A TYR* 4.1 0.4 - - + -
618A THR* 3.3 26.5 - - + +
620A VAL 3.1 6.7 + - - -
621A PHE* 3.3 30.6 - - + -
622A LEU 2.9 23.7 + - - +
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Residues in contact with VAL 551 (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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549A CYS* 4.4 9.0 - - - +
550A VAL* 1.3 75.8 - - - +
552A VAL* 1.3 57.0 + - - +
559A LYS* 3.9 24.0 - - + +
562A LEU* 5.4 2.5 - - + -
563A LEU* 4.3 29.2 - - + -
598A LEU* 4.5 4.5 - - + -
599A TRP 3.0 15.4 + - - +
600A ASP* 4.7 1.8 - - - -
601A THR* 2.7 32.7 + - - -
622A LEU* 3.5 24.9 - - + +
624A CYS* 3.7 27.1 - - - -
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Residues in contact with VAL 552 (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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550A VAL* 4.0 17.0 + - + -
551A VAL* 1.3 78.0 - - - +
553A GLY* 1.3 60.7 + - - +
559A LYS* 3.4 10.5 - - - +
601A THR* 3.7 14.1 - - - +
611A ARG* 4.3 1.6 - - - -
615A TYR* 3.8 24.5 - - + +
621A PHE* 4.6 6.5 - - + -
622A LEU 2.9 8.8 + - - +
623A ILE* 3.5 27.3 - - + -
624A CYS* 2.8 25.5 + - - +
640A TRP* 3.9 23.3 - - + -
644A VAL* 4.2 10.3 - - + -
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Residues in contact with GLY 553 (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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552A VAL* 1.3 79.6 - - - +
554A ASP* 1.3 70.0 + - - +
557A VAL* 4.4 0.7 - - - -
559A LYS* 3.1 16.4 + - - +
601A THR* 5.0 0.2 + - - -
603A GLY* 3.1 12.6 - - - -
624A CYS 3.5 14.8 - - - -
640A TRP* 3.3 25.2 - - - -
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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