Contacts of the helix formed by residues 560 - 570 (chain A) in PDB entry 1WKB
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 THR 560 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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161A LYS* 5.3 2.5 - - - +
165A TRP* 5.5 0.2 - - - -
557A GLU 4.1 9.2 - - - +
558A LYS* 2.9 21.0 + - + +
559A LEU* 1.3 75.9 - - - +
561A PRO* 1.3 77.6 - - + +
562A GLU* 3.4 19.0 + - - +
563A PHE* 3.0 20.2 + - - +
564A PHE* 3.2 13.4 + - - -
580A LEU* 5.8 0.7 - - - +
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Residues in contact with PRO 561 (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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161A LYS* 6.1 2.9 - - - +
164A GLU* 6.0 0.9 - - + -
165A TRP* 3.4 30.4 - - + +
168A TRP* 3.9 32.5 - - + +
169A LYS* 5.2 3.4 - - - -
559A LEU 4.7 0.9 - - - +
560A THR* 1.3 89.5 - - - +
562A GLU* 1.3 55.3 + - - +
565A ASP* 2.9 39.8 + - - +
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Residues in contact with GLU 562 (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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560A THR* 3.0 12.4 + - - +
561A PRO* 1.3 78.1 - - - +
563A PHE* 1.3 66.9 + - - +
565A ASP* 3.2 12.0 + - - +
566A TYR* 3.2 20.8 + - - +
570A GLU* 4.7 1.4 - - - +
576A LYS* 3.3 29.7 + - - +
579A GLU* 4.1 1.2 - - - +
580A LEU* 4.1 13.2 - - + +
583A LYS* 2.8 38.7 + - - +
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Residues in contact with PHE 563 (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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545A ILE* 6.1 0.2 - - + -
558A LYS 4.4 2.9 - - - +
559A LEU* 3.8 27.6 - - + -
560A THR* 3.0 22.8 + - - +
562A GLU* 1.3 80.2 - - - +
564A PHE* 1.3 78.6 + + - +
566A TYR* 3.2 6.1 + - - +
567A ILE* 3.2 43.7 + - + +
580A LEU* 3.9 23.5 - - + +
584A THR* 3.9 17.7 - - + -
586A ILE* 4.3 12.1 - - + -
591A ILE* 3.9 30.3 - - + -
594A MET* 3.7 33.2 - - + -
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Residues in contact with PHE 564 (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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158A PRO 4.1 6.5 - - - -
161A LYS 3.7 1.8 - - - -
162A PHE* 3.5 37.7 - + + -
165A TRP* 3.6 45.1 - + + -
538A TYR* 5.3 1.1 - + - -
541A ILE* 3.8 25.1 - - + -
545A ILE* 5.3 1.8 - - + -
559A LEU* 3.6 38.8 - - + -
560A THR 3.2 17.6 + - - -
563A PHE* 1.3 89.9 - + - +
565A ASP* 1.3 60.3 + - - +
567A ILE* 3.3 2.8 + - + -
568A PHE* 2.9 54.1 + + + +
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Residues in contact with ASP 565 (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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165A TRP* 2.8 20.4 + - - +
169A LYS* 2.9 24.9 + - - -
561A PRO* 2.9 26.1 + - - +
562A GLU* 3.2 11.1 + - - +
564A PHE* 1.3 76.8 - - - +
566A TYR* 1.3 58.0 + - - +
569A LEU* 2.9 38.9 + - + +
570A GLU* 3.0 26.4 + - - +
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Residues in contact with TYR 566 (chain A).
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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562A GLU 3.2 6.1 + - - +
563A PHE 3.5 8.1 - - - +
564A PHE 3.2 0.4 - - - -
565A ASP* 1.3 80.1 - - - +
567A ILE* 1.3 70.0 + - + +
570A GLU* 3.5 30.1 + - + +
571A GLU 3.3 20.9 - - - -
572A PHE* 3.4 5.2 - - - -
573A SER* 2.9 20.2 + - - -
576A LYS* 4.0 16.4 - - + -
577A GLU* 2.4 47.1 + - + -
580A LEU* 3.7 29.2 - - + -
591A ILE* 4.0 13.9 - - + -
595A LYS* 2.9 43.2 + - + +
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Residues in contact with ILE 567 (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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541A ILE* 3.9 16.2 - - + -
563A PHE* 3.2 45.5 + - + +
564A PHE* 3.6 9.2 - - + +
566A TYR* 1.3 78.3 - - + +
568A PHE* 1.3 87.0 + - + +
591A ILE* 3.8 30.7 - - + +
594A MET* 4.2 12.3 - - + -
595A LYS* 2.9 36.5 + - + +
598A PHE* 3.7 13.5 - - + -
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Residues in contact with PHE 568 (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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162A PHE* 3.7 21.1 - + - -
165A TRP* 3.7 16.2 - + + -
537A ALA* 3.4 30.3 - - + -
540A THR* 4.3 0.7 - - - -
541A ILE* 3.8 14.8 - - + -
564A PHE* 2.9 53.7 + + + +
567A ILE* 1.3 87.6 - - + +
569A LEU* 1.3 70.1 + - + +
598A PHE* 3.4 45.7 - + + -
629A PHE* 3.9 18.8 - + + -
630A ARG* 2.9 20.0 + - - -
633A HIS* 4.2 2.4 - - - -
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Residues in contact with LEU 569 (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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165A TRP* 4.3 12.3 - - + -
169A LYS* 3.8 15.7 - - + +
173A LYS* 5.9 1.6 - - - +
565A ASP* 2.9 36.1 + - + +
568A PHE* 1.3 89.2 - - + +
570A GLU* 1.3 65.7 + - + +
571A GLU* 5.3 0.9 - - - +
628A ILE* 3.3 36.1 - - + +
629A PHE* 4.3 9.6 - - + -
630A ARG* 3.5 30.0 + - + +
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Residues in contact with GLU 570 (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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562A GLU 4.7 0.7 - - - +
565A ASP* 3.0 32.4 + - - +
566A TYR* 3.5 26.9 + - + +
569A LEU* 1.3 84.0 - - + +
571A GLU* 1.3 68.1 + - - +
576A LYS* 3.5 26.9 + - - +
595A LYS* 2.6 29.4 + - - -
599A GLU* 4.2 0.3 - - - +
630A ARG* 3.9 7.7 + - - -
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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