Contacts of the helix formed by residues 558 - 569 (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 GLY 558 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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556A ALA 3.3 3.8 + - - -
557A VAL* 1.3 79.5 - - - +
559A LYS* 1.3 66.8 + - - +
561A CYS* 3.8 0.9 - - - +
562A LEU* 2.9 32.4 + - - +
658A THR* 5.0 2.0 - - - -
1724A GTP 2.9 41.7 + - - -
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Residues in contact with LYS 559 (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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551A VAL* 3.9 19.5 - - + +
552A VAL* 3.4 33.0 - - - +
553A GLY* 3.1 12.5 + - - +
554A ASP 3.0 17.4 + - - -
557A VAL* 3.7 11.4 - - + -
558A GLY* 1.3 77.9 - - - +
560A THR* 1.3 61.4 + - - +
562A LEU* 3.4 11.5 - - - +
563A LEU* 3.2 26.9 + - - +
600A ASP* 3.8 12.8 - - - +
601A THR* 3.4 25.6 - - - -
603A GLY 4.4 1.6 - - - +
624A CYS* 4.1 7.9 - - + -
658A THR* 5.5 0.2 - - - +
1724A GTP 2.7 49.8 + - - +
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Residues in contact with THR 560 (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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559A LYS* 1.3 75.3 - - - +
561A CYS* 1.3 57.9 + - - +
563A LEU* 3.2 4.2 + - - +
564A ILE* 2.9 49.8 + - + +
572A PRO* 5.5 1.3 - - + -
576A ILE 5.6 2.9 - - - +
578A THR* 2.8 5.2 + - - +
583A TYR* 3.7 13.0 - - - +
600A ASP* 2.6 21.1 + - - +
1724A GTP 2.9 15.0 + - - +
1726A MG 2.1 30.4 - - - -
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Residues in contact with CYS 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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558A GLY 3.8 0.7 - - - +
559A LYS 3.3 0.2 - - - -
560A THR* 1.3 75.4 - - - +
562A LEU* 1.3 57.6 + - - +
564A ILE* 3.8 1.0 - - - +
565A SER* 2.9 31.4 + - - -
571A PHE* 3.8 14.6 - - + -
572A PRO* 3.4 31.4 - - + +
573A GLY 4.5 3.1 - - - -
702A ALA* 3.5 6.5 - - + +
1724A GTP 2.8 70.1 + - + +
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Residues in contact with LEU 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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551A VAL* 5.4 2.7 - - + -
558A GLY 2.9 18.0 + - - +
559A LYS* 3.4 18.2 - - - +
560A THR 3.3 0.2 - - - -
561A CYS* 1.3 76.1 - - - +
563A LEU* 1.3 66.2 + - + +
565A SER* 3.8 1.5 - - - -
566A TYR* 2.9 30.8 + - - +
622A LEU* 5.0 8.1 - - + -
624A CYS* 4.3 11.4 - - - -
656A VAL* 4.7 2.9 - - + -
658A THR* 3.8 27.6 - - + -
700A CYS* 4.4 11.9 - - - -
702A ALA* 3.7 14.5 - - + +
708A LEU* 3.9 16.8 - - + +
711A VAL* 5.5 1.8 - - + -
712A PHE* 3.4 30.7 - - + -
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Residues in contact with LEU 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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551A VAL* 4.3 15.3 - - + -
559A LYS 3.2 14.3 + - - +
560A THR 3.7 5.2 - - - +
562A LEU* 1.3 79.1 - - + +
564A ILE* 1.3 60.0 + - - +
566A TYR* 4.6 2.0 - - - -
567A THR* 2.8 36.9 + - - +
583A TYR* 3.8 24.0 - - + -
598A LEU* 3.9 27.4 - - + -
600A ASP* 3.6 43.1 - - + +
712A PHE* 3.8 29.6 - - + -
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Residues in contact with ILE 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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443A GLU* 5.7 2.5 - - + -
560A THR* 2.9 35.6 + - + +
561A CYS 4.0 2.7 - - - +
563A LEU* 1.3 76.5 - - - +
565A SER* 1.3 57.9 + - - +
567A THR* 3.9 5.4 - - - -
568A THR* 2.7 52.1 + - + +
570A ALA* 4.4 8.1 - - + +
572A PRO* 3.6 43.1 - - + -
583A TYR* 3.5 22.0 - - + +
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Residues in contact with SER 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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561A CYS 2.9 19.4 + - - -
562A LEU 3.8 0.7 - - - -
564A ILE* 1.3 77.8 - - - +
566A TYR* 1.3 58.0 + - - +
569A ASN* 2.8 22.2 + - - +
570A ALA 3.4 18.6 + - - -
571A PHE* 5.2 0.4 - - - -
702A ALA* 2.9 28.9 + - - -
705A GLN* 3.0 36.0 + - - +
708A LEU* 3.4 9.5 - - - +
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Residues in contact with TYR 566 (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 LEU 2.9 18.8 + - - +
563A LEU* 3.9 2.7 - - - +
565A SER* 1.3 79.5 - - - +
567A THR* 1.3 72.7 + - + +
568A THR 3.7 0.2 + - - -
569A ASN* 4.5 6.5 - - - +
585A ALA* 3.8 22.2 - - + -
587A VAL* 3.1 31.6 - - + +
596A LEU* 4.9 0.4 - - + -
598A LEU* 4.6 3.8 - - + -
705A GLN* 4.8 0.9 - - - +
708A LEU* 3.6 16.8 - - + +
709A LYS* 4.3 26.8 + - + -
712A PHE* 3.4 57.2 - + + +
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Residues in contact with THR 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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443A GLU* 3.9 10.3 + - - +
563A LEU 2.8 23.2 + - - +
564A ILE* 3.7 0.7 + - - -
566A TYR* 1.3 94.8 - - + +
568A THR* 1.3 71.6 + - - +
583A TYR* 3.7 29.5 - - + -
584A SER 3.6 26.9 - - - +
585A ALA* 4.6 2.5 - - + -
598A LEU* 4.6 4.5 - - + -
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Residues in contact with THR 568 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
443A GLU* 3.5 37.0 - - + +
564A ILE* 2.7 32.6 + - + +
567A THR* 1.3 88.7 - - - +
569A ASN* 1.3 69.7 + - - +
570A ALA* 3.0 21.1 + - - +
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Residues in contact with ASN 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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565A SER* 2.8 17.2 + - - +
566A TYR 4.5 5.6 - - - +
567A THR 3.9 0.4 - - - -
568A THR* 1.3 79.5 + - - +
570A ALA* 1.3 60.6 + - - +
705A GLN* 3.0 32.2 + - - +
709A LYS* 5.3 5.2 + - - -
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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