Contacts of the helix formed by residues 565 - 572 (chain B) in PDB entry 1K2P
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 PRO 565 (chain B).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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563B TRP 4.3 3.6 - - - +
564B SER* 1.3 86.0 - - - +
566B PRO* 1.3 72.3 - - + +
567B GLU* 2.9 29.8 + - + +
568B VAL* 2.9 37.7 + - + +
569B LEU* 3.1 4.4 + - - +
573B LYS 5.4 0.2 - - - +
578B SER* 3.7 30.5 - - - +
581B TRP* 3.7 24.5 - - + -
641B ARG* 3.9 7.0 - - - +
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Residues in contact with PRO 566 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
564B SER 3.8 0.4 - - - -
565B PRO* 1.3 81.1 - - + +
567B GLU* 1.3 74.0 + - - +
569B LEU* 3.3 21.0 + - + +
570B MET* 3.3 29.8 + - + +
581B TRP* 3.4 23.3 - - + -
610B ILE* 3.5 21.1 - - + +
611B ALA* 4.6 7.6 - - + +
636B GLU* 3.3 41.1 - - + +
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Residues in contact with GLU 567 (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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565B PRO* 3.2 10.9 - - + +
566B PRO* 1.3 95.9 - - - +
568B VAL* 1.3 58.2 + - - +
570B MET* 5.0 0.4 - - - -
571B TYR* 3.1 49.8 + - - +
572B SER 3.5 2.3 + - - -
573B LYS* 3.5 33.0 + - + +
636B GLU* 3.3 22.4 - - - +
638B ALA* 4.4 7.8 - - + +
641B ARG* 2.9 27.4 + - - -
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Residues in contact with VAL 568 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
559B PHE* 3.4 20.8 - - + -
564B SER* 3.2 17.7 - - - +
565B PRO* 2.9 42.8 + - + +
567B GLU* 1.3 72.1 - - - +
569B LEU* 1.3 59.2 + - + +
570B MET 3.0 10.4 + - - -
572B SER* 3.1 26.4 + - - +
573B LYS 3.1 33.0 - - - +
574B PHE* 3.7 9.9 - - + +
578B SER* 4.0 11.2 - - - +
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Residues in contact with LEU 569 (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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559B PHE* 4.0 22.2 - - + -
561B VAL* 3.5 46.9 - - + +
564B SER* 3.5 28.0 - - - +
565B PRO 3.1 11.1 + - - +
566B PRO* 3.3 16.3 + - + +
568B VAL* 1.3 74.0 - - - +
570B MET* 1.3 63.0 + - + +
607B ALA* 4.6 27.1 - - + +
610B ILE* 4.5 21.5 - - + -
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Residues in contact with MET 570 (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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559B PHE* 5.3 3.8 - - - -
566B PRO* 3.3 32.4 + - + +
567B GLU* 5.0 0.2 - - - -
568B VAL 3.0 1.0 - - - -
569B LEU* 1.3 87.0 - - + +
571B TYR* 1.3 85.4 + - + +
572B SER* 3.6 2.5 + - - -
611B ALA* 4.9 16.4 - - + -
636B GLU* 5.3 2.9 - - - +
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Residues in contact with TYR 571 (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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567B GLU* 3.1 27.1 + - - +
570B MET* 1.3 99.2 - - + +
572B SER* 1.3 70.2 + - - +
573B LYS* 3.3 35.0 + - + +
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Residues in contact with SER 572 (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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552B THR 5.7 0.4 - - - -
556B GLY 5.9 1.4 + - - -
559B PHE* 3.2 33.1 - - - -
567B GLU 3.5 0.6 + - - -
568B VAL* 3.1 21.9 + - - +
570B MET 3.6 0.7 + - - -
571B TYR* 1.3 78.5 - - - +
573B LYS* 1.3 58.3 + - - +
574B PHE* 3.2 43.6 + - - -
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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