Contacts of the strand formed by residues 567 - 572 (chain A) in PDB entry 1LVK
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 GLU 567 (chain A).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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544A ILE* 3.3 13.9 - - - +
548A HIS* 3.5 2.1 + - - -
561A PRO* 3.0 23.0 - - + +
564A SER* 3.4 22.5 + - - +
565A LYS 3.6 0.2 - - - -
566A THR* 1.3 88.4 + - - +
568A PHE* 1.3 63.1 + - - +
578A MET* 3.2 23.7 - - + +
579A TYR 2.9 15.3 - - - +
580A GLU* 3.6 25.2 - - - +
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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
----------------------------------------------------------
469A LEU* 4.9 1.6 - - + -
525A ILE* 3.7 19.1 - - + -
544A ILE* 4.0 14.8 - - + -
547A LEU* 3.8 11.0 - - + -
548A HIS* 4.0 3.4 - - + -
558A TYR* 3.4 40.6 - + + +
559A GLU 3.7 6.5 - - - +
561A PRO* 4.2 0.9 - - - -
567A GLU* 1.3 76.5 - - - +
569A GLY* 1.3 60.1 - - - +
570A VAL* 3.4 29.2 - - + -
577A VAL 3.8 0.2 - - - +
578A MET* 3.2 7.3 - - - +
579A TYR* 2.7 61.8 + + + +
581A ILE* 3.7 23.8 - - + -
584A TRP* 3.9 15.3 - + - -
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Residues in contact with GLY 569 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
558A TYR* 3.3 9.0 - - - -
559A GLU 2.8 42.3 + - - -
568A PHE* 1.3 74.9 - - - +
570A VAL* 1.3 65.9 + - - +
576A GLN* 4.2 11.2 - - - -
577A VAL 3.2 8.3 - - - -
578A MET* 3.5 14.8 - - - -
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Residues in contact with VAL 570 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
469A LEU* 4.8 3.4 - - + -
513A THR* 4.0 10.5 - - + -
516A LEU* 4.4 10.8 - - + -
517A ILE* 4.9 4.3 - - + -
525A ILE* 3.9 14.8 - - + -
557A LYS 3.3 7.0 - - - +
558A TYR* 5.1 0.2 - - + -
568A PHE* 3.4 30.5 - - + -
569A GLY* 1.3 74.7 - - - +
571A THR* 1.3 69.0 + - - +
572A HIS* 3.3 38.1 + - + +
576A GLN* 3.2 4.3 - - - +
577A VAL 2.8 34.9 + - - -
579A TYR* 3.8 11.0 - - + -
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Residues in contact with THR 571 (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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513A THR* 2.9 25.5 + - - +
556A ALA 4.5 4.0 + - - -
557A LYS* 2.8 45.8 + - + +
558A TYR 5.8 0.3 - - - -
570A VAL* 1.3 71.6 - - - +
572A HIS* 1.3 71.4 + - - +
575A GLY* 4.7 6.7 - - - -
576A GLN* 4.1 17.3 + - + +
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Residues in contact with HIS 572 (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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458A PHE* 4.2 10.0 - + + -
469A LEU* 4.7 1.1 - - + -
472A ASN* 3.5 23.9 - - + +
476A GLU* 2.8 25.9 + - - +
513A THR* 3.8 3.5 - - - +
517A ILE* 3.9 20.6 - - + -
570A VAL* 3.3 32.8 + - + +
571A THR* 1.3 83.8 - - - +
573A TYR* 1.3 67.0 + - - +
574A ALA* 3.2 5.4 - - + +
575A GLY* 2.9 26.4 + - - +
577A VAL* 3.6 23.6 - - + -
579A TYR* 2.6 28.4 + - - -
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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