Contacts of the helix formed by residues 567 - 572 (chain A) in PDB entry 5KZX
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 567 (chain A).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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538A LEU* 3.9 21.7 - - + +
559A ALA 4.0 9.4 - - - -
560A SER 4.3 1.8 - - - +
561A SER 3.5 10.1 - - - +
562A HIS* 3.8 31.0 - - + +
563A GLN 4.6 0.2 - - - +
566A SER* 1.3 83.2 + - - +
568A HIS* 1.3 66.5 + - - +
569A TYR* 3.7 10.9 - - - +
570A ASN* 3.1 29.1 + - - +
571A LEU* 3.3 13.1 + - - +
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Residues in contact with HIS 568 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
279A TRP* 5.2 2.2 - + - -
468A ILE* 4.4 0.2 - - - +
522A PRO* 3.7 19.3 - - + +
556A THR* 4.2 0.2 + - - -
557A ILE* 3.5 38.2 - - + +
558A CYS 3.6 11.4 - - - +
559A ALA* 3.7 3.4 - - - +
561A SER* 3.0 32.3 + - - +
563A GLN* 2.8 30.8 + - + +
566A SER 4.0 0.4 + - - -
567A THR* 1.3 73.1 - - - +
569A TYR* 1.3 59.6 + - - +
571A LEU 4.3 0.2 - - - +
572A HIS* 2.8 78.7 + + + +
575A TYR* 4.3 7.9 - + - -
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Residues in contact with TYR 569 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
244A GLN* 2.9 31.0 + - + +
279A TRP* 4.1 20.2 - - - -
315A SER 5.0 0.3 - - - +
316A ASN* 3.7 18.8 + - - -
317A ALA 4.7 0.7 + - - -
333A THR* 2.6 43.8 + - - -
334A GLY* 4.6 2.0 - - - -
538A LEU* 3.4 48.7 - - + -
541A PRO* 3.9 6.0 - - + +
552A LEU* 3.8 23.3 - - + -
559A ALA* 2.7 27.8 + - + +
567A THR* 3.7 9.4 - - - +
568A HIS* 1.3 74.9 - - - +
570A ASN* 1.3 73.8 + - - +
572A HIS 4.5 0.3 + - - -
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Residues in contact with ASN 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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191A TYR* 3.4 40.5 + - + +
315A SER* 2.7 37.0 + - - +
316A ASN* 2.8 29.5 + - - +
334A GLY* 4.8 0.5 - - - -
335A GLY 4.6 3.1 + - - -
538A LEU* 6.3 0.2 - - - +
566A SER* 2.8 26.5 + - - +
567A THR* 3.1 15.8 + - - +
569A TYR* 1.3 86.9 - - - +
571A LEU* 1.3 56.3 + - - +
572A HIS 3.6 0.4 - - - -
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Residues in contact with LEU 571 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
191A TYR* 3.6 26.7 - - + +
194A PRO* 4.9 1.3 - - + -
491A THR* 4.2 15.7 - - + -
563A GLN* 3.6 37.3 - - + +
565A LEU* 4.2 15.0 - - + -
566A SER* 3.5 43.3 - - - +
567A THR 3.3 8.2 + - - +
568A HIS 3.1 1.6 + - - +
570A ASN* 1.3 75.9 - - - +
572A HIS* 1.3 56.4 + - - +
573A ASN 3.3 2.5 - - - -
574A LEU* 2.8 47.1 + - + +
575A TYR* 3.4 4.9 + - - -
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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
----------------------------------------------------------
279A TRP* 3.3 39.2 - + + -
280A ASN* 2.6 29.1 + - - -
521A GLU 3.1 32.9 + - - +
556A THR* 3.2 31.5 + - + -
568A HIS* 2.8 50.0 + - - +
569A TYR 4.5 0.2 + - - -
570A ASN 3.6 1.0 - - - -
571A LEU* 1.3 74.6 - - - +
573A ASN* 1.3 75.4 + - - +
575A TYR* 3.0 18.4 + - - +
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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