Contacts of the strand formed by residues 566 - 571 (chain A) in PDB entry 6R4F
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 HIS 566 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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538A LYS 3.2 15.8 + - - +
539A SER* 3.2 17.7 + - - +
540A VAL 3.2 19.8 + - - +
541A LEU* 5.8 0.7 - - - +
560A LYS* 4.0 23.4 + - + -
565A MET* 1.3 70.7 - - - +
567A SER* 1.3 63.2 + - - +
568A GLU* 4.1 20.0 + - + +
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Residues in contact with SER 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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540A VAL* 3.2 28.3 - - - -
542A ILE* 4.5 1.8 - - - -
556A ALA* 2.6 37.7 + - - +
559A ILE* 3.2 26.2 - - - +
560A LYS* 2.5 39.9 + - - +
565A MET 2.9 5.5 + - - -
566A HIS* 1.3 72.8 - - - +
568A GLU* 1.3 54.9 + - - +
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Residues in contact with GLU 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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540A VAL 3.1 6.3 + - - -
541A LEU* 3.6 20.3 - - + +
542A ILE 2.9 23.6 + - - +
556A ALA* 3.7 5.2 - - - -
560A LYS* 4.3 7.2 - - - +
566A HIS* 4.3 19.6 + - + +
567A SER* 1.3 76.6 - - - +
569A GLY* 1.3 73.2 + - - +
570A ILE* 3.8 17.8 + - + +
582A LEU* 5.1 6.1 - - - +
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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
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542A ILE 3.2 9.0 - - - -
549A TYR* 5.4 0.2 - - - -
552A CYS* 3.6 28.0 - - - -
553A LEU* 4.0 18.0 - - - +
556A ALA* 3.3 9.5 - - - +
568A GLU* 1.3 78.9 - - - +
570A ILE* 1.3 63.7 + - - +
571A LEU 4.3 0.5 + - - -
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Residues in contact with ILE 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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541A LEU* 4.0 39.3 - - + -
542A ILE 2.8 12.3 + - - +
543A MET* 3.4 14.4 - - + +
544A GLY 3.4 17.7 + - - -
552A CYS* 3.7 4.8 - - - -
568A GLU* 4.2 19.5 - - + +
569A GLY* 1.3 77.9 - - - +
571A LEU* 1.3 74.8 - - - +
572A ALA 3.2 3.3 + - - -
574A GLU* 5.2 1.6 - - + -
575A LEU* 4.3 22.2 - - + +
579A PRO* 4.2 31.0 - - + +
582A LEU* 5.3 3.8 - - + -
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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
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544A GLY 3.4 12.3 - - - +
545A ARG* 4.0 15.0 - - + -
546A GLY 4.7 2.0 - - - +
549A TYR* 3.6 53.0 - - + +
569A GLY 4.2 0.4 - - - -
570A ILE* 1.3 76.7 - - - +
572A ALA* 1.3 67.9 + - - +
573A GLY* 4.2 8.5 - - - +
574A GLU* 2.8 43.2 + - + +
575A LEU 3.8 0.2 + - - -
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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