Contacts of the strand formed by residues 564 - 569 (chain B) in PDB entry 4CCN
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 564 (chain B).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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560B GLY* 3.3 5.2 - - - -
561B GLU 2.8 35.0 + - - +
562B GLY 2.8 23.5 + - - -
563B GLY* 1.3 84.8 - - - +
565B LEU* 1.3 64.2 + - - +
566B PHE* 3.6 22.1 - + + -
586B GLU* 2.8 28.6 + - - +
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Residues in contact with LEU 565 (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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558B LEU* 4.7 17.9 - - + -
559B VAL 3.6 8.1 - - - +
560B GLY* 4.5 7.6 - - - -
563B GLY 5.6 1.6 - - - +
564B HIS* 1.3 78.9 - - - +
566B PHE* 1.3 62.1 + - - +
586B GLU* 3.4 10.3 + - - +
587B ILE* 2.8 52.3 + - + +
589B PRO* 4.5 14.4 - - + -
592B ALA* 3.3 34.5 - - + -
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Residues in contact with PHE 566 (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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557B ARG 3.4 2.8 - - - +
558B LEU* 4.2 2.7 - - - -
559B VAL 2.9 38.3 + - - +
561B GLU* 4.1 22.2 - - + -
564B HIS* 3.6 35.7 - + + -
565B LEU* 1.3 76.1 - - - +
567B LEU* 1.3 59.1 + - - +
568B TYR* 3.5 25.3 + + + -
584B CYS* 3.6 26.2 - - + -
585B LEU 3.7 1.3 - - - -
586B GLU* 3.9 34.3 - - + -
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Residues in contact with LEU 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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550B MET* 5.3 1.1 - - + -
556B ALA* 4.1 19.5 - - + -
557B ARG 3.5 20.0 - - - +
558B LEU* 4.1 10.9 - - + +
565B LEU 4.3 0.4 + - - -
566B PHE* 1.3 69.8 - - - +
568B TYR* 1.3 60.2 + - - +
569B TYR* 3.5 4.9 - - - -
584B CYS* 3.2 3.8 - - - -
585B LEU* 2.9 41.7 + - + +
587B ILE* 4.0 12.3 - - + +
595B MET* 3.9 22.9 - - + -
599B LEU* 4.2 9.0 - - + -
626B LEU* 3.5 32.3 - - + -
631B LEU* 3.7 18.4 - - + -
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Residues in contact with TYR 568 (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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503B LYS* 3.3 44.8 + - + +
506B ILE* 4.0 18.4 - - + +
556B ALA* 3.1 4.5 - - - +
557B ARG* 2.7 40.9 + - + +
559B VAL* 3.9 13.0 - - + -
561B GLU* 2.8 25.9 + - - -
566B PHE* 3.5 29.8 - - + +
567B LEU* 1.3 73.2 - - - +
569B TYR* 1.3 59.3 + - - +
582B PRO* 4.3 22.2 - - + -
583B LYS 3.4 12.3 - - - +
584B CYS* 3.5 28.1 - - + -
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Residues in contact with TYR 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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506B ILE* 3.2 14.3 - - - +
507B HIS* 5.9 0.2 - - - -
555B ILE 2.9 12.8 - - - +
556B ALA* 4.1 4.3 - - + -
567B LEU 3.5 11.4 - - - -
568B TYR* 1.3 73.2 - - - +
570B THR* 1.3 58.2 + - - +
571B VAL* 3.4 28.9 - - + -
572B GLU* 4.2 8.7 - - + -
573B ASN* 4.0 6.8 - - - +
583B LYS* 3.2 32.0 + - + +
584B CYS* 3.6 27.8 + - - -
585B LEU* 3.9 15.3 - - + +
629B LYS* 3.1 32.4 - - + -
631B LEU* 3.4 32.8 - - + -
903B SO4 3.4 16.8 + - - -
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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