Contacts of the helix formed by residues 565 - 580 (chain B) in PDB entry 4RS6
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 PHE 565 (chain B).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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535B MET* 5.5 1.3 - - - -
546B TYR* 2.9 52.9 - + - -
554B SER* 5.3 7.0 - - - -
556B PHE* 4.3 28.3 - + + -
561B ALA* 5.4 0.4 - - + -
562B PRO* 2.8 26.3 + - + +
564B GLN* 1.3 116.0 - - + +
566B ILE* 1.3 64.8 + - - +
567B SER 3.4 2.0 - - - -
568B GLN* 3.1 20.3 + - + +
569B VAL* 3.1 23.2 + - + +
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Residues in contact with ILE 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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558B ALA 5.6 0.4 - - - +
559B THR 5.2 4.5 - - - +
561B ALA* 3.2 35.9 - - + +
562B PRO 3.4 0.9 + - - +
563B GLU* 3.1 28.5 + - + +
564B GLN 3.6 0.2 - - - -
565B PHE* 1.3 75.6 - - - +
567B SER* 1.3 68.8 + - - +
569B VAL* 3.2 8.0 + - + +
570B THR* 3.1 34.0 + - + +
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Residues in contact with SER 567 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
563B GLU 4.7 0.6 + - - -
564B GLN 5.8 2.5 - - - -
565B PHE 3.4 0.4 - - - -
566B ILE* 1.3 78.7 - - - +
568B GLN* 1.3 65.8 + - - +
570B THR* 2.6 23.8 + - - -
571B VAL* 3.2 15.3 + - - +
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Residues in contact with GLN 568 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
529B PHE* 3.6 30.0 - - + -
531B ASN* 4.4 7.5 + - - +
533B ALA* 3.6 28.9 - - - +
535B MET* 3.6 17.7 - - - +
546B TYR* 4.6 5.3 + - - -
564B GLN 3.8 10.4 - - - +
565B PHE* 3.1 29.6 + - - +
566B ILE 3.0 0.8 - - - -
567B SER* 1.3 84.4 - - - +
569B VAL* 1.3 65.0 + - - +
571B VAL* 3.3 7.8 + - + +
572B LEU* 3.0 21.5 + - - +
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Residues in contact with VAL 569 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
535B MET* 3.6 22.9 - - + -
544B VAL* 4.3 8.1 - - + -
556B PHE* 4.1 24.0 - - + -
558B ALA* 4.2 24.2 - - + +
561B ALA* 4.2 9.4 - - + -
565B PHE 3.1 15.4 + - - +
566B ILE* 3.2 9.8 + - + +
568B GLN* 1.3 76.0 - - - +
570B THR* 1.3 62.9 + - + +
572B LEU* 3.0 5.1 + - + +
573B LYS* 2.8 46.5 + - + +
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Residues in contact with THR 570 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
566B ILE* 3.1 27.5 + - + +
567B SER* 2.6 25.6 + - - -
569B VAL* 1.3 77.4 - - + +
571B VAL* 1.3 64.1 + - - +
573B LYS* 3.1 13.8 + - + +
574B TYR* 3.0 20.8 + - - +
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Residues in contact with VAL 571 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
514B TYR* 3.9 36.6 - - + -
529B PHE* 3.7 23.1 - - + -
567B SER 3.2 17.2 + - - +
568B GLN* 3.4 9.4 - - + +
569B VAL 3.1 0.2 - - - -
570B THR* 1.3 79.3 + - - +
572B LEU* 1.3 62.6 + - - +
574B TYR* 3.0 17.8 + - + +
575B PHE* 3.1 34.7 + - + -
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Residues in contact with LEU 572 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
525B VAL* 4.0 17.3 - - + +
527B VAL* 3.5 31.0 - - + -
529B PHE* 4.9 1.1 - - + -
535B MET* 3.1 41.3 - - + +
536B SER 4.0 12.1 - - - +
537B LEU* 4.0 26.0 - - + +
544B VAL* 4.3 11.2 - - + -
568B GLN 3.0 13.2 + - - +
569B VAL* 3.0 10.7 + - + +
571B VAL* 1.3 76.8 - - - +
573B LYS* 1.3 63.2 + - + +
575B PHE* 3.3 4.2 + - - +
576B SER* 3.0 21.5 + - - -
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Residues in contact with LYS 573 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
537B LEU* 4.9 12.8 - - + -
541B LYS 5.5 4.7 - - - -
558B ALA* 4.2 26.3 - - + +
559B THR* 5.2 9.9 - - - +
569B VAL* 2.8 29.6 + - + +
570B THR* 3.3 14.3 - - + +
572B LEU* 1.3 76.6 - - + +
574B TYR* 1.3 59.4 + - - +
576B SER* 3.2 6.6 + - - -
577B HIS* 2.9 29.7 + - - +
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Residues in contact with TYR 574 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
510B TYR* 4.0 29.8 + + - -
514B TYR* 3.8 41.5 - + + -
570B THR 3.0 11.7 + - - +
571B VAL* 3.3 13.0 - - - +
573B LYS* 1.3 76.5 - - - +
575B PHE* 1.3 72.1 + + - +
577B HIS* 3.3 10.0 + - - +
578B TYR* 3.0 37.1 + + + +
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Residues in contact with PHE 575 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
508B VAL* 3.7 38.4 - - + -
510B TYR* 3.9 23.8 - + + -
514B TYR* 3.9 17.0 - + + -
515B GLY 3.7 24.2 - - - -
517B GLY* 3.7 9.0 - - - -
525B VAL* 4.8 1.6 - - + -
527B VAL* 3.7 32.3 - - + -
571B VAL* 3.1 38.5 + - + -
572B LEU 3.6 6.5 - - - +
573B LYS 3.2 0.2 - - - -
574B TYR* 1.3 80.8 - + - +
576B SER* 1.3 66.4 + - - +
578B TYR* 3.1 5.7 + - + +
579B MET* 3.0 35.2 + - + +
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Residues in contact with SER 576 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
525B VAL* 4.2 18.4 - - - +
537B LEU* 3.9 18.9 - - - +
541B LYS* 2.8 35.8 + - - -
572B LEU 3.0 13.1 + - - -
573B LYS* 3.5 9.4 - - - -
575B PHE* 1.3 78.8 - - - +
577B HIS* 1.3 62.8 + - - +
579B MET* 3.3 2.9 + - - +
580B GLU* 3.1 23.1 + - - +
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Residues in contact with HIS 577 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
573B LYS 2.9 16.9 + - - +
574B TYR* 3.6 10.8 + - - +
576B SER* 1.3 78.8 - - - +
578B TYR* 1.3 64.5 + - - +
580B GLU* 2.5 62.1 + - - +
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Residues in contact with TYR 578 (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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512A ASN* 5.8 1.4 + - - -
507B TRP 5.7 0.2 - - - -
508B VAL* 4.0 31.4 - - + +
510B TYR* 3.5 33.1 + + - -
574B TYR* 3.0 27.8 + + + +
575B PHE* 3.4 12.1 - - + +
577B HIS* 1.3 83.5 + - - +
579B MET* 1.3 69.5 + - + +
580B GLU 3.3 5.9 - - - +
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Residues in contact with MET 579 (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 LYS* 2.9 50.7 + - + +
507B TRP 4.1 1.3 - - - +
508B VAL* 3.8 26.7 - - + -
517B GLY 4.2 1.6 - - - -
518B TYR* 3.4 37.5 - - - +
519B GLN* 3.7 30.1 - - + +
525B VAL* 3.8 21.3 - - + -
575B PHE* 3.0 17.6 + - + +
576B SER 4.0 2.9 - - - +
577B HIS 3.2 0.2 - - - -
578B TYR* 1.3 81.4 - - + +
580B GLU* 1.3 65.3 + - - +
581B GLU* 3.3 1.6 + - - +
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Residues in contact with GLU 580 (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 LYS* 4.8 1.3 - - - +
519B GLN* 5.1 1.5 + - - -
541B LYS* 5.2 12.0 - - - +
576B SER* 3.1 10.3 + - - +
577B HIS* 2.5 59.7 + - - +
578B TYR 3.3 9.0 - - - +
579B MET* 1.3 75.0 - - - +
581B GLU* 1.3 64.5 + - - +
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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
------------------------------------------------------------
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