Contacts of the helix formed by residues 565 - 579 (chain B) in PDB entry 2XWU
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 TYR 565 (chain B).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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524B PRO 4.6 3.3 + - - -
527B ILE* 3.5 24.4 - - + +
528B ASN* 3.5 42.0 + - - +
531B LEU* 3.9 24.2 - - + -
561B ASP 3.9 13.9 - - - -
562B LEU* 3.1 26.1 + - + +
564B PRO* 1.3 81.2 - - + +
566B ALA* 1.3 64.7 + - - +
567B ALA 3.0 4.5 + - - -
568B ASN* 3.1 13.4 + - + +
569B ILE* 3.0 26.0 + - + +
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Residues in contact with ALA 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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562B LEU 3.1 10.3 + - - +
563B PRO 3.2 16.6 - - - +
564B PRO 3.2 1.6 - - - -
565B TYR* 1.3 78.4 - - - +
567B ALA* 1.3 58.8 + - - +
570B VAL* 2.7 37.6 + - + +
597B LEU* 3.8 24.2 - - + -
601B LEU* 3.4 32.5 - - + -
609B ASN* 5.9 0.4 - - - -
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Residues in contact with ALA 567 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
563B PRO 4.7 0.2 + - - -
564B PRO 4.2 8.6 + - - +
565B TYR 3.0 0.6 - - - -
566B ALA* 1.3 81.3 - - - +
568B ASN* 1.3 62.2 + - - +
570B VAL* 3.9 4.7 - - - +
571B ALA* 3.2 21.7 + - - +
609B ASN* 5.4 5.6 - - - +
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Residues in contact with ASN 568 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
531B LEU* 5.9 1.4 - - + +
535B LEU* 3.5 23.8 - - + +
565B TYR* 3.1 15.3 + - + +
567B ALA* 1.3 77.3 - - - +
569B ILE* 1.3 64.9 + - + +
571B ALA* 3.2 7.6 + - - +
572B VAL* 3.0 31.2 + - - +
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Residues in contact with ILE 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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531B LEU* 4.1 30.1 - - + -
535B LEU* 4.4 17.2 - - + +
551B LEU* 4.3 22.7 - - + -
555B CYS* 4.6 7.9 - - - -
562B LEU* 4.4 13.2 - - + -
565B TYR* 3.2 21.3 - - + +
568B ASN* 1.3 76.2 - - + +
570B VAL* 1.3 64.0 + - - +
571B ALA 3.1 0.3 + - - -
572B VAL* 3.2 3.1 + - - +
573B SER* 2.9 35.2 + - - +
594B LEU* 4.5 4.3 - - + -
597B LEU* 3.7 39.9 - - + -
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Residues in contact with VAL 570 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
566B ALA* 2.7 27.2 + - + +
567B ALA* 3.9 3.6 - - - +
569B ILE* 1.3 74.6 - - - +
571B ALA* 1.3 60.0 + - - +
573B SER* 3.9 1.0 - - - -
574B GLN* 2.9 55.5 + - + +
594B LEU* 4.3 11.9 - - + -
597B LEU* 3.6 18.8 - - + -
598B LEU* 4.1 15.3 - - + -
609B ASN* 4.2 26.9 - - + +
612B SER* 5.3 0.2 - - - -
613B LEU* 4.3 13.7 - - + -
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Residues in contact with ALA 571 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
567B ALA 3.2 12.5 + - - +
568B ASN* 3.2 14.3 + - - +
569B ILE 3.1 0.8 - - - -
570B VAL* 1.3 75.4 - - - +
572B VAL* 1.3 66.7 + - + +
574B GLN* 3.3 10.1 + - - +
575B ASP* 3.1 23.9 + - - +
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Residues in contact with VAL 572 (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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535B LEU* 3.5 45.5 - - + +
538B LEU* 4.3 14.8 - - + +
568B ASN* 3.0 27.1 + - - +
569B ILE 3.9 2.9 - - - +
571B ALA* 1.3 77.0 - - + +
573B SER* 1.3 61.1 + - - +
575B ASP* 4.0 6.8 - - + +
576B VAL* 3.3 25.0 + - + +
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Residues in contact with SER 573 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
535B LEU* 5.6 0.2 - - - +
538B LEU* 4.4 6.3 - - - +
551B LEU* 4.3 10.4 - - - +
569B ILE* 2.9 23.7 + - - +
570B VAL 3.9 4.3 - - - -
572B VAL* 1.3 76.9 - - - +
574B GLN* 1.3 65.2 + - - +
576B VAL* 3.5 5.6 + - - +
577B LEU* 3.1 30.0 + - - +
590B LEU* 3.6 25.9 - - - +
594B LEU* 3.7 21.8 - - - +
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Residues in contact with GLN 574 (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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570B VAL* 2.9 39.1 + - - +
571B ALA* 3.7 6.6 - - - +
573B SER* 1.3 78.1 - - - +
575B ASP* 1.3 62.3 + - - +
577B LEU* 3.3 11.0 + - + +
578B MET* 3.0 23.7 + - - +
612B SER* 3.0 49.7 - - - +
613B LEU* 3.5 20.7 - - + +
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Residues in contact with ASP 575 (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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571B ALA 3.1 16.2 + - - +
572B VAL* 4.0 7.8 - - - +
574B GLN* 1.3 76.0 - - - +
576B VAL* 1.3 67.5 + - - +
578B MET* 3.0 18.7 + - - +
579B LYS* 3.1 50.4 + - - +
581B ILE* 5.6 0.5 - - - +
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Residues in contact with VAL 576 (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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538B LEU* 3.2 33.0 - - + +
539B GLY* 3.8 3.8 - - - +
572B VAL* 3.3 21.8 + - + +
573B SER* 3.7 6.3 - - - +
575B ASP* 1.3 84.2 - - - +
577B LEU* 1.3 62.4 + - - +
579B LYS 3.5 1.3 + - - -
581B ILE* 3.4 42.4 + - + +
582B HIS* 3.0 38.7 + - + +
590B LEU* 4.4 6.5 - - + -
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Residues in contact with LEU 577 (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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573B SER 3.1 28.9 + - - +
574B GLN* 3.6 10.8 - - - +
576B VAL* 1.3 74.7 - - + +
578B MET* 1.3 68.2 + - - +
579B LYS 3.0 3.2 + - - -
580B GLN* 3.1 16.3 + - - +
582B HIS* 5.3 2.2 - - + +
587B CYS* 4.2 33.4 - - + +
590B LEU* 4.2 30.7 - - + -
591B MET* 4.5 14.1 - - - -
613B LEU* 4.8 11.0 - - + -
617B TYR* 3.6 34.2 + - + +
643B LEU* 5.3 4.0 - - + -
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Residues in contact with MET 578 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
574B GLN 3.0 9.4 + - - +
575B ASP* 3.0 13.8 + - - +
577B LEU* 1.3 81.2 - - - +
579B LYS* 1.3 57.8 + - + +
580B GLN* 3.0 19.3 + - - +
616B PRO* 4.2 24.9 - - + -
617B TYR* 5.1 5.6 - - + -
620B GLN* 4.7 15.5 - - - +
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Residues in contact with LYS 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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575B ASP* 3.1 43.4 + - - +
577B LEU 3.0 1.6 + - - -
578B MET* 1.3 80.3 - - + +
580B GLN* 1.3 78.3 + - - +
581B ILE* 3.1 30.5 + - + +
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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
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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