Contacts of the helix formed by residues 558 - 569 (chain B) in PDB entry 2XER
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 ARG 558 (chain B).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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536B VAL* 3.6 28.5 + - + -
539B TYR* 3.8 32.7 + - + -
540B GLU* 4.1 16.6 + - - -
543B TYR* 3.1 31.5 + - - +
556B ASP* 3.1 12.6 + - - +
557B ASP* 1.3 78.2 - - - +
559B LYS* 1.3 62.7 + - - +
561B LYS* 3.3 6.9 + - - +
562B ILE* 3.0 26.9 + - + +
603B PHE* 5.0 1.4 - - - -
638C SER* 4.1 9.9 + - - -
641C SER* 2.8 39.0 + - - -
642C LEU* 3.2 26.6 - - + +
645C TYR* 3.6 12.2 + - + +
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Residues in contact with LYS 559 (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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556B ASP* 4.5 0.6 + - - -
557B ASP* 3.3 1.0 - - - +
558B ARG* 1.3 77.7 - - - +
560B HIS* 1.3 59.6 + - + +
562B ILE* 2.8 30.6 + - + +
563B CYS* 3.2 21.4 + - - +
645C TYR* 3.6 46.2 - - + +
646C HIS* 6.5 0.2 - - + -
691C ILE 5.2 0.8 + - - -
694C SER* 3.4 29.8 + - - -
695C ARG* 3.5 25.6 - - - +
698C ASP* 2.5 33.0 + - - +
742C ASN* 4.8 2.1 - - - +
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Residues in contact with HIS 560 (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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532B LEU* 6.4 0.7 - - + -
557B ASP* 2.7 40.0 + - - +
558B ARG 3.4 0.2 - - - -
559B LYS* 1.3 82.6 - - - +
561B LYS* 1.3 63.0 + - + +
563B CYS* 3.7 6.4 + - - +
564B SER* 2.9 35.8 + - - -
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Residues in contact with LYS 561 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
532B LEU* 4.0 18.5 - - + +
535B ASP* 3.3 44.6 + - + +
536B VAL* 3.8 16.2 - - + -
539B TYR* 3.1 27.8 + - + +
557B ASP* 3.4 26.0 - - - +
558B ARG 3.3 7.1 + - - +
559B LYS 3.1 0.6 - - - -
560B HIS* 1.3 79.0 - - + +
562B ILE* 1.3 64.4 + - - +
564B SER* 3.4 8.6 - - - -
565B MET* 3.0 32.5 + - - +
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Residues in contact with ILE 562 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
536B VAL* 3.8 25.4 - - + -
558B ARG* 3.0 19.2 + - + +
559B LYS* 2.8 13.2 + - + +
561B LYS* 1.3 77.9 - - - +
563B CYS* 1.3 66.1 + - - +
565B MET* 3.3 13.2 + - - +
566B TYR* 3.2 19.6 + - - +
600B ILE* 6.2 0.2 - - + -
603B PHE* 3.3 49.4 - - + +
604B LEU* 4.3 14.7 - - + +
608B GLN* 4.6 3.1 - - - +
642C LEU* 6.1 1.3 - - + -
645C TYR* 5.1 8.3 - - + -
646C HIS* 4.0 16.4 - - + -
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Residues in contact with CYS 563 (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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559B LYS* 3.2 18.7 + - - +
560B HIS* 4.1 8.7 - - - +
562B ILE* 1.3 84.3 - - - +
564B SER* 1.3 61.0 - - - +
566B TYR* 3.3 7.9 + - - +
567B ASP* 3.0 28.7 + - - +
608B GLN* 4.7 14.4 - - - +
646C HIS* 6.2 3.1 - - - -
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Residues in contact with SER 564 (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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532B LEU* 3.9 18.0 - - - +
560B HIS* 2.9 31.9 + - - -
561B LYS* 3.4 12.0 - - - -
562B ILE 3.2 0.2 - - - -
563B CYS* 1.3 76.6 - - - +
565B MET* 1.3 65.2 + - - +
567B ASP* 2.6 24.2 - - - +
568B ASN* 3.0 18.1 + - - +
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Residues in contact with MET 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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529B THR* 3.5 23.7 - - + +
532B LEU* 3.7 18.6 - - + +
533B LEU* 3.4 46.7 - - + -
536B VAL* 4.3 11.4 - - - -
561B LYS 3.0 17.8 + - - +
562B ILE* 3.6 12.6 - - - +
564B SER* 1.3 75.1 - - - +
566B TYR* 1.3 61.9 + - - +
568B ASN* 3.2 4.9 - - - +
569B LEU* 3.1 29.2 + - - +
600B ILE* 3.5 44.4 - - + -
603B PHE* 5.8 1.3 - - - -
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Residues in contact with TYR 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 ILE 3.2 12.2 + - - +
563B CYS* 3.7 7.9 - - - +
564B SER 3.1 0.8 - - - -
565B MET* 1.3 74.2 - - - +
567B ASP* 1.3 63.7 + - + +
568B ASN 3.0 4.5 - - - -
569B LEU* 3.0 10.4 + - + +
570B ARG* 2.7 50.2 + - + +
604B LEU* 4.1 16.8 - - + +
608B GLN* 3.4 63.4 - - + +
611B ASP* 2.6 30.1 + - - +
612B ILE* 4.0 10.5 - - + -
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Residues in contact with ASP 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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563B CYS 3.0 15.1 + - - +
564B SER* 2.6 33.5 - - - +
566B TYR* 1.3 81.6 - - + +
568B ASN* 1.3 63.5 + - - +
570B ARG 3.7 13.0 - - - +
571B GLY* 3.4 20.7 - - - -
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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
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525B ILE* 4.3 22.3 + - + +
528B LYS* 4.5 7.3 - - - +
529B THR* 2.8 37.5 + - + +
532B LEU* 4.3 9.8 - - - +
564B SER* 3.0 19.2 + - - +
565B MET 3.2 12.1 - - - +
566B TYR 3.0 0.6 - - - -
567B ASP* 1.3 83.4 + - - +
569B LEU* 1.3 58.5 + - + +
570B ARG 3.5 0.2 + - - -
583B HIS* 2.7 34.9 + - - -
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Residues in contact with LEU 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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525B ILE* 5.9 0.2 - - + -
529B THR* 4.8 4.5 - - + +
565B MET 3.1 18.2 - - - +
566B TYR* 3.0 10.6 + - - +
568B ASN* 1.3 76.2 - - + +
570B ARG* 1.3 73.6 + - + +
571B GLY 3.8 0.4 - - - -
583B HIS* 3.7 9.9 - - - -
584B PHE* 3.4 29.1 - - + +
587B ILE* 3.9 23.3 - - + -
596B MET* 4.1 23.1 - - + -
597B VAL* 4.1 20.6 - - + -
600B ILE* 4.2 24.5 - - + -
604B LEU* 4.8 7.4 - - + -
612B ILE* 4.5 14.4 - - + -
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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