Contacts of the helix formed by residues 558 - 569 (chain C) 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 C).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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637B LEU* 5.8 1.4 - - - +
638B SER* 4.6 7.7 + - - +
641B SER* 3.2 33.5 + - - -
642B LEU* 4.2 10.0 - - + +
645B TYR* 4.1 9.2 - - + -
536C VAL* 4.1 25.3 - - + +
539C TYR* 3.3 45.3 + - - -
540C GLU* 2.6 30.9 + - - +
556C ASP* 2.9 36.2 + - - +
557C ASP* 1.3 77.6 - - - +
559C LYS* 1.3 65.5 + - - +
561C LYS* 2.9 8.9 + - - -
562C ILE* 2.7 45.4 + - + +
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Residues in contact with LYS 559 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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645B TYR* 3.5 33.8 - - + +
694B SER* 2.5 51.2 + - - +
695B ARG* 3.1 27.8 - - - +
698B ASP* 2.9 44.5 + - - +
742B ASN* 3.2 12.9 - - - +
556C ASP* 5.8 0.2 - - - +
557C ASP* 4.7 3.8 - - - +
558C ARG* 1.3 79.8 - - - +
560C HIS* 1.3 60.7 + - - +
562C ILE* 4.3 3.8 - - - +
563C CYS* 3.3 28.5 + - - -
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Residues in contact with HIS 560 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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532C LEU* 5.9 2.3 - - + +
557C ASP* 3.2 30.8 + - - +
558C ARG 3.2 0.4 - - - -
559C LYS* 1.3 76.4 - - - +
561C LYS* 1.3 79.6 + - + +
563C CYS* 3.4 6.9 + - - +
564C SER* 3.0 41.7 + - - -
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Residues in contact with LYS 561 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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532C LEU* 3.6 29.2 - - + +
535C ASP* 3.1 35.0 + - + +
536C VAL* 3.6 23.8 - - + -
557C ASP* 3.1 38.5 + - - +
558C ARG* 2.9 6.6 + - - +
560C HIS* 1.3 84.4 - - + +
562C ILE* 1.3 59.1 + - - +
564C SER* 3.0 8.7 + - - -
565C MET* 2.8 32.1 + - - +
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Residues in contact with ILE 562 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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642B LEU* 4.4 13.9 - - + -
645B TYR* 4.9 9.0 - - + -
646B HIS* 4.5 9.2 - - + -
536C VAL* 4.6 9.0 - - + -
558C ARG* 2.7 43.2 + - + +
559C LYS* 4.3 4.0 - - - +
561C LYS* 1.3 70.5 - - - +
563C CYS* 1.3 65.3 + - - +
565C MET* 3.2 11.5 + - - +
566C TYR* 3.0 22.3 + - - +
603C PHE* 3.5 44.0 - - + +
604C LEU* 3.8 18.1 - - + +
608C GLN* 4.3 8.7 - - - +
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Residues in contact with CYS 563 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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698B ASP* 5.3 9.0 - - - -
559C LYS* 3.3 20.3 + - - +
560C HIS* 3.4 10.0 + - - +
561C LYS 3.3 0.6 - - - -
562C ILE* 1.3 79.3 - - - +
564C SER* 1.3 58.1 + - - +
566C TYR* 3.2 6.5 + - - +
567C ASP* 2.8 40.3 + - - +
608C GLN* 4.9 12.6 - - - +
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Residues in contact with SER 564 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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532C LEU* 3.7 17.0 - - - -
560C HIS* 3.0 36.3 + - - -
561C LYS* 3.0 11.3 + - - -
563C CYS* 1.3 75.5 - - - +
565C MET* 1.3 56.9 + - - +
567C ASP* 3.3 7.1 + - - -
568C ASN* 2.9 40.1 + - - +
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Residues in contact with MET 565 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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529C THR* 4.3 9.3 - - + +
532C LEU* 3.5 28.5 - - + +
533C LEU* 3.5 37.9 - - + +
536C VAL* 4.3 11.7 - - - -
561C LYS 2.8 17.5 + - - +
562C ILE* 3.5 17.0 - - - +
564C SER* 1.3 76.4 - - - +
566C TYR* 1.3 62.0 + - - +
568C ASN* 3.2 7.1 + - - +
569C LEU* 3.1 29.4 + - - +
600C ILE* 3.3 50.5 - - + -
603C PHE* 5.2 4.3 - - + -
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Residues in contact with TYR 566 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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562C ILE 3.0 12.5 + - - +
563C CYS 3.6 6.1 - - - +
565C MET* 1.3 73.8 - - - +
567C ASP* 1.3 69.9 + - - +
568C ASN 2.9 4.7 - - - -
569C LEU* 3.0 6.5 + - - +
570C ARG* 2.8 43.7 + - + +
571C GLY* 6.1 0.9 - - - -
604C LEU* 4.2 11.4 - - + +
607C GLU 5.4 0.3 - - - -
608C GLN* 3.5 53.8 - - + +
611C ASP* 2.6 32.8 + - - +
612C ILE* 3.5 33.4 - - + -
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Residues in contact with ASP 567 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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563C CYS* 2.8 29.7 + - - +
564C SER* 3.8 7.7 - - - +
566C TYR* 1.3 81.4 - - - +
568C ASN* 1.3 61.2 + - - +
570C ARG 2.7 23.3 - - - +
571C GLY* 4.3 11.3 - - - +
572C LYS 5.2 2.8 - - - +
583C HIS* 5.5 0.3 + - - -
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Residues in contact with ASN 568 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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525C ILE* 3.7 19.1 + - + +
528C LYS* 4.7 9.1 - - - +
529C THR* 3.2 31.5 + - - +
532C LEU* 4.1 16.6 - - - +
564C SER* 2.9 26.5 + - - +
565C MET 3.4 5.6 - - - +
566C TYR 2.9 0.4 - - - -
567C ASP* 1.3 83.6 - - - +
569C LEU* 1.3 56.6 + - - +
583C HIS* 2.6 32.1 + - - -
587C ILE* 3.9 1.0 - - - +
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Residues in contact with LEU 569 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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529C THR* 4.2 6.3 - - + +
565C MET 3.2 13.9 - - - +
566C TYR* 3.0 6.8 + - - +
568C ASN* 1.3 79.7 - - - +
570C ARG* 1.3 62.6 + - + +
583C HIS* 3.3 18.8 - - - +
584C PHE* 3.4 33.2 - - + +
587C ILE* 3.6 24.7 - - + -
596C MET* 3.8 22.7 - - + -
597C VAL* 4.1 20.6 - - + -
600C ILE* 3.8 31.4 - - + -
604C LEU* 5.2 2.0 - - + -
612C ILE* 4.9 14.1 - - + -
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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