Contacts of the helix formed by residues 581 - 587 (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 ASP 581 (chain C).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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570C ARG* 3.4 15.3 + - - +
579C PRO 5.1 0.2 - - - +
580C SER* 1.3 72.8 - - - +
582C ASP* 1.3 66.6 + - - +
584C PHE* 3.0 5.5 + - - +
585C VAL* 2.7 27.4 + - + +
615C THR* 3.6 6.2 - - + +
618C ARG* 2.7 44.5 + - - +
619C ASN* 2.9 35.0 + - - +
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Residues in contact with ASP 582 (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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518C LYS* 4.8 3.3 - - - +
580C SER* 3.1 15.7 + - - +
581C ASP* 1.3 78.2 - - - +
583C HIS* 1.3 66.5 + - - +
585C VAL* 3.0 7.0 + - - +
586C GLN* 2.9 57.1 + - - +
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Residues in contact with HIS 583 (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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522C THR* 5.1 4.0 + - - -
525C ILE* 4.0 28.9 - - + -
567C ASP 5.5 0.6 + - - -
568C ASN* 2.6 24.5 + - - -
569C LEU 3.3 25.6 - - - +
570C ARG* 5.3 1.3 - - - -
571C GLY 5.4 9.2 - - - +
573C LEU* 6.0 5.1 - - + +
580C SER* 4.0 7.1 + - - +
581C ASP 3.2 0.8 + - - -
582C ASP* 1.3 81.7 + - - +
584C PHE* 1.3 61.2 + - - +
586C GLN* 3.4 20.4 + - - +
587C ILE* 3.4 23.7 + - + +
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Residues in contact with PHE 584 (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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569C LEU* 3.4 37.9 - - + +
570C ARG* 3.9 20.2 - - - +
580C SER 4.7 0.4 + - - -
581C ASP 3.0 6.3 + - - +
583C HIS* 1.3 77.0 - - - +
585C VAL* 1.3 64.9 + - + +
587C ILE* 2.9 23.7 + - + +
588C MET* 3.0 44.9 + - + +
597C VAL* 4.3 12.8 - - + -
612C ILE* 3.9 29.6 - - + -
615C THR* 3.5 28.3 - - + -
616C THR* 3.6 26.2 - - - -
623C LEU* 5.2 1.1 - - + -
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Residues in contact with VAL 585 (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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581C ASP* 2.7 29.0 + - + +
582C ASP* 3.5 6.5 - - - +
584C PHE* 1.3 75.9 - - + +
586C GLN* 1.3 63.7 + - + +
588C MET* 3.3 15.3 + - - +
589C CYS* 3.3 15.0 + - - -
615C THR* 4.7 4.7 - - + +
619C ASN* 3.3 40.6 - - + +
622C PHE* 3.8 33.2 - - + -
623C LEU* 3.8 7.0 - - + +
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Residues in contact with GLN 586 (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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518C LYS* 3.1 41.2 - - - +
522C THR* 3.1 36.3 + - + +
582C ASP* 2.9 51.0 + - - +
583C HIS* 3.6 13.3 + - - +
584C PHE 3.1 0.2 - - - -
585C VAL* 1.3 78.5 - - + +
587C ILE* 1.3 61.9 + - - +
589C CYS* 3.7 14.3 + - - +
590C ILE* 3.9 9.2 - - - +
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Residues in contact with ILE 587 (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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522C THR* 4.2 16.8 - - + +
525C ILE* 4.2 11.9 - - + -
526C ILE* 4.2 13.7 - - + -
568C ASN 3.9 15.3 - - - +
569C LEU* 3.6 25.6 - - + -
583C HIS* 3.6 24.2 - - + +
584C PHE* 2.9 11.3 + - + +
586C GLN* 1.3 78.8 - - - +
588C MET* 1.3 57.2 + - + +
589C CYS 3.1 6.1 + - - -
590C ILE* 3.3 11.3 + - - +
593C GLY* 3.5 34.6 - - - +
596C MET* 4.3 10.1 - - + -
597C VAL* 4.4 11.0 - - + -
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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