Contacts of the helix formed by residues 564 - 571 (chain C) in PDB entry 1CX2
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 ILE 564 (chain C).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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197C MET* 5.0 4.3 - - + -
201C PHE* 3.7 13.2 - - + -
301C TYR* 4.1 12.3 - - + +
343C ILE* 3.6 4.4 - - + +
347C ASP* 2.8 20.1 + - - +
563C SER* 1.3 71.7 - - - +
565C GLN* 1.3 69.4 + - + +
567C LEU* 3.1 15.5 + - + -
568C ILE* 3.1 43.4 + - + +
578C THR* 5.0 3.5 + - - -
579C SER* 4.5 19.7 - - - +
580C PHE* 3.1 46.9 - - + -
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Residues in contact with GLN 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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563C SER* 3.7 11.4 - - - +
564C ILE* 1.3 84.6 - - + +
566C SER* 1.3 60.7 + - - +
568C ILE* 4.1 2.1 - - - +
569C CYS* 3.1 32.3 + - + +
576C PRO 3.6 19.8 + - - -
577C PHE* 3.8 16.2 - - - +
578C THR* 3.6 30.4 + - - +
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Residues in contact with SER 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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561C THR 4.2 10.6 + - - -
562C ALA* 5.2 1.3 - - - -
563C SER* 2.5 28.8 + - - -
565C GLN* 1.3 75.4 - - - +
567C LEU* 1.3 68.5 + - - +
568C ILE 3.0 2.0 - - - -
569C CYS* 4.3 5.8 - - - +
570C ASN* 2.8 43.6 + - - +
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Residues in contact with LEU 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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201C PHE* 4.8 3.1 - - + -
301C TYR* 5.1 2.2 - - + -
304C ILE* 3.8 21.4 - - + +
305C TRP* 3.7 47.6 - - + +
308C GLU* 4.0 29.8 - - + +
339C GLU* 4.8 3.8 - - - +
343C ILE* 4.1 11.2 - - + -
563C SER 2.8 15.1 + - - +
564C ILE* 3.1 25.5 + - + +
566C SER* 1.3 76.6 - - - +
568C ILE* 1.3 58.1 + - - +
570C ASN* 4.9 1.6 - - - +
571C ASN* 3.1 36.2 + - - +
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Residues in contact with ILE 568 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
197C MET* 4.3 11.9 - - + -
301C TYR* 4.6 6.7 - - + -
304C ILE* 4.4 18.4 - - + -
423C VAL* 3.9 16.2 - - + -
564C ILE* 3.1 38.0 + - + +
565C GLN 4.1 1.1 - - - +
566C SER 3.0 0.6 - - - -
567C LEU* 1.3 75.8 - - - +
569C CYS* 1.3 60.0 + - - +
570C ASN 3.0 3.8 - - - -
571C ASN 2.9 0.9 + - - -
572C VAL* 2.6 49.8 + - + +
576C PRO* 3.3 33.2 - - + +
578C THR* 3.3 23.3 - - - +
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Residues in contact with CYS 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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565C GLN* 3.1 27.9 + - + +
566C SER* 3.1 7.4 + - - +
568C ILE* 1.3 78.6 - - - +
570C ASN* 1.3 60.5 + - - +
572C VAL 4.6 1.2 + - - +
574C GLY 4.6 3.3 - - - +
575C CYS* 2.0 74.9 - - - +
576C PRO 4.2 0.4 - - - -
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Residues in contact with ASN 570 (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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308C GLU* 4.6 4.1 + - - +
311C ARG* 3.8 43.2 + - - +
566C SER* 2.8 34.2 + - - +
567C LEU* 4.9 0.9 - - - +
569C CYS* 1.3 76.3 - - - +
571C ASN* 1.3 74.1 + - - +
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Residues in contact with ASN 571 (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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304C ILE* 3.9 19.8 + - + +
307C ARG* 3.1 40.8 + - + +
308C GLU* 3.0 60.1 + - - +
311C ARG* 4.7 4.0 - - - +
419C LEU* 5.9 0.5 - - - +
567C LEU* 3.1 25.2 + - - +
568C ILE 2.9 1.8 + - - -
570C ASN* 1.3 86.6 - - - +
572C VAL* 1.3 61.4 + - + +
573C LYS 3.9 1.9 + - - -
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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