Contacts of the helix formed by residues 415 - 419 (chain C) in PDB entry 2XLR
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 THR 415 (chain C).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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408C HIS 5.4 0.3 + - - -
412C ASN* 3.0 40.8 + - - +
414C MET* 1.3 86.0 - - + +
416C PHE* 1.3 66.4 + - - +
417C ARG 3.0 3.6 - - - -
418C ASP* 2.9 34.8 + - - +
419C HIS* 3.9 12.7 + - - -
437C TRP* 5.9 0.2 - - - -
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Residues in contact with PHE 416 (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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78C ASP* 3.7 10.8 - - - -
102C TYR* 3.3 26.1 + + - -
216C ASP* 5.2 1.8 - - - -
405C TRP* 3.6 28.5 - - - -
408C HIS* 3.8 30.1 - - + +
409C LYS* 3.8 27.8 - - + -
412C ASN 3.3 5.6 + - - +
413C ILE* 3.2 32.5 - - + -
414C MET 3.7 1.1 - - - -
415C THR* 1.3 76.7 - - - +
417C ARG* 1.3 102.4 + - + +
418C ASP 3.1 4.4 + - - -
419C HIS* 3.3 21.7 + - - +
421C TYR* 4.2 0.5 + - - -
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Residues in contact with ARG 417 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
76C TRP* 3.2 38.8 + - + +
77C SER 2.9 26.4 + - - -
78C ASP* 3.4 16.0 - - - +
100C ALA* 6.1 0.9 - - - +
101C SER 5.9 0.2 + - - -
102C TYR* 3.3 32.4 + - + +
216C ASP* 2.9 34.7 + - - -
219C SER* 5.7 0.6 - - - -
220C GLN* 4.5 4.8 - - - +
414C MET 5.2 1.3 + - - +
415C THR 3.0 1.4 + - - -
416C PHE* 1.3 112.4 - - + +
418C ASP* 1.3 62.2 + - - +
419C HIS 3.4 1.1 - - - +
433C HIS* 6.2 0.3 - - - +
437C TRP* 3.7 50.0 - - + +
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Residues in contact with ASP 418 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
76C TRP* 5.8 0.7 - - - -
414C MET 4.8 0.5 - - - +
415C THR* 2.9 29.3 + - - +
417C ARG* 1.3 79.7 - - - +
419C HIS* 1.3 65.5 + - + +
420C SER* 4.4 1.4 + - - -
432C LYS* 3.4 35.0 + - - +
433C HIS* 5.6 1.2 + - - +
435C THR 4.5 1.2 - - - +
436C PRO* 3.4 16.0 - - - +
437C TRP* 2.8 37.7 + - - +
438C ILE* 5.0 1.9 + - - +
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Residues in contact with HIS 419 (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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100C ALA* 5.9 0.5 - - - +
101C SER* 3.8 7.8 + - - -
102C TYR* 3.7 17.2 - - - -
408C HIS* 3.5 55.7 + + + +
411C GLU* 4.3 11.2 + - - -
415C THR* 3.9 16.8 + - - -
416C PHE* 3.3 17.7 + - - +
417C ARG 4.1 0.7 - - - +
418C ASP* 1.3 84.3 - - + +
420C SER* 1.3 62.3 + - - +
421C TYR* 3.7 10.3 - - + +
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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