Contacts of the helix formed by residues 468 - 475 (chain B) in PDB entry 1XI1
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 PRO 468 (chain B).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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248B PHE* 4.0 5.2 - - + -
448B CYS* 4.0 20.4 - - + -
451B ARG* 3.2 28.5 - - - +
462B LEU* 3.6 27.1 - - + -
466B GLU 3.1 4.7 - - - +
467B ILE* 1.3 85.5 - - - +
469B ASP* 1.3 64.9 + - - +
470B VAL* 4.1 8.5 - - + -
471B ILE* 3.2 26.0 + - + -
472B LYS* 3.1 14.7 + - - +
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Residues in contact with ASP 469 (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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467B ILE 3.4 1.8 + - - -
468B PRO* 1.3 72.0 - - - +
470B VAL* 1.3 66.3 + - + +
471B ILE 3.2 0.9 + - - -
472B LYS* 3.2 51.3 + - - +
473B ASP 4.7 0.9 + - - -
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Residues in contact with VAL 470 (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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447B ALA* 3.5 39.6 - - + +
448B CYS* 4.1 7.6 - - - -
468B PRO* 4.1 7.0 - - + -
469B ASP* 1.3 79.8 - - + +
471B ILE* 1.3 69.7 + - + +
473B ASP* 5.2 2.7 + - - +
474B ILE* 4.8 5.0 - - - +
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Residues in contact with ILE 471 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
248B PHE* 3.9 31.0 - - + -
444B ALA* 4.6 13.5 - - + +
447B ALA* 5.2 2.5 - - + -
448B CYS* 3.8 24.7 - - - -
460B ILE* 4.5 7.2 - - + -
467B ILE* 4.3 0.9 - - + -
468B PRO* 3.2 36.8 + - + +
469B ASP 3.2 0.6 - - - -
470B VAL* 1.3 82.8 - - + +
472B LYS* 1.3 64.8 + - - +
473B ASP 3.2 2.7 - - - -
474B ILE* 2.9 32.1 + - + +
475B VAL* 2.8 30.1 - - + +
483B TRP* 5.5 4.9 - - + -
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Residues in contact with LYS 472 (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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467B ILE* 3.7 31.2 - - + -
468B PRO 3.1 12.7 + - - +
469B ASP* 3.2 52.7 + - - +
470B VAL 3.6 0.2 - - - -
471B ILE* 1.3 77.5 - - - +
473B ASP* 1.3 67.0 + - - +
474B ILE 3.1 1.4 + - - -
475B VAL* 3.4 15.8 + - - +
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Residues in contact with ASP 473 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
469B ASP 4.7 1.0 + - - -
470B VAL 5.2 2.2 + - - +
471B ILE* 3.2 1.2 - - - +
472B LYS* 1.3 81.0 - - - +
474B ILE* 1.3 66.1 + - + +
475B VAL 3.6 1.3 - - - -
482B TYR* 3.8 14.5 + - - -
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Residues in contact with ILE 474 (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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444B ALA* 5.1 5.4 - - + -
470B VAL 4.8 3.1 - - - +
471B ILE* 2.9 35.4 + - + +
473B ASP* 1.3 86.4 - - + +
475B VAL* 1.3 58.5 + - - +
482B TYR* 3.6 18.6 - - + -
483B TRP* 2.8 48.9 + - + +
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Residues in contact with VAL 475 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
248B PHE* 4.3 10.1 - - + -
467B ILE* 4.3 22.0 - - + -
471B ILE* 2.8 47.3 - - + +
472B LYS* 3.4 14.4 + - - +
473B ASP 3.6 1.1 - - - -
474B ILE* 1.3 80.9 - - - +
476B ASP* 1.3 69.1 + - - +
477B PRO* 5.7 0.9 - - + -
482B TYR* 4.0 2.5 - - - -
483B TRP* 3.0 16.2 - - + +
485B HIS* 4.4 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