Contacts of the helix formed by residues 461 - 468 (chain A) in PDB entry 2ILU
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 461 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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111A TYR* 2.8 42.5 + - - +
115A MET* 3.8 2.6 - - - +
157A PHE* 5.2 0.2 - - - -
161A ARG* 2.7 39.6 + - - -
165A PRO* 5.9 1.0 - - - +
443A GLU* 4.0 7.8 - - - +
444A ALA 4.1 7.4 - - - +
445A MET* 3.3 15.0 - - - +
447A GLY 3.1 14.2 - - - +
448A PHE* 3.7 2.1 - - - -
449A HIS* 3.4 12.9 + - - +
460A ALA* 1.3 75.8 - - - +
462A GLY* 1.3 64.3 + - - +
464A HIS 4.1 0.3 + - - -
465A GLY* 2.8 28.5 + - - -
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Residues in contact with GLY 462 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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114A TYR* 3.3 21.5 - - - -
115A MET* 3.7 6.4 - - - +
118A TRP* 3.9 6.1 + - - -
445A MET 2.8 15.1 + - - -
446A GLN 3.8 6.3 - - - -
447A GLY 3.3 11.9 - - - -
461A ASP* 1.3 78.0 - - - +
463A LYS* 1.3 58.8 + - - -
464A HIS 3.4 0.2 - - - -
466A LEU* 3.0 21.1 + - - +
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Residues in contact with LYS 463 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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118A TRP* 3.5 38.1 - - + -
122A TYR* 6.5 0.9 - - + -
446A GLN 4.9 1.2 + - - -
447A GLY 4.8 0.2 + - - -
462A GLY* 1.3 69.3 - - - -
464A HIS* 1.3 86.6 - - + +
466A LEU* 3.2 6.6 + - + +
467A HIS* 3.0 50.2 + - + +
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Residues in contact with HIS 464 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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447A GLY 5.6 0.2 + - - -
448A PHE* 3.5 47.2 - + + -
462A GLY 3.4 0.6 - - - -
463A LYS* 1.3 99.2 + - + +
465A GLY* 1.3 66.4 + - - +
467A HIS* 3.4 13.8 + - - +
468A GLU* 3.3 23.9 + - - +
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Residues in contact with GLY 465 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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165A PRO* 5.0 4.9 - - - -
448A PHE* 3.6 3.5 - - - -
459A GLY 4.2 3.2 - - - +
460A ALA* 3.7 12.3 - - - -
461A ASP* 2.8 37.4 + - - -
464A HIS* 1.3 77.0 - - - +
466A LEU* 1.3 64.4 + - - +
468A GLU* 3.2 17.8 + - - +
469A TYR* 3.9 10.0 - - - -
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Residues in contact with LEU 466 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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115A MET* 4.4 4.8 - - - -
118A TRP* 3.7 46.7 - - + +
122A TYR* 3.6 35.4 - - + -
165A PRO* 4.1 24.9 - - + +
168A LEU* 4.4 8.1 - - + -
169A THR* 3.8 23.7 - - + +
462A GLY 3.0 13.5 + - - +
463A LYS* 3.2 9.6 + - + +
465A GLY* 1.3 76.9 - - - +
467A HIS* 1.3 68.6 + - + +
469A TYR* 3.1 21.5 + - - +
470A LEU 4.1 0.2 + - - -
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Residues in contact with HIS 467 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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122A TYR* 4.2 17.9 - - - +
123A GLU 4.8 2.5 + - - -
140A LYS* 3.6 25.4 + - - -
247A LYS* 4.8 0.3 + - - -
463A LYS* 3.0 46.7 + - + +
464A HIS* 3.8 15.2 + - - +
465A GLY 3.3 0.2 - - - -
466A LEU* 1.3 75.0 - - + +
468A GLU* 1.3 62.9 - - - +
469A TYR 3.0 5.4 - - - -
470A LEU* 2.9 49.6 + - + +
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Residues in contact with GLU 468 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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143A LEU* 3.6 7.8 - - - +
224A MET* 3.7 5.6 - - + +
247A LYS* 2.7 44.6 + - - +
248A VAL 5.6 0.3 - - - +
249A OCS 3.5 27.4 + - - +
448A PHE* 4.3 7.2 - - + -
458A GLY* 3.4 21.2 - - - -
459A GLY 3.5 24.7 + - - +
464A HIS 3.3 15.6 + - - +
465A GLY 3.2 10.1 + - - +
467A HIS* 1.3 75.8 - - - +
469A TYR* 1.3 61.4 + - + +
470A LEU 3.3 0.8 + - - -
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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