Contacts of the helix formed by residues 422 - 428 (chain A) in PDB entry 1IEW
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 ASN 422 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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418A SER 3.7 17.3 + - - +
419A HIS* 4.1 6.3 + - - +
420A ALA 3.9 1.4 - - - -
421A ASP* 1.3 77.1 - - - +
423A LEU* 1.3 64.2 + - - +
424A GLY 3.2 0.2 + - - -
425A TYR* 3.1 43.2 + - + +
426A GLN* 3.1 22.4 + - - +
438A THR* 3.0 22.0 + - - -
439A GLY* 2.8 27.0 + - - +
446A THR* 3.8 4.1 - - - +
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Residues in contact with LEU 423 (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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422A ASN* 1.3 72.8 + - - +
424A GLY* 1.3 63.9 + - - +
426A GLN* 3.4 28.7 + - - +
427A CYS* 3.2 33.5 + - - -
439A GLY 3.6 12.3 + - - +
440A ARG* 4.3 14.9 - - - +
441A THR* 5.1 0.9 - - - +
442A THR* 3.2 44.2 - - + +
444A GLY* 3.8 17.9 - - - +
445A THR 4.2 8.1 - - - +
446A THR* 3.5 15.5 - - + +
548A SER* 3.9 22.7 - - - +
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Residues in contact with GLY 424 (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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422A ASN* 3.2 2.3 + - - -
423A LEU* 1.3 72.3 - - - +
425A TYR* 1.3 64.9 + - - +
427A CYS* 3.0 7.3 + - - +
428A GLY* 3.0 20.3 + - - +
431A THR* 5.6 1.3 - - - -
437A ASP 3.0 26.3 + - - +
439A GLY 2.8 19.1 + - - -
441A THR* 4.5 9.9 - - - -
488A PRO* 3.7 3.3 - - - +
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Residues in contact with TYR 425 (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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418A SER* 3.8 15.9 - - - -
419A HIS* 3.6 39.9 - + + +
422A ASN* 3.1 40.7 + - + +
424A GLY* 1.3 74.4 - - - +
426A GLN* 1.3 63.0 + - - +
427A CYS 3.2 0.9 + - - -
428A GLY* 3.3 11.8 + - - -
438A THR* 3.5 18.2 + - - -
486A GLU 4.8 3.1 - - - +
487A HIS* 3.5 27.4 + + - -
488A PRO* 3.4 30.0 - - + +
523A ILE* 3.6 14.6 - - - +
545A LEU* 4.1 2.9 - - - +
5C NAG 2.7 44.1 + - - -
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Residues in contact with GLN 426 (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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419A HIS* 5.1 6.9 + - + +
422A ASN 3.1 11.8 + - - +
423A LEU* 3.5 13.4 - - - +
424A GLY 3.2 0.2 - - - -
425A TYR* 1.3 80.3 - - - +
427A CYS* 1.3 57.2 + - - +
445A THR 3.2 19.7 + - - -
446A THR* 3.2 26.0 - - - +
447A ILE* 3.6 14.0 + - + +
523A ILE* 4.3 14.6 - - + -
545A LEU* 3.5 2.1 - - - -
546A PRO* 3.3 27.7 - - + +
547A GLY 2.6 42.5 + - - +
548A SER 3.5 9.1 + - - -
550A GLY* 3.5 13.3 - - - +
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Residues in contact with CYS 427 (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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98A HIS* 3.5 5.0 - - - -
108A ILE* 3.9 16.2 - - + -
111A HIS* 3.3 23.0 + - - -
423A LEU* 3.2 29.3 + - - +
424A GLY* 3.0 6.9 + - - +
426A GLN* 1.3 76.9 - - - +
428A GLY* 1.3 65.3 + - - +
431A THR* 3.5 28.3 - - + +
441A THR* 6.0 0.4 - - - -
442A THR* 5.2 2.5 - - - -
545A LEU* 4.1 4.9 - - - +
547A GLY* 3.6 29.6 - - - -
548A SER* 3.8 9.4 - - - -
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Residues in contact with GLY 428 (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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424A GLY 3.0 12.1 + - - +
425A TYR 3.3 9.9 + - - -
427A CYS* 1.3 75.0 - - - +
429A GLY* 1.3 62.9 + - - -
431A THR* 2.8 23.4 + - - -
436A GLY* 3.8 6.6 - - - -
488A PRO* 3.8 19.2 - - - +
545A LEU* 4.1 15.9 - - - -
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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