Contacts of the helix formed by residues 489 - 496 (chain A) in PDB entry 4E2I
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 GLN 489 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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450A VAL 4.0 7.9 - - - +
451A ASN* 4.4 14.7 + - - +
452A LEU 4.9 2.2 - - - +
453A PRO* 5.5 7.0 - - + -
454A LEU* 4.5 13.1 - - + +
476A LYS* 3.5 1.7 - - - +
478A THR* 6.2 0.8 - - - +
488A GLY* 1.3 89.2 + - - -
490A GLY* 1.3 57.2 + - - +
491A ILE 3.5 0.4 - - - -
492A ASN* 3.9 22.6 + - - +
493A ASN* 2.7 53.7 + - - +
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Residues in contact with GLY 490 (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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450A VAL* 3.7 23.9 + - - +
451A ASN* 4.3 4.2 + - - -
475A VAL* 3.7 9.2 - - - -
476A LYS 2.7 23.6 + - - +
489A GLN* 1.3 79.7 - - - +
491A ILE* 1.3 61.2 + - - -
493A ASN* 3.3 2.3 + - - +
494A LEU* 3.1 23.7 + - - +
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Residues in contact with ILE 491 (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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475A VAL* 3.6 28.0 - - + +
476A LYS 3.0 5.7 + - - +
477A GLY* 3.4 31.4 - - - +
478A THR 5.3 0.2 - - - +
490A GLY* 1.3 72.0 - - - -
492A ASN* 1.3 65.1 + - - +
494A LEU* 3.3 19.3 + - + +
495A ASP* 3.3 11.8 + - - +
528A MET* 3.6 22.7 - - + -
531A TYR* 4.4 3.4 - - + -
532A SER 3.8 16.8 - - - +
533A VAL* 4.7 0.2 - - + -
534A PRO* 3.5 34.8 - - + -
537A LEU* 3.8 7.3 - - + +
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Residues in contact with ASN 492 (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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476A LYS 4.9 1.4 + - - -
477A GLY* 5.0 0.8 - - - -
478A THR* 4.4 20.9 - - - +
488A GLY 3.3 24.7 + - - -
489A GLN* 3.7 23.8 + - - +
490A GLY 3.2 0.4 - - - -
491A ILE* 1.3 78.9 - - - +
493A ASN* 1.3 61.0 + - - +
495A ASP* 3.0 17.8 + - - +
496A ASN* 2.7 28.3 + - - +
476B LYS* 3.8 8.1 + - - +
486B PRO* 5.9 2.3 - - - +
487B SER 5.7 0.7 - - - +
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Residues in contact with ASN 493 (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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450A VAL* 3.7 28.3 + - + -
452A LEU 3.9 6.3 + - - -
454A LEU* 3.2 40.8 - - - +
457A LEU* 3.3 25.6 - - + +
489A GLN* 2.7 40.0 + - - +
490A GLY 3.7 3.1 - - - +
492A ASN* 1.3 72.8 - - - +
494A LEU* 1.3 62.0 + - - +
496A ASN* 3.0 18.3 + - - +
497A LEU* 3.2 22.2 - - - +
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Residues in contact with LEU 494 (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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450A VAL* 4.6 6.5 - - + -
472A PHE* 4.2 26.7 - - + -
475A VAL* 4.0 17.0 - - + -
490A GLY 3.1 16.6 + - - +
491A ILE* 3.4 17.3 - - + +
492A ASN 3.1 0.4 - - - -
493A ASN* 1.3 76.2 - - - +
495A ASP* 1.3 61.1 + - - +
497A LEU* 3.2 18.0 + - + +
501A LEU* 3.3 29.3 - - + +
526A VAL* 3.8 34.1 - - + -
528A MET* 4.9 2.0 - - + -
537A LEU* 3.6 27.4 - - + -
541A PHE* 5.0 3.1 - - + -
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Residues in contact with ASP 495 (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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491A ILE 3.3 7.0 + - - +
492A ASN* 3.0 10.8 + - - +
494A LEU* 1.3 74.8 - - - +
496A ASN* 1.3 58.9 + - - +
497A LEU 2.9 9.1 + - - -
498A ARG* 2.8 46.2 + - - +
534A PRO* 4.5 5.1 - - + +
536A THR* 2.9 25.8 + - - -
537A LEU* 4.2 11.5 + - + +
451B ASN* 4.4 0.7 + - - -
476B LYS* 3.1 29.6 - - - +
486B PRO* 3.3 15.6 - - + +
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Residues in contact with ASN 496 (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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454A LEU* 3.8 26.3 - - + +
457A LEU* 6.1 0.4 - - + -
492A ASN* 2.7 36.1 + - - +
493A ASN* 3.0 13.6 + - - +
495A ASP* 1.3 75.8 - - - +
497A LEU* 1.3 70.7 + - + +
498A ARG 3.8 0.7 - - - -
449B ASN* 3.4 7.8 + - - -
451B ASN* 3.3 40.1 - - + +
452B LEU* 3.8 2.0 - - + +
476B LYS* 3.0 27.7 + - - +
488B GLY* 4.6 5.5 - - - -
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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