Contacts of the helix formed by residues 489 - 496 (chain L) 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 L).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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450L VAL 3.9 7.9 - - - +
451L ASN* 4.4 14.6 + - - +
452L LEU 4.9 2.0 - - - +
453L PRO* 5.5 6.5 - - + -
454L LEU* 4.5 13.1 - - + +
476L LYS* 3.5 1.5 - - - +
488L GLY* 1.3 89.8 + - - -
490L GLY* 1.3 57.2 + - - +
491L ILE 3.5 0.7 - - - -
492L ASN* 3.9 23.3 + - - +
493L ASN* 2.7 53.4 + - - +
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Residues in contact with GLY 490 (chain L).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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450L VAL* 3.7 24.2 + - - +
451L ASN* 4.3 3.8 + - - -
475L VAL* 3.7 8.7 - - - -
476L LYS 2.7 24.9 + - - +
489L GLN* 1.3 79.1 - - - +
491L ILE* 1.3 61.2 + - - -
493L ASN* 3.3 2.4 + - - +
494L LEU* 3.1 23.4 + - - +
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Residues in contact with ILE 491 (chain L).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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475L VAL* 3.6 28.2 - - + +
476L LYS 3.0 5.5 + - - -
477L GLY* 3.4 32.8 - - - +
478L THR 5.3 0.2 - - - +
490L GLY* 1.3 71.6 - - - -
492L ASN* 1.3 66.4 + - - +
494L LEU* 3.3 18.6 + - + +
495L ASP* 3.3 11.4 + - - +
528L MET* 3.6 22.2 - - + -
531L TYR* 4.4 3.6 - - + -
532L SER 3.8 16.8 - - - +
533L VAL* 4.7 0.2 - - + -
534L PRO* 3.5 34.8 - - + -
537L LEU* 3.8 8.1 - - + +
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Residues in contact with ASN 492 (chain L).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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476G LYS* 4.1 7.5 + - - +
486G PRO* 6.2 0.2 - - - +
476L LYS 4.9 2.0 + - - -
477L GLY* 5.0 0.8 - - - -
478L THR* 4.4 20.5 - - - +
488L GLY 3.3 24.2 + - - -
489L GLN* 3.7 24.0 + - - +
490L GLY 3.2 0.4 - - - -
491L ILE* 1.3 78.3 - - - +
493L ASN* 1.3 59.8 + - - +
495L ASP* 3.0 17.6 + - - +
496L ASN* 2.7 29.1 + - - +
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Residues in contact with ASN 493 (chain L).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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450L VAL* 3.7 28.1 + - + -
452L LEU 3.9 6.5 + - - -
454L LEU* 3.2 41.0 - - - +
457L LEU* 3.4 25.0 - - + +
489L GLN* 2.7 39.4 + - - +
490L GLY 3.7 3.1 - - - +
492L ASN* 1.3 73.2 - - - +
494L LEU* 1.3 62.8 + - - +
496L ASN* 3.0 18.0 + - - +
497L LEU* 3.2 22.6 + - + +
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Residues in contact with LEU 494 (chain L).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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450L VAL* 4.6 6.7 - - + -
472L PHE* 4.2 26.0 - - + -
475L VAL* 4.0 16.6 - - + -
490L GLY 3.1 15.7 + - - +
491L ILE* 3.4 17.5 - - + +
493L ASN* 1.3 76.6 - - - +
495L ASP* 1.3 61.8 + - - +
497L LEU* 3.2 16.4 + - + +
501L LEU* 3.3 29.6 - - + +
526L VAL* 3.8 36.1 - - + -
528L MET* 4.9 2.2 - - + -
537L LEU* 3.6 27.1 - - + -
541L PHE* 4.9 2.0 - - + -
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Residues in contact with ASP 495 (chain L).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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451G ASN* 4.2 0.7 + - - -
476G LYS* 3.0 31.0 - - - +
486G PRO* 3.5 14.7 - - + +
491L ILE 3.3 7.0 + - - +
492L ASN* 3.0 10.8 + - - +
494L LEU* 1.3 74.3 - - - +
496L ASN* 1.3 57.3 + - - +
497L LEU 2.9 9.9 + - - -
498L ARG* 2.8 45.4 + - - +
534L PRO* 4.4 6.3 - - + +
536L THR* 2.9 25.6 + - - -
537L LEU* 4.2 10.8 + - + +
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Residues in contact with ASN 496 (chain L).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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449G ASN* 3.3 12.5 + - - -
451G ASN* 3.3 44.1 - - + +
452G LEU* 3.4 2.3 - - + +
476G LYS* 3.3 24.8 + - - +
488G GLY* 4.7 5.4 - - - -
454L LEU* 3.8 23.8 - - + +
492L ASN* 2.7 35.3 + - - +
493L ASN* 3.0 13.8 + - - +
495L ASP* 1.3 76.3 - - - +
497L LEU* 1.3 64.5 + - + +
498L ARG 3.8 0.9 - - - -
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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