Contacts of the helix formed by residues 489 - 496 (chain H) 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 H).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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450H VAL 4.0 7.9 - - - +
451H ASN* 4.4 14.5 + - - +
452H LEU 4.9 3.4 - - - +
453H PRO* 5.5 5.6 - - + -
454H LEU* 4.5 13.0 - - + +
476H LYS* 3.5 1.7 - - - +
478H THR* 6.2 0.4 - - - +
488H GLY* 1.3 89.5 + - - -
490H GLY* 1.3 60.2 + - - +
491H ILE 3.5 0.7 - - - -
492H ASN* 3.9 24.6 + - - +
493H ASN* 2.7 49.9 + - - +
496H ASN* 5.9 0.2 + - - -
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Residues in contact with GLY 490 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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450H VAL* 3.6 24.1 + - - +
451H ASN* 4.3 4.2 + - - -
475H VAL* 3.7 8.7 - - - -
476H LYS 2.7 24.2 + - - +
489H GLN* 1.3 80.1 - - - +
491H ILE* 1.3 61.7 + - - -
493H ASN* 3.7 2.6 - - - +
494H LEU* 3.1 23.2 + - - +
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Residues in contact with ILE 491 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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475H VAL* 3.5 27.8 - - + +
476H LYS 3.0 5.5 + - - -
477H GLY* 3.4 30.7 - - - +
478H THR 5.3 0.2 - - - +
490H GLY* 1.3 71.2 - - - -
492H ASN* 1.3 66.2 + - - +
494H LEU* 3.3 18.5 + - + +
495H ASP* 3.4 11.1 + - - +
528H MET* 3.6 22.7 - - + -
531H TYR* 4.4 3.8 - - + -
532H SER 3.8 16.2 - - - +
533H VAL* 4.7 0.2 - - + -
534H PRO* 3.5 34.8 - - + -
537H LEU* 3.8 7.5 - - + +
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Residues in contact with ASN 492 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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476H LYS 4.9 1.8 + - - -
477H GLY* 5.1 0.6 - - - -
478H THR* 4.4 21.5 - - - +
488H GLY 3.4 24.2 + - - -
489H GLN* 3.4 23.9 + - - +
490H GLY 3.2 0.6 - - - -
491H ILE* 1.3 78.7 - - - +
493H ASN* 1.3 59.7 + - - +
495H ASP* 3.0 18.4 + - - +
496H ASN* 2.7 27.1 + - - +
476I LYS* 4.1 5.1 + - - +
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Residues in contact with ASN 493 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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450H VAL* 3.7 27.9 + - + -
452H LEU 4.0 6.1 + - - -
454H LEU* 3.2 41.2 - - - +
457H LEU* 3.3 25.2 - - + +
489H GLN* 2.7 38.6 + - - +
490H GLY 3.7 4.3 - - - +
492H ASN* 1.3 73.4 - - - +
494H LEU* 1.3 62.9 + - - +
496H ASN* 3.0 18.3 + - - +
497H LEU* 3.2 21.8 + - + +
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Residues in contact with LEU 494 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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450H VAL* 4.6 7.2 - - + -
472H PHE* 4.2 25.8 - - + -
475H VAL* 4.0 16.4 - - + -
490H GLY 3.1 16.0 + - - +
491H ILE* 3.4 17.3 - - + +
492H ASN 3.1 0.4 - - - -
493H ASN* 1.3 76.8 - - - +
495H ASP* 1.3 59.7 + - - +
497H LEU* 3.2 16.1 + - + +
501H LEU* 3.2 30.0 - - + +
526H VAL* 3.7 35.0 - - + -
528H MET* 4.9 1.8 - - + -
537H LEU* 3.6 28.0 - - + -
541H PHE* 4.9 2.9 - - + -
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Residues in contact with ASP 495 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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491H ILE 3.4 7.0 + - - +
492H ASN* 3.0 11.4 + - - +
494H LEU* 1.3 74.5 - - - +
496H ASN* 1.3 58.8 + - - +
497H LEU 2.9 9.6 + - - -
498H ARG* 2.8 47.7 + - - +
534H PRO* 4.5 6.2 - - + +
536H THR* 2.9 26.0 + - - -
537H LEU* 4.2 11.5 + - + +
451I ASN* 4.5 0.5 + - - -
476I LYS* 3.0 29.8 - - - +
486I PRO* 3.3 13.9 - - + +
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Residues in contact with ASN 496 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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454H LEU* 3.8 27.0 - - + +
457H LEU* 6.1 0.4 - - + -
492H ASN* 2.7 36.9 + - - +
493H ASN* 3.0 13.4 + - - +
495H ASP* 1.3 75.9 - - - +
497H LEU* 1.3 69.7 + - + +
498H ARG 3.8 1.3 - - - -
449I ASN* 3.5 2.9 + - - -
451I ASN* 3.3 39.7 - - + +
452I LEU* 3.5 6.0 - - + +
476I LYS* 3.2 24.7 + - - +
488I GLY* 4.7 6.2 - - - -
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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