Contacts of the helix formed by residues 489 - 496 (chain D) 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 D).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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450D VAL 4.0 7.6 - - - +
451D ASN* 4.4 15.4 + - - +
452D LEU 4.9 1.8 - - - +
453D PRO* 5.5 5.8 - - + -
454D LEU* 4.5 13.2 - - + +
476D LYS* 3.5 1.5 - - - +
478D THR* 6.2 0.4 - - - +
488D GLY* 1.3 91.0 + - - -
490D GLY* 1.3 55.8 + - - +
491D ILE 3.5 0.9 - - - -
492D ASN* 3.9 23.4 + - - +
493D ASN* 2.7 52.8 + - - +
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Residues in contact with GLY 490 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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450D VAL* 3.7 23.7 + - - +
451D ASN* 4.3 4.4 + - - -
475D VAL* 3.8 8.7 - - - -
476D LYS 2.7 23.1 + - - +
489D GLN* 1.3 79.9 - - - +
491D ILE* 1.3 61.2 + - - -
493D ASN* 3.3 2.4 + - - +
494D LEU* 3.1 22.9 + - - +
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Residues in contact with ILE 491 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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475D VAL* 3.5 28.5 - - + +
476D LYS 3.0 5.8 + - - +
477D GLY* 3.4 31.6 - - - +
478D THR 5.3 0.2 - - - +
490D GLY* 1.3 71.2 - - - -
492D ASN* 1.3 65.8 + - - +
494D LEU* 3.3 19.1 + - + +
495D ASP* 3.3 11.6 + - - +
528D MET* 3.6 22.7 - - + -
531D TYR* 4.4 3.6 - - + -
532D SER 3.8 16.4 - - - +
533D VAL* 4.7 0.2 - - + -
534D PRO* 3.5 34.5 - - + -
537D LEU* 3.8 6.9 - - + +
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Residues in contact with ASN 492 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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476D LYS 4.9 1.4 + - - -
477D GLY* 5.0 0.8 - - - -
478D THR* 4.4 21.1 - - - +
488D GLY 3.3 24.5 + - - -
489D GLN* 3.4 24.4 + - - +
490D GLY 3.2 0.2 - - - -
491D ILE* 1.3 79.7 - - - +
493D ASN* 1.3 59.0 + - - +
495D ASP* 3.0 17.8 + - - +
496D ASN* 2.7 29.2 + - - +
476E LYS* 4.2 5.9 + - - +
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Residues in contact with ASN 493 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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450D VAL* 3.7 27.9 + - + -
452D LEU 3.9 6.1 + - - -
454D LEU* 3.2 42.1 - - - +
457D LEU* 3.3 25.8 - - + +
489D GLN* 2.7 40.2 + - - +
490D GLY 3.7 3.4 - - - +
492D ASN* 1.3 72.8 - - - +
494D LEU* 1.3 61.8 + - - +
496D ASN* 3.0 17.9 + - - +
497D LEU* 3.2 22.3 - - + +
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Residues in contact with LEU 494 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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450D VAL* 4.6 6.5 - - + -
472D PHE* 4.2 26.7 - - + -
475D VAL* 4.0 16.4 - - + -
490D GLY 3.1 16.4 + - - +
491D ILE* 3.4 18.2 - - + +
492D ASN 3.1 0.2 - - - -
493D ASN* 1.3 76.4 - - - +
495D ASP* 1.3 61.0 + - - +
497D LEU* 3.2 16.6 + - + +
501D LEU* 3.3 29.7 - - + +
526D VAL* 3.8 35.0 - - + -
528D MET* 4.9 2.0 - - + -
537D LEU* 3.6 27.1 - - + -
541D PHE* 4.9 2.9 - - + -
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Residues in contact with ASP 495 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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491D ILE 3.3 7.2 + - - +
492D ASN* 3.0 11.2 + - - +
494D LEU* 1.3 74.9 - - - +
496D ASN* 1.3 57.5 + - - +
497D LEU 2.9 10.2 + - - -
498D ARG* 2.8 45.5 + - - +
534D PRO* 4.4 7.1 - - + +
536D THR* 2.9 25.5 + - - -
537D LEU* 4.2 11.5 + - + +
451E ASN* 4.4 0.3 + - - -
476E LYS* 3.0 31.1 - - - +
486E PRO* 3.4 12.7 - - + +
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Residues in contact with ASN 496 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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454D LEU* 3.8 24.0 - - + +
457D LEU* 6.1 0.2 - - + -
492D ASN* 2.7 37.1 + - - +
493D ASN* 3.0 13.0 + - - +
495D ASP* 1.3 75.0 - - - +
497D LEU* 1.3 69.6 + - + +
498D ARG 3.8 1.1 - - - -
449E ASN* 3.4 8.3 + - - -
451E ASN* 3.4 43.6 - - + +
452E LEU* 3.4 2.9 - - + +
476E LYS* 3.3 23.2 + - - +
488E GLY* 4.8 5.2 - - - -
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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