Contacts of the helix formed by residues 456 - 462 (chain E) 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 ARG 456 (chain E).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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454D LEU 4.4 6.1 - - - +
455D ASP* 3.0 40.0 + - - +
456D ARG* 3.7 17.2 - - - +
458D ASN* 3.4 41.5 + - - +
459D PHE* 3.7 22.3 - - - -
510D GLU* 5.3 1.8 - - - -
452E LEU* 4.9 9.4 - - + -
453E PRO* 3.6 7.1 + - + +
455E ASP* 1.3 90.4 - - + +
457E LEU* 1.3 63.8 + - - +
458E ASN 3.1 3.1 - - - -
459E PHE* 3.0 35.1 + - + +
460E GLU* 3.1 14.7 + - - +
456F ARG* 3.4 22.8 - - - +
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Residues in contact with LEU 457 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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449E ASN 4.4 7.6 - - - +
450E VAL* 3.8 31.4 - - + -
452E LEU* 5.2 1.8 - - - +
453E PRO 3.5 5.9 + - - +
454E LEU* 3.6 30.1 - - + +
455E ASP 3.1 0.6 - - - -
456E ARG* 1.3 79.0 - - - +
458E ASN* 1.3 54.2 + - - +
460E GLU* 3.7 4.0 - - + +
461E LEU* 2.7 67.2 + - + +
493E ASN* 3.3 24.2 - - - +
497E LEU* 4.3 13.9 - - + -
452F LEU* 4.5 14.6 - - + -
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Residues in contact with ASN 458 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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454E LEU 3.6 10.0 - - - +
455E ASP 4.4 1.6 - - - +
456E ARG 3.1 0.2 - - - -
457E LEU* 1.3 78.9 - - - +
459E PHE* 1.3 65.7 + - + +
460E GLU 3.1 1.3 + - - -
461E LEU* 4.3 6.4 - - - +
462E GLY* 3.5 15.2 + - - -
500E TYR* 5.7 1.4 + - - -
510E GLU* 3.6 40.6 + - + +
452F LEU* 3.1 32.9 - - - +
456F ARG* 3.8 26.2 + - + +
459F PHE* 5.7 2.0 - - - +
460F GLU* 4.1 12.7 + - - +
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Residues in contact with PHE 459 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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458D ASN* 5.6 1.3 - - - +
459D PHE* 6.3 3.8 - + - -
508D ASN* 5.9 0.7 - - - +
510D GLU* 4.5 20.4 - - - +
515D ASN* 5.0 9.7 + - - +
455E ASP 4.0 10.8 - - - -
456E ARG* 3.0 26.2 + - + +
458E ASN* 1.3 76.7 - - + +
460E GLU* 1.3 58.2 + - - +
462E GLY* 4.4 3.8 + - - -
463E VAL* 4.6 6.8 - - - +
510E GLU* 3.7 24.8 - - + +
513E HIS* 5.6 13.5 - + - -
456F ARG* 3.6 33.7 - - - -
459F PHE* 6.2 4.7 - + - -
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Residues in contact with GLU 460 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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458D ASN* 4.6 7.3 + - - -
500D TYR* 4.0 15.7 + - - -
508D ASN* 3.4 27.0 - - + +
448E LEU* 3.2 18.6 - - + +
449E ASN* 2.7 51.2 + - - +
452E LEU* 4.4 16.1 - - - +
456E ARG 3.1 12.8 + - - +
457E LEU* 3.9 6.1 - - + +
458E ASN 3.1 0.2 - - - -
459E PHE* 1.3 79.5 - - - +
461E LEU* 1.3 59.6 + - + +
462E GLY 3.0 4.7 - - - -
463E VAL* 3.0 25.6 - - - +
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Residues in contact with LEU 461 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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448E LEU* 3.9 13.5 - - + -
449E ASN 6.0 0.4 - - - +
450E VAL* 5.1 0.4 - - + -
457E LEU* 2.7 57.0 + - + +
458E ASN* 3.8 6.5 + - - +
460E GLU* 1.3 73.0 - - + +
462E GLY* 1.3 57.0 + - - +
463E VAL 3.0 9.6 + - - -
464E ALA 3.5 8.4 + - - -
472E PHE* 4.4 12.8 - - + -
497E LEU* 3.9 21.1 - - + -
500E TYR* 4.0 19.7 - - + +
509E LEU* 3.4 21.9 - - + +
521E PHE* 3.8 31.6 - - + -
452F LEU* 5.8 2.7 - - + -
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Residues in contact with GLY 462 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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458E ASN 3.5 9.6 + - - -
459E PHE 5.1 2.7 - - - -
460E GLU* 3.0 3.0 - - - +
461E LEU* 1.3 77.4 - - - +
463E VAL* 1.3 60.4 + - - +
464E ALA 3.5 0.4 - - - -
465E ILE* 3.0 33.7 - - - +
509E LEU* 4.4 6.3 - - - -
510E GLU 3.7 23.3 - - - +
511E LYS* 4.5 7.8 - - - +
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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