Contacts of the helix formed by residues 497 - 503 (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 LEU 497 (chain E).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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450E VAL* 5.0 7.2 - - + -
457E LEU* 4.3 12.3 - - + -
461E LEU* 3.9 35.4 - - + -
472E PHE* 5.3 6.3 - - + -
493E ASN 3.2 21.5 - - - +
494E LEU* 3.2 12.5 + - + +
495E ASP 2.9 0.8 - - - -
496E ASN* 1.3 88.8 - - + +
498E ARG* 1.3 64.3 + - - +
499E ASP* 3.5 2.9 - - - -
500E TYR* 3.6 43.1 - - + -
501E LEU* 3.1 26.7 + - + +
521E PHE* 6.2 0.4 - - + -
452F LEU* 4.2 14.8 - - + -
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Residues in contact with ARG 498 (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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494E LEU 5.0 0.7 - - - -
495E ASP* 2.8 50.7 + - - +
496E ASN 3.8 1.0 - - - -
497E LEU* 1.3 73.0 - - - +
499E ASP* 1.3 65.3 + - - +
501E LEU* 2.9 18.1 + - - +
502E ASP* 2.7 24.4 + - - +
536E THR* 2.9 36.2 + - - +
537E LEU* 5.3 0.6 - - - +
540E ARG* 3.2 24.1 - - - +
451F ASN* 5.1 1.2 - - - +
473F GLU 4.9 1.6 - - - +
474F ASP* 3.0 64.4 + - + +
476F LYS* 5.5 1.3 - - - -
529F ASN* 3.2 14.8 + - - +
531F TYR* 3.4 20.6 + - - -
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Residues in contact with ASP 499 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
498E ARG* 1.3 78.5 + - - +
500E TYR* 1.3 75.3 + - - +
502E ASP* 3.5 9.8 + - - -
503E GLY* 2.8 30.8 + - - -
505E VAL* 3.6 17.0 - - + +
507E VAL* 3.1 29.2 - - - +
433F THR* 5.4 0.2 - - - -
447F ALA* 5.2 4.6 - - - +
448F LEU 5.1 3.3 - - - +
449F ASN* 3.9 18.8 - - - +
473F GLU* 3.5 39.5 - - + +
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Residues in contact with TYR 500 (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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420E ARG* 3.2 18.5 + - - -
421E TYR* 3.9 0.9 + - - -
458E ASN* 5.7 1.6 + - - -
461E LEU* 4.0 20.3 - - + +
497E LEU* 3.4 43.1 - - + +
498E ARG 3.1 0.4 - - - -
499E ASP* 1.3 114.5 - - - +
501E LEU* 1.3 59.5 + - + +
507E VAL* 3.8 24.5 - - + -
508E ASN 3.5 21.1 + - - -
509E LEU* 4.7 3.4 - - + -
521E PHE* 3.3 52.0 - + + +
449F ASN* 4.7 12.7 - - + +
452F LEU* 5.7 4.4 - - + +
460F GLU* 4.3 15.9 + - - -
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Residues in contact with LEU 501 (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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418E LYS* 4.4 6.2 + - - -
420E ARG* 3.3 13.5 + - - +
421E TYR* 3.8 46.2 - - + +
472E PHE* 4.9 8.3 - - + -
494E LEU* 3.3 35.0 - - + +
495E ASP* 5.3 0.4 - - - -
497E LEU* 3.1 15.5 + - + +
498E ARG* 2.9 10.3 + - - +
500E TYR* 1.3 77.7 - - + +
502E ASP* 1.3 64.8 + - - +
521E PHE* 6.2 0.4 - - + -
526E VAL* 5.1 2.7 - - + -
537E LEU* 3.8 21.5 - - + -
540E ARG* 3.9 30.4 - - + +
541E PHE* 5.5 4.0 - - + -
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Residues in contact with ASP 502 (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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417E PRO* 3.4 7.8 - - - +
418E LYS* 3.1 46.3 + - + +
420E ARG* 3.2 14.0 + - - -
498E ARG* 2.7 22.6 + - - +
499E ASP* 3.2 7.3 + - - +
501E LEU* 1.3 77.6 - - - +
503E GLY* 1.3 60.5 + - - +
504E SER* 3.4 6.1 - - - +
540E ARG* 2.8 36.2 + - - -
433F THR* 3.7 27.5 + - + +
473F GLU* 4.4 0.2 - - - +
474F ASP* 4.4 1.0 - - - +
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Residues in contact with GLY 503 (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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417E PRO* 5.0 0.4 - - - -
420E ARG* 3.2 20.6 - - - +
499E ASP 2.8 18.2 + - - -
500E TYR 4.8 0.2 - - - -
502E ASP* 1.3 73.5 - - - +
504E SER* 1.3 59.5 + - - +
505E VAL 3.2 8.5 + - - -
507E VAL* 6.2 0.2 - - - -
520E ILE* 3.1 27.2 - - - +
521E PHE* 4.7 2.2 - - - -
567F ARG* 3.6 18.0 + - - -
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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