Contacts of the helix formed by residues 497 - 503 (chain F) 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 F).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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452A LEU* 4.1 14.4 - - + -
450F VAL* 5.0 6.7 - - + -
457F LEU* 4.3 13.7 - - + -
461F LEU* 3.9 31.9 - - + -
472F PHE* 5.3 6.7 - - + -
493F ASN 3.2 20.9 - - - +
494F LEU* 3.2 12.7 + - + +
495F ASP 2.9 0.6 - - - -
496F ASN* 1.3 87.7 - - + +
498F ARG* 1.3 65.4 + - - +
499F ASP* 3.5 2.5 - - - -
500F TYR* 3.6 46.7 - - + -
501F LEU* 3.1 26.4 + - + +
521F PHE* 6.2 0.7 - - + -
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Residues in contact with ARG 498 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
451A ASN* 4.9 3.0 - - - +
473A GLU 5.1 1.1 - - - +
474A ASP* 3.5 42.1 + - + +
476A LYS* 4.7 3.2 - - + +
486A PRO* 4.3 0.8 - - - +
529A ASN* 3.7 12.7 + - - -
531A TYR* 3.3 25.2 + - - -
494F LEU 5.0 0.7 - - - -
495F ASP* 2.8 49.0 + - - +
496F ASN 3.8 1.0 - - - -
497F LEU* 1.3 72.4 - - - +
499F ASP* 1.3 67.5 + - - +
501F LEU* 2.9 17.4 + - - +
502F ASP* 2.7 24.0 + - - +
536F THR* 2.9 35.9 + - - +
537F LEU* 5.3 0.6 - - - +
540F ARG* 3.2 36.9 - - - +
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Residues in contact with ASP 499 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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433A THR* 5.9 0.4 - - - -
447A ALA 5.5 2.6 - - - +
448A LEU 5.2 2.4 - - - +
449A ASN* 3.5 25.9 - - - +
473A GLU* 3.6 26.2 - - + +
498F ARG* 1.3 79.4 + - - +
500F TYR* 1.3 73.8 + - - -
502F ASP* 3.6 9.8 + - - -
503F GLY* 2.8 31.4 + - - -
505F VAL* 3.6 24.3 - - + +
507F VAL* 3.1 29.4 - - - +
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Residues in contact with TYR 500 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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449A ASN* 4.7 13.0 - - + -
452A LEU* 5.3 6.0 - - + +
460A GLU* 4.2 15.6 + - - -
420F ARG* 3.2 18.0 + - - -
421F TYR* 3.9 0.9 + - - -
458F ASN* 5.8 1.4 + - - -
461F LEU* 4.0 20.1 - - + +
497F LEU* 3.3 42.6 - - + +
498F ARG 3.1 0.4 - - - -
499F ASP* 1.3 115.9 - - - +
501F LEU* 1.3 59.8 + - + +
507F VAL* 3.8 25.6 - - + -
508F ASN 3.5 22.0 + - - -
509F LEU* 4.7 3.1 - - + -
521F PHE* 3.3 52.8 - + + +
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Residues in contact with LEU 501 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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418F LYS* 4.4 5.8 + - - -
420F ARG* 3.3 13.2 + - - +
421F TYR* 3.8 45.6 - - + -
472F PHE* 4.9 9.0 - - + -
494F LEU* 3.3 33.4 - - + +
495F ASP* 5.4 0.2 - - - -
497F LEU* 3.1 15.7 + - + +
498F ARG* 2.9 9.3 + - - +
500F TYR* 1.3 79.1 - - + +
502F ASP* 1.3 63.0 + - - +
521F PHE* 6.2 0.4 - - + -
526F VAL* 5.1 3.1 - - + -
537F LEU* 3.8 21.5 - - + -
540F ARG* 3.9 31.2 - - + +
541F PHE* 5.5 4.0 - - + -
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Residues in contact with ASP 502 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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433A THR* 4.3 16.0 - - + +
473A GLU* 4.7 0.2 - - - +
474A ASP* 4.2 4.7 - - - +
417F PRO* 3.4 7.8 - - - +
418F LYS* 3.1 47.9 + - + +
420F ARG* 3.2 14.2 + - - -
498F ARG 2.7 22.9 + - - +
499F ASP* 3.6 7.6 - - - +
501F LEU* 1.3 77.1 - - - +
503F GLY* 1.3 60.6 + - - +
504F SER* 3.4 13.0 - - - +
540F ARG* 2.8 34.8 + - - -
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Residues in contact with GLY 503 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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567A ARG* 3.9 14.8 + - - -
417F PRO* 5.0 1.3 - - - -
420F ARG* 3.2 21.3 - - - +
499F ASP 2.8 19.0 + - - -
500F TYR 4.8 0.4 - - - -
502F ASP* 1.3 73.0 - - - +
504F SER* 1.3 59.7 + - - +
505F VAL 3.2 8.5 - - - -
520F ILE* 3.1 28.3 - - - +
521F PHE 4.7 2.0 - - - -
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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