Contacts of the helix formed by residues 497 - 503 (chain G) 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 G).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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450G VAL* 5.0 6.3 - - + -
457G LEU* 4.3 14.1 - - + -
461G LEU* 3.9 35.7 - - + -
472G PHE* 5.4 6.3 - - + -
493G ASN 3.2 20.4 - - - +
494G LEU* 3.2 12.1 + - + +
495G ASP 2.9 1.2 - - - -
496G ASN* 1.3 88.5 - - + +
498G ARG* 1.3 64.1 + - - +
499G ASP* 3.5 2.9 - - - -
500G TYR* 3.6 42.4 - - + -
501G LEU* 3.1 26.2 + - + +
521G PHE* 6.2 0.7 - - + -
452H LEU* 4.0 14.8 - - + -
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Residues in contact with ARG 498 (chain G).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
494G LEU 5.0 0.4 - - - -
495G ASP* 2.8 49.1 + - - +
496G ASN 3.8 0.8 - - - -
497G LEU* 1.3 73.0 - - - +
499G ASP* 1.3 67.1 + - - +
501G LEU* 2.9 17.3 + - - +
502G ASP* 2.7 24.4 + - - +
536G THR* 2.9 35.9 + - - +
537G LEU* 5.3 0.6 - - - +
540G ARG* 3.2 36.4 - - - +
451H ASN* 4.9 2.3 - - - +
473H GLU 5.0 1.1 - - - +
474H ASP* 3.4 42.8 - - + +
476H LYS* 4.7 2.6 - - + +
486H PRO* 4.3 0.8 - - - +
529H ASN* 3.6 13.9 + - - +
531H TYR* 3.2 26.0 + - - -
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Residues in contact with ASP 499 (chain G).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
498G ARG* 1.3 79.8 + - - +
500G TYR* 1.3 73.4 + - - +
502G ASP* 3.5 9.4 - - - -
503G GLY* 2.8 31.0 + - - -
505G VAL* 3.6 21.4 - - + +
507G VAL* 3.1 29.4 - - - +
433H THR* 5.8 0.4 - - - -
447H ALA 5.5 2.6 - - - +
448H LEU 5.2 2.3 - - - +
449H ASN* 3.5 25.5 - - - +
473H GLU* 3.6 29.6 - - + +
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Residues in contact with TYR 500 (chain G).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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420G ARG* 3.2 17.5 + - - -
421G TYR* 3.9 1.0 + - - -
458G ASN* 5.7 1.2 + - - -
461G LEU* 4.0 21.1 - - + +
497G LEU* 3.4 42.0 - - + +
499G ASP* 1.3 117.0 - - - +
501G LEU* 1.3 60.0 + - + +
507G VAL* 3.8 26.0 - - + -
508G ASN 3.5 21.6 + - - -
509G LEU* 4.7 3.1 - - + -
521G PHE* 3.3 52.8 - + + +
449H ASN* 4.7 13.4 - - + +
452H LEU* 5.3 5.9 - - + +
460H GLU* 4.2 15.9 + - - -
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Residues in contact with LEU 501 (chain G).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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418G LYS* 4.4 6.0 + - - -
420G ARG* 3.3 13.5 + - - +
421G TYR* 3.8 44.6 - - + -
472G PHE* 4.9 8.7 - - + -
494G LEU* 3.3 34.3 - - + +
495G ASP* 5.4 0.2 - - - -
497G LEU* 3.1 14.9 + - + +
498G ARG* 2.9 9.9 + - - +
500G TYR* 1.3 79.8 - - + +
502G ASP* 1.3 64.9 + - - +
521G PHE* 6.2 0.4 - - + -
526G VAL* 5.1 3.4 - - + -
537G LEU* 3.8 22.2 - - + -
540G ARG* 3.9 30.1 - - + +
541G PHE* 5.5 3.6 - - + -
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Residues in contact with ASP 502 (chain G).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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417G PRO* 3.4 7.4 - - - +
418G LYS* 3.1 46.6 + - + +
420G ARG* 3.2 14.5 + - - -
498G ARG 2.7 22.5 + - - +
499G ASP* 3.2 7.6 + - - +
501G LEU* 1.3 77.0 - - - +
503G GLY* 1.3 60.8 + - - +
504G SER* 3.4 12.8 - - - +
540G ARG* 2.8 36.3 + - - -
433H THR* 4.3 15.6 - - + +
473H GLU* 4.7 0.2 - - - +
474H ASP* 4.2 4.5 - - - +
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Residues in contact with GLY 503 (chain G).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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417G PRO* 5.0 1.1 - - - -
420G ARG* 3.2 21.0 - - - +
499G ASP 2.8 18.3 + - - -
500G TYR 4.8 0.2 - - - -
502G ASP* 1.3 74.0 - - - +
504G SER* 1.3 58.7 + - - +
505G VAL 3.2 8.7 - - - -
520G ILE* 3.1 28.5 - - - +
521G PHE 4.7 2.2 - - - -
567H ARG* 3.9 15.6 + - - -
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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