Contacts of the helix formed by residues 497 - 503 (chain H) 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 H).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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450H VAL* 5.0 6.7 - - + -
457H LEU* 4.3 13.5 - - + -
461H LEU* 3.9 35.4 - - + -
472H PHE* 5.3 6.7 - - + -
493H ASN 3.2 20.9 - - - +
494H LEU* 3.2 11.9 + - + +
495H ASP 2.9 1.0 - - - -
496H ASN* 1.3 85.8 - - + +
498H ARG* 1.3 65.8 + - - +
499H ASP* 3.5 2.9 - - - -
500H TYR* 3.3 44.1 + - + -
501H LEU* 3.1 26.3 + - + +
521H PHE* 6.2 0.7 - - + -
452I LEU* 3.9 14.8 - - + -
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Residues in contact with ARG 498 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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494H LEU 5.0 0.7 - - - -
495H ASP* 2.8 49.2 + - - +
496H ASN 3.8 0.8 - - - -
497H LEU* 1.3 72.0 - - - +
499H ASP* 1.3 67.0 + - - +
501H LEU* 2.9 18.1 + - - +
502H ASP* 2.7 24.2 + - - +
536H THR* 2.9 35.7 + - - +
537H LEU* 5.7 0.4 - - - +
540H ARG* 3.2 36.9 - - - +
451I ASN* 4.8 3.1 - - - +
473I GLU 5.0 0.4 - - - +
474I ASP* 3.6 44.7 + - + +
476I LYS* 4.9 3.4 - - + +
486I PRO* 4.1 1.4 - - - +
529I ASN* 3.8 10.9 + - - -
531I TYR* 3.2 27.0 + - - -
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Residues in contact with ASP 499 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
498H ARG* 1.3 78.1 + - - +
500H TYR* 1.3 74.7 + - - +
502H ASP* 3.5 10.1 - - - -
503H GLY* 2.8 31.7 + - - -
504H SER 4.6 0.5 + - - -
505H VAL* 3.6 19.1 - - + +
507H VAL* 3.1 29.4 - - - +
433I THR* 6.1 0.2 - - - -
447I ALA 5.5 1.6 - - - +
448I LEU 5.1 2.6 - - - +
449I ASN* 3.3 28.6 - - - +
473I GLU* 3.5 31.2 - - + +
474I ASP* 4.8 0.2 + - - -
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Residues in contact with TYR 500 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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420H ARG* 3.2 17.8 + - - -
421H TYR* 3.9 1.0 + - - -
458H ASN* 5.7 1.0 + - - -
461H LEU* 4.0 20.7 - - + +
497H LEU* 3.4 42.8 - - + +
498H ARG 3.1 0.4 - - - -
499H ASP* 1.3 115.1 - - - +
501H LEU* 1.3 58.7 + - + +
507H VAL* 3.8 24.5 - - + -
508H ASN 3.5 21.7 + - - -
509H LEU* 4.7 2.9 - - + -
521H PHE* 3.3 52.3 - + + +
449I ASN* 4.5 12.8 - - + -
452I LEU* 5.0 5.6 - - + +
460I GLU* 4.0 16.0 + - - -
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Residues in contact with LEU 501 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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418H LYS* 4.4 6.3 + - - -
420H ARG* 3.3 13.3 + - - +
421H TYR* 3.8 45.0 - - + -
472H PHE* 4.9 8.5 - - + -
494H LEU* 3.2 32.8 - - + +
495H ASP* 5.4 0.2 - - - -
497H LEU* 3.1 15.9 + - + +
498H ARG* 2.9 9.7 + - - +
500H TYR* 1.3 78.9 - - + +
502H ASP* 1.3 64.2 + - - +
521H PHE* 6.2 0.4 - - + -
526H VAL* 5.1 3.1 - - + -
537H LEU* 3.8 22.2 - - + -
540H ARG* 3.9 31.7 - - + +
541H PHE* 5.5 4.3 - - + -
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Residues in contact with ASP 502 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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417H PRO* 3.4 7.6 - - - +
418H LYS* 3.1 47.4 + - + +
420H ARG* 3.2 14.5 + - - -
498H ARG 2.7 22.0 + - - +
499H ASP* 3.1 7.7 + - - +
501H LEU* 1.3 77.6 - - - +
503H GLY* 1.3 61.9 + - - +
504H SER* 3.4 12.6 - - - +
540H ARG* 2.8 36.3 + - - -
433I THR* 4.4 14.8 + - + +
473I GLU* 4.7 0.2 - - - +
474I ASP* 4.0 5.0 - - - +
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Residues in contact with GLY 503 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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417H PRO* 4.9 2.0 - - - -
420H ARG* 3.2 20.6 - - - +
499H ASP 2.8 19.0 + - - -
500H TYR 4.8 0.4 - - - -
502H ASP* 1.3 74.7 - - - +
504H SER* 1.3 59.0 + - - +
505H VAL 3.2 8.5 - - - -
520H ILE* 3.1 28.7 - - - +
521H PHE 4.7 2.2 - - - -
567I ARG* 4.2 14.3 + - - -
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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