Contacts of the helix formed by residues 497 - 503 (chain A) 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 A).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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450A VAL* 5.0 6.1 - - + -
457A LEU* 4.3 13.5 - - + -
461A LEU* 3.9 35.4 - - + -
472A PHE* 5.3 6.5 - - + -
493A ASN 3.2 20.9 - - - +
494A LEU* 3.2 11.8 + - + +
495A ASP 2.9 1.2 - - - -
496A ASN* 1.3 86.4 - - - +
498A ARG* 1.3 65.0 + - - +
499A ASP* 3.5 3.1 - - - -
500A TYR* 3.6 42.0 - - + -
501A LEU* 3.1 26.2 + - + +
521A PHE* 6.2 0.7 - - + -
452B LEU* 4.0 14.8 - - + -
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Residues in contact with ARG 498 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
494A LEU 5.0 0.7 - - - -
495A ASP* 2.8 48.4 + - - +
496A ASN 3.8 0.8 - - - -
497A LEU* 1.3 73.0 - - - +
499A ASP* 1.3 67.3 + - - +
501A LEU* 2.9 18.2 + - - +
502A ASP* 2.7 24.5 + - - +
536A THR* 2.9 35.4 + - - +
537A LEU* 5.3 0.6 - - - +
540A ARG* 3.2 36.5 - - - +
451B ASN* 4.9 1.7 - - - +
473B GLU 5.0 0.7 - - - +
474B ASP* 3.2 44.7 + - + +
476B LYS* 5.2 2.4 - - + +
486B PRO* 4.3 0.6 - - - +
529B ASN* 3.3 15.2 + - - +
531B TYR* 3.1 24.6 + - - -
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Residues in contact with ASP 499 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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498A ARG* 1.3 78.2 + - - +
500A TYR* 1.3 73.8 + - - +
502A ASP* 3.5 9.4 - - - -
503A GLY* 2.8 31.0 + - - -
505A VAL* 3.6 21.1 - - + +
507A VAL* 3.1 29.1 - - - +
433B THR* 5.7 0.2 - - - -
447B ALA 5.5 1.7 - - - +
448B LEU 5.1 2.9 - - - +
449B ASN* 3.5 25.5 - - - +
473B GLU* 3.4 32.1 - - + +
474B ASP* 4.6 0.2 + - - -
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Residues in contact with TYR 500 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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420A ARG* 3.2 17.8 + - - -
421A TYR* 3.9 1.0 + - - -
458A ASN* 5.8 0.9 + - - -
461A LEU* 4.0 21.3 - - + +
497A LEU* 3.4 42.4 - - + +
498A ARG 3.1 0.2 - - - -
499A ASP* 1.3 115.4 - - - +
501A LEU* 1.3 58.4 + - + +
507A VAL* 3.8 25.8 - - + -
508A ASN 3.5 21.4 + - - -
509A LEU* 4.7 2.9 - - + -
521A PHE* 3.3 52.3 - + + +
449B ASN* 4.5 13.9 - - + +
452B LEU* 5.3 5.4 - - + +
460B GLU* 4.2 15.9 + - - -
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Residues in contact with LEU 501 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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418A LYS* 4.4 6.2 + - - -
420A ARG* 3.3 13.5 + - - +
421A TYR* 3.8 46.5 - - + -
472A PHE* 4.9 8.3 - - + -
494A LEU* 3.3 33.0 - - + +
495A ASP* 5.4 0.2 - - - -
497A LEU* 3.1 15.3 + - + +
498A ARG* 2.9 9.5 + - - +
500A TYR* 1.3 80.3 - - + +
502A ASP* 1.3 64.1 + - - +
521A PHE* 6.2 0.2 - - + -
526A VAL* 5.1 2.9 - - + -
537A LEU* 3.8 21.8 - - + -
540A ARG* 3.9 31.5 - - + +
541A PHE* 5.5 3.6 - - + -
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Residues in contact with ASP 502 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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417A PRO* 3.4 8.2 - - - +
418A LYS* 3.1 46.6 + - + +
420A ARG* 3.2 14.7 + - - -
498A ARG 2.7 22.7 + - - +
499A ASP* 3.5 6.9 + - - +
501A LEU* 1.3 76.5 - - - +
503A GLY* 1.3 61.7 + - - +
504A SER* 3.4 8.5 - - - +
540A ARG* 2.8 34.8 + - - -
433B THR* 4.1 23.3 - - + +
474B ASP* 4.1 3.5 - - - +
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Residues in contact with GLY 503 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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417A PRO* 5.0 0.9 - - - -
420A ARG* 3.2 20.6 - - - +
499A ASP 2.8 18.5 + - - -
500A TYR 4.8 0.2 - - - -
502A ASP* 1.3 74.7 - - - +
504A SER* 1.3 59.3 + - - +
505A VAL 3.2 8.3 - - - -
520A ILE* 3.1 28.8 - - - +
521A PHE* 4.7 2.2 - - - -
567B ARG* 3.9 15.7 + - - -
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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