Contacts of the helix formed by residues 456 - 462 (chain C) 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 ARG 456 (chain C).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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454B LEU 4.6 5.6 - - - +
455B ASP* 3.4 32.9 + - - +
456B ARG* 3.7 22.2 - - - +
458B ASN* 3.7 37.6 + - - +
459B PHE* 3.6 25.1 - - - -
510B GLU* 5.4 2.0 - - - -
452C LEU* 4.9 9.2 - - + -
453C PRO* 3.6 6.6 + - + +
455C ASP* 1.3 90.2 - - + +
457C LEU* 1.3 63.0 + - - +
458C ASN 3.1 3.1 - - - -
459C PHE* 3.0 36.6 + - + +
460C GLU* 3.1 15.0 + - - +
456D ARG* 3.4 23.4 - - - +
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Residues in contact with LEU 457 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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449C ASN 4.4 8.3 - - - +
450C VAL* 3.8 31.4 - - + -
452C LEU* 5.2 1.1 - - - +
453C PRO 3.5 6.5 + - - +
454C LEU* 3.6 31.2 - - + +
455C ASP 3.1 0.6 - - - -
456C ARG* 1.3 78.5 - - - +
458C ASN* 1.3 54.2 + - - +
460C GLU* 3.2 4.2 + - + +
461C LEU* 2.8 66.2 + - + +
493C ASN* 3.3 24.9 - - + +
497C LEU* 4.3 17.5 - - + -
452D LEU* 4.5 10.5 - - + -
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Residues in contact with ASN 458 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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454C LEU 3.6 10.9 - - - +
455C ASP 3.9 1.7 + - - +
456C ARG 3.1 0.6 - - - -
457C LEU* 1.3 78.3 - - - +
459C PHE* 1.3 65.9 + - + +
460C GLU 3.1 1.1 + - - -
461C LEU* 4.3 6.1 - - - +
462C GLY* 3.5 15.4 + - - -
500C TYR* 5.8 1.4 + - - -
510C GLU* 3.5 40.8 + - + +
452D LEU* 3.0 35.2 - - - +
456D ARG* 3.8 26.2 + - + +
459D PHE* 5.8 1.2 - - - +
460D GLU* 4.1 12.3 + - - +
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Residues in contact with PHE 459 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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458B ASN* 5.8 1.1 - - - +
459B PHE* 6.4 1.8 - + - -
510B GLU* 4.6 19.2 - - - +
515B ASN* 5.2 9.5 + - - +
455C ASP 4.0 11.0 - - - -
456C ARG* 3.0 24.9 + - + +
458C ASN* 1.3 76.5 - - + +
460C GLU* 1.3 58.0 + - - +
462C GLY* 4.4 3.2 + - - -
463C VAL* 4.6 7.3 - - - +
510C GLU* 3.7 24.1 - - + +
513C HIS* 5.5 13.7 - + - -
456D ARG* 3.5 34.1 - - - -
459D PHE* 6.2 4.9 - + - -
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Residues in contact with GLU 460 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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458B ASN* 4.4 15.2 + - - +
500B TYR* 4.2 13.8 + - - -
508B ASN* 3.7 27.5 + - + +
448C LEU* 3.2 18.8 - - + +
449C ASN* 2.7 51.1 + - - +
452C LEU* 4.4 11.0 - - - +
456C ARG 3.1 13.1 + - - +
457C LEU* 3.9 6.3 - - + +
459C PHE* 1.3 79.1 - - - +
461C LEU* 1.3 58.9 + - + +
462C GLY 3.0 4.9 - - - -
463C VAL* 3.0 25.1 - - - +
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Residues in contact with LEU 461 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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448C LEU* 3.9 14.6 - - + -
449C ASN 6.0 0.2 - - - +
450C VAL* 5.1 0.2 - - + -
457C LEU* 2.8 59.0 + - + +
458C ASN* 4.5 5.4 - - - +
460C GLU* 1.3 73.9 - - + +
462C GLY* 1.3 56.6 + - - +
463C VAL 3.0 10.3 + - - -
464C ALA* 3.5 8.4 + - - +
472C PHE* 4.4 13.0 - - + -
497C LEU* 3.9 20.4 - - + -
500C TYR* 4.0 19.7 - - + +
509C LEU* 3.3 21.5 - - + +
521C PHE* 3.8 31.9 - - + -
452D LEU* 5.8 3.1 - - + -
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Residues in contact with GLY 462 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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458C ASN 3.5 9.6 + - - -
459C PHE 5.1 2.2 - - - -
460C GLU* 3.0 3.0 - - - +
461C LEU* 1.3 77.2 - - - +
463C VAL* 1.3 60.8 + - - +
464C ALA 3.5 0.4 - - - -
465C ILE* 3.0 33.2 - - - +
509C LEU* 4.3 6.1 - - - -
510C GLU 3.7 23.3 - - - +
511C LYS* 4.5 8.0 - - - +
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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