Contacts of the helix formed by residues 456 - 462 (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 ARG 456 (chain G).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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452G LEU* 4.9 8.7 - - + -
453G PRO* 3.6 7.2 + - + +
455G ASP* 1.3 98.3 - - + +
457G LEU* 1.3 64.3 + - - +
458G ASN 3.1 2.9 - - - -
459G PHE* 3.0 35.6 + - + +
460G GLU* 3.1 14.0 + - - +
456H ARG* 3.6 12.4 - - - +
454L LEU 4.4 5.8 - - - +
455L ASP* 3.0 38.4 + - - +
456L ARG* 3.7 16.0 - - - +
458L ASN* 3.3 40.7 + - - +
459L PHE* 3.5 26.9 - - - -
510L GLU* 5.1 2.2 - - - -
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Residues in contact with LEU 457 (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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449G ASN 4.4 7.9 - - - +
450G VAL* 3.8 31.4 - - + -
452G LEU* 5.2 1.3 - - - +
453G PRO 3.5 6.1 + - - +
454G LEU* 3.6 30.7 - - + +
455G ASP 3.1 0.8 - - - -
456G ARG* 1.3 78.2 - - - +
458G ASN* 1.3 54.5 + - - +
460G GLU* 3.2 4.4 + - + +
461G LEU* 2.7 67.3 + - + +
493G ASN* 3.3 24.9 - - + +
497G LEU* 4.3 16.8 - - + -
452H LEU* 4.6 11.0 - - + -
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Residues in contact with ASN 458 (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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454G LEU 3.6 12.1 - - - +
455G ASP 3.9 1.3 - - - +
456G ARG 3.1 0.4 - - - -
457G LEU* 1.3 79.0 - - - +
459G PHE* 1.3 65.4 + - + +
460G GLU 3.1 1.0 + - - -
461G LEU* 4.3 6.1 - - - +
462G GLY* 3.5 15.1 + - - -
500G TYR* 5.7 1.8 + - - -
510G GLU* 3.5 40.2 + - + +
452H LEU* 3.4 29.2 - - - +
456H ARG* 3.6 30.9 + - + +
459H PHE* 5.7 1.6 - - - +
460H GLU* 4.4 9.7 + - - +
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Residues in contact with PHE 459 (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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455G ASP 4.0 11.4 - - - -
456G ARG* 3.0 25.1 + - + +
458G ASN* 1.3 77.3 - - + +
460G GLU* 1.3 57.8 + - - +
462G GLY* 4.4 3.6 + - - -
463G VAL* 4.6 6.4 - - - +
510G GLU* 3.7 25.1 - - - +
513G HIS* 5.6 13.9 - + - -
456H ARG* 3.7 31.9 - - - -
459H PHE* 6.3 3.4 - + - -
458L ASN* 5.5 1.6 - - - +
459L PHE* 6.2 4.0 - + - -
508L ASN* 5.7 1.2 - - - +
510L GLU* 4.3 23.4 - - - +
513L HIS 6.1 0.7 - - - -
515L ASN* 4.8 11.6 + - - +
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Residues in contact with GLU 460 (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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448G LEU* 3.2 18.0 - - + +
449G ASN* 2.7 51.1 + - - +
452G LEU* 4.4 16.2 - - - +
456G ARG* 3.1 13.2 + - - +
457G LEU* 3.8 6.1 - - + +
459G PHE* 1.3 80.4 - - - +
461G LEU* 1.3 59.7 + - + +
462G GLY 3.0 4.9 - - - -
463G VAL* 3.0 25.1 - - - +
458L ASN* 4.5 8.3 + - - +
500L TYR* 3.8 17.4 + - - -
508L ASN* 3.3 30.1 - - + +
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Residues in contact with LEU 461 (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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448G LEU* 3.9 14.4 - - + -
449G ASN 6.0 0.4 - - - +
450G VAL* 5.1 0.2 - - + -
457G LEU* 2.7 57.8 + - + +
458G ASN* 4.5 5.8 - - - +
460G GLU* 1.3 71.6 - - - +
462G GLY* 1.3 56.1 + - - +
463G VAL 3.0 9.9 + - - -
464G ALA 3.5 8.8 + - - -
472G PHE* 4.4 13.5 - - + -
497G LEU* 3.9 20.9 - - + -
500G TYR* 4.0 18.8 - - + +
509G LEU* 3.3 22.3 - - + +
521G PHE* 3.8 32.2 - - + -
452H LEU* 5.8 3.1 - - + -
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Residues in contact with GLY 462 (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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458G ASN 3.5 9.6 + - - -
459G PHE 5.1 2.2 - - - -
460G GLU* 3.0 2.6 - - - +
461G LEU* 1.3 77.2 - - - +
463G VAL* 1.3 60.3 + - - +
464G ALA 3.5 0.7 - - - -
465G ILE* 3.1 33.0 - - - +
509G LEU* 4.3 6.1 - - - -
510G GLU 3.7 23.5 - - - +
511G LYS* 4.5 7.8 - - - +
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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