Contacts of the helix formed by residues 449 - 454 (chain B) in PDB entry 3E0D
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 449 (chain B).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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386B ARG* 4.1 4.3 - - - +
426B SER 4.9 0.3 - - - +
429B GLY* 3.4 15.1 - - - -
447B GLY 3.7 12.3 - - - +
448B LEU* 1.3 80.6 - - - +
450B PHE* 1.3 64.7 + - - +
451B GLU* 4.0 14.4 - - + +
452B ARG* 3.3 20.6 + - + +
453B PHE 3.8 2.4 + - - -
745B GLU* 3.7 37.4 + - + +
748B MET* 5.4 5.4 - - + -
749B GLN* 4.4 30.7 - - + +
759B LEU* 5.0 15.0 - - + -
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Residues in contact with PHE 450 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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386B ARG* 3.5 9.0 - - - +
389B TYR* 4.6 6.1 - + + -
390B GLU* 3.2 69.8 - - + +
393B VAL* 3.8 30.7 - - + -
394B ILE* 4.0 11.0 - - + -
429B GLY 3.1 12.3 + - - -
430B SER* 3.6 17.7 - - - -
449B LEU* 1.3 72.1 - - - +
451B GLU* 1.3 77.8 + - + +
453B PHE* 3.0 22.0 + + - +
454B LEU* 3.0 50.0 + - + +
456B PRO* 5.2 1.3 - - + -
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Residues in contact with GLU 451 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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386B ARG* 5.5 3.6 + - - -
389B TYR* 3.5 25.2 + - - +
449B LEU* 3.2 13.6 - - + +
450B PHE* 1.3 91.5 + - + +
452B ARG* 1.3 60.2 + - - +
453B PHE 3.3 0.2 - - - -
454B LEU 3.4 20.5 - - - +
455B ASN* 3.6 14.2 + - - +
456B PRO* 4.1 23.6 - - + -
748B MET* 4.6 6.9 - - + +
759B LEU* 4.7 36.1 - - + +
760B GLY* 5.0 0.6 - - - +
763B ASP* 4.8 1.7 - - - -
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Residues in contact with ARG 452 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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426B SER* 3.5 21.2 + - - -
449B LEU* 3.3 19.6 + - + +
450B PHE 3.1 1.0 - - - -
451B GLU* 1.3 78.3 - - - +
453B PHE* 1.3 61.4 + - - +
455B ASN 5.3 0.2 - - - -
744B GLN* 2.7 29.0 + - - +
745B GLU* 3.9 11.4 - - + +
748B MET* 3.1 33.0 - - + +
763B ASP* 3.7 11.5 + - - +
766B ARG* 2.0 58.7 - - - +
767B ARG* 4.5 5.9 + - - +
814B ASN* 3.5 25.5 - - - +
1222B DTP 4.2 16.1 + - - -
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Residues in contact with PHE 453 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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403B PHE* 3.4 35.9 - + - -
426B SER* 3.3 36.4 + - - +
427B ALA* 3.7 21.5 - - - -
430B SER* 3.7 24.9 - - - +
433B ALA* 5.4 1.3 - - + -
449B LEU 3.8 3.0 + - - +
450B PHE* 3.0 15.3 + + - +
452B ARG* 1.3 81.0 - - - +
454B LEU* 1.3 76.3 + - + +
455B ASN 4.0 1.1 + - - -
462B PRO* 3.9 27.0 - - + +
463B ASP 4.1 7.6 - - - -
464B ILE* 3.8 25.6 - - + -
767B ARG* 5.2 4.2 + - - -
1222B DTP 5.5 0.9 + - - -
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Residues in contact with LEU 454 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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393B VAL* 5.3 0.7 - - + -
394B ILE* 3.5 39.5 - - + +
397B MET* 4.0 24.7 - - + -
399B PHE* 4.3 7.2 - - + -
403B PHE* 4.5 12.3 - - + -
450B PHE* 3.0 34.4 + - + +
451B GLU* 3.4 8.9 - - - +
453B PHE* 1.3 83.4 - - + +
455B ASN* 1.3 60.1 + - - +
456B PRO* 3.1 13.2 - - - +
460B SER 3.9 20.9 - - - +
462B PRO* 4.2 19.7 - - + -
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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