Contacts of the helix formed by residues 407 - 415 (chain A) in PDB entry 4EEP
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 SER 407 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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389A LYS 2.5 29.5 + - - -
391A PHE* 3.1 40.6 + - - -
405A PHE* 4.3 7.4 - - - -
406A ALA* 1.3 75.9 - - - +
408A ASP* 1.3 64.9 + - - +
409A SER 3.8 1.5 + - - -
410A PHE* 3.1 19.4 + - - +
411A LEU* 3.4 11.3 + - - +
418A ARG* 3.8 1.6 - - - +
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Residues in contact with ASP 408 (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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407A SER* 1.3 72.5 - - - +
409A SER* 1.3 62.5 - - - +
411A LEU* 3.3 19.8 + - + +
412A GLU* 3.3 11.3 + - - +
418A ARG* 2.9 28.6 + - - +
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Residues in contact with SER 409 (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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389A LYS* 3.6 34.8 + - - +
390A ASN* 3.1 23.3 - - - +
407A SER* 3.1 1.4 + - - -
408A ASP* 1.3 77.0 - - - +
410A PHE* 1.3 64.5 + - - +
412A GLU* 3.1 18.1 + - - +
413A LEU* 3.0 19.2 + - - +
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Residues in contact with PHE 410 (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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390A ASN* 3.5 8.9 + - + -
391A PHE 3.8 9.6 - - - +
392A VAL* 3.7 26.2 - - + -
403A ILE* 4.9 0.2 - - + -
406A ALA* 4.1 4.9 - - + -
407A SER* 3.1 22.1 + - - +
409A SER* 1.3 76.5 - - - +
411A LEU* 1.3 61.0 + - - +
413A LEU* 3.3 4.0 + - + +
414A THR* 2.9 55.1 + - + +
421A ILE* 3.4 36.6 - - + -
426A CYS* 4.0 8.7 - - - -
428A PHE* 4.8 3.8 - + - -
429A LEU* 3.9 17.7 - - + -
489A GLN* 3.3 42.2 - - + -
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Residues in contact with LEU 411 (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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406A ALA* 4.2 15.5 - - + -
407A SER 3.5 9.4 - - - +
408A ASP* 3.3 12.8 - - - +
410A PHE* 1.3 78.8 - - - +
412A GLU* 1.3 55.8 + - - +
414A THR* 4.0 1.8 - - - -
415A GLU* 2.9 27.4 + - - -
416A TYR 3.3 21.0 - - - +
417A SER* 4.7 1.8 - - - -
418A ARG* 3.6 56.3 - - + +
421A ILE* 3.6 24.5 - - + -
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Residues in contact with GLU 412 (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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390A ASN* 5.6 0.2 - - - +
408A ASP 3.3 8.1 + - - +
409A SER* 3.1 18.3 + - - +
411A LEU* 1.3 78.5 - - - +
413A LEU* 1.3 66.6 + - - +
414A THR 3.4 0.3 + - - -
415A GLU* 3.6 12.2 + - - +
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Residues in contact with LEU 413 (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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390A ASN* 3.7 28.3 - - + +
409A SER 3.0 12.8 + - - +
410A PHE* 3.3 8.0 + - + +
412A GLU* 1.3 80.0 + - - +
414A THR* 1.3 74.2 + - + +
415A GLU* 4.5 1.6 - - - +
429A LEU* 6.3 0.2 - - + -
460A THR* 3.6 16.3 - - - +
466A PHE* 4.1 22.4 - - + -
489A GLN* 3.7 27.8 - - + +
490A LEU 4.9 0.4 - - - +
491A ASP* 3.7 35.9 - - + +
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Residues in contact with THR 414 (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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410A PHE* 2.9 54.2 + - + +
411A LEU* 3.7 1.2 + - - -
413A LEU* 1.3 88.9 - - + +
415A GLU* 1.3 69.8 + - - +
416A TYR* 3.2 29.3 + - - +
429A LEU* 3.7 20.2 - - + -
460A THR* 3.4 8.4 - - - +
461A LYS 2.9 21.7 + - - -
466A PHE* 5.0 4.0 - - + -
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Residues in contact with GLU 415 (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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411A LEU 2.9 11.8 + - - -
412A GLU 3.6 10.0 + - - +
413A LEU 3.5 2.6 - - - +
414A THR* 1.3 78.3 - - - +
416A TYR* 1.3 62.7 + - - +
420A GLU* 4.3 0.9 - - - +
460A THR* 3.2 26.8 + - - +
461A LYS* 3.6 19.3 + - + +
462A SER* 2.6 35.3 + - - -
464A LYS* 3.6 19.0 + - - +
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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