Contacts of the helix formed by residues 475 - 484 (chain E) in PDB entry 4E3C
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 MET 475 (chain E).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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477D GLN* 2.9 17.5 - - - +
472E MET* 3.0 38.3 + - + +
473E ALA* 4.3 3.4 - - - +
474E SER* 1.3 81.2 + - - +
476E SER* 1.3 66.3 + - - +
477E GLN 3.2 0.2 - - - -
478E GLN* 2.8 39.8 + - - +
479E LEU* 2.9 38.5 + - + +
633E VAL 5.3 0.2 - - - +
636E MET* 3.8 15.7 - - + -
637E ASN* 3.7 34.1 - - - +
641E LYS* 5.3 2.0 - - - +
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Residues in contact with SER 476 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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473E ALA 3.2 13.2 + - - -
474E SER* 2.8 0.4 - - - -
475E MET* 1.3 82.6 - - - +
477E GLN* 1.3 56.9 + - - +
479E LEU* 3.1 3.1 + - - +
480E LYS* 2.9 31.4 + - - +
526E ARG 3.1 15.8 + - - -
530E VAL* 3.8 13.2 - - - +
636E MET* 2.7 45.3 - - - +
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Residues in contact with GLN 477 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
474D SER* 3.3 25.6 + - - +
475D MET* 5.3 4.2 + - - -
477D GLN* 3.3 20.9 - - + +
478D GLN* 4.7 2.5 + - + +
474E SER* 3.0 33.2 + - - +
476E SER* 1.3 77.6 + - - +
478E GLN* 1.3 59.6 + - - +
480E LYS* 4.6 4.3 - - - +
481E ALA* 3.0 26.6 + - - +
527E GLU* 6.5 0.9 - - - -
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Residues in contact with GLN 478 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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477D GLN* 3.1 51.1 + - + +
478D GLN* 3.3 18.4 - - - +
481D ALA* 3.0 19.4 - - + +
475E MET* 2.8 31.7 + - - +
477E GLN* 1.3 81.3 - - - +
479E LEU* 1.3 75.2 + - - +
481E ALA* 3.3 2.4 + - - +
482E LYS* 2.8 36.4 + - - +
641E LYS* 5.0 4.5 + - - -
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Residues in contact with LEU 479 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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475E MET* 2.9 57.8 + - + +
476E SER* 3.6 9.2 - - - +
478E GLN* 1.3 95.2 - - - +
480E LYS* 1.3 64.8 + - - +
482E LYS* 3.2 14.2 + - + +
483E LEU* 3.2 20.4 + - - +
636E MET* 5.1 12.6 - - + +
637E ASN* 5.2 0.4 - - - +
640E GLU* 4.2 19.1 - - + +
641E LYS* 3.6 44.9 - - + +
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Residues in contact with LYS 480 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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476E SER 2.9 15.0 + - - +
477E GLN* 4.6 4.3 - - - +
479E LEU* 1.3 76.0 - - - +
481E ALA* 1.3 63.5 + - - +
483E LEU* 3.3 44.8 + - + +
484E ASP* 3.6 12.2 + - - +
522E GLU* 4.9 11.7 + - - -
524E CYS 4.6 1.0 + - - -
525E GLY* 3.8 30.2 - - - +
526E ARG 4.1 14.1 - - - +
527E GLU* 3.1 53.6 - - + +
640E GLU* 4.1 9.1 - - - +
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Residues in contact with ALA 481 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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478D GLN* 3.5 30.5 - - + +
482D LYS* 4.9 5.4 - - - +
477E GLN 3.0 21.2 + - - +
478E GLN 3.3 5.6 + - - +
479E LEU 3.2 0.4 - - - -
480E LYS* 1.3 78.2 - - - +
482E LYS* 1.3 64.7 + - - +
484E ASP* 3.2 27.6 + - - +
485E PHE 3.9 1.4 + - - -
527E GLU* 6.1 0.2 - - - -
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Residues in contact with LYS 482 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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478D GLN 4.0 1.1 - - - +
481D ALA* 3.1 46.7 + - + +
482D LYS* 3.8 30.7 - - + +
484D ASP* 4.7 7.9 + - - +
485D PHE* 5.2 9.4 - - - +
478E GLN* 2.8 23.2 + - + +
479E LEU* 3.2 15.6 + - + +
481E ALA* 1.3 78.2 - - - +
483E LEU* 1.3 52.9 + - - +
485E PHE* 2.8 45.7 + - + +
641E LYS* 3.9 23.8 - - - +
645E ARG* 6.3 0.4 - - - +
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Residues in contact with LEU 483 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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479E LEU 3.2 6.2 + - - +
480E LYS* 3.3 37.0 - - - +
481E ALA 3.3 0.2 - - - -
482E LYS* 1.3 78.2 - - - +
484E ASP* 1.3 72.6 + - - +
485E PHE* 3.2 1.1 - - - -
486E PHE* 2.9 29.8 - - - +
487E LYS* 4.1 5.1 + - + +
521E VAL* 3.5 27.8 - - + +
522E GLU* 4.6 11.7 - - - +
524E CYS 3.4 16.2 - - - +
640E GLU* 2.8 33.4 - - + +
644E VAL* 4.8 12.3 - - + -
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Residues in contact with ASP 484 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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480E LYS* 3.6 18.0 + - - +
481E ALA* 3.2 17.0 + - - +
482E LYS 2.9 0.8 + - - -
483E LEU* 1.3 86.0 - - - +
485E PHE* 1.3 65.4 + - - +
486E PHE 2.9 2.0 - - - -
487E LYS* 2.9 27.0 + - - +
488E THR* 3.8 6.6 + - - -
522E GLU* 5.5 1.0 - - - +
527E GLU* 5.3 3.5 - - - +
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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