Contacts of the helix formed by residues 475 - 484 (chain A) 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 A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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472A MET* 3.0 33.3 + - + +
473A ALA* 4.3 1.1 - - - -
474A SER* 1.3 78.8 + - - +
476A SER* 1.3 59.0 + - - +
477A GLN* 3.2 0.7 - - - -
478A GLN* 2.8 47.9 + - - +
479A LEU* 2.8 39.4 + - + +
636A MET* 3.1 35.7 - - + -
637A ASN* 3.5 36.3 - - - +
641A LYS* 5.1 4.9 - - + +
478F GLN* 6.4 0.2 - - - -
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Residues in contact with SER 476 (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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473A ALA 3.2 16.5 + - - -
474A SER 2.8 0.4 - - - -
475A MET* 1.3 88.2 - - - +
477A GLN* 1.3 56.8 + - - +
479A LEU* 3.1 4.0 + - - +
480A LYS* 2.9 31.8 + - - +
526A ARG 2.8 27.4 + - - +
527A GLU* 4.5 4.0 + - - -
530A VAL* 4.0 11.0 - - - +
531A LYS 5.4 0.7 + - - -
636A MET* 3.5 18.7 - - - -
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Residues in contact with GLN 477 (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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474A SER* 3.0 38.2 + - - +
476A SER* 1.3 79.2 + - - +
478A GLN* 1.3 58.0 + - + +
480A LYS* 4.6 3.5 - - - +
481A ALA* 3.0 27.4 + - - +
527A GLU* 6.1 3.1 - - - -
474F SER* 5.5 2.8 + - - -
475F MET* 3.5 15.8 - - - +
477F GLN* 5.7 5.9 - - - +
478F GLN* 2.2 51.5 + - + +
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Residues in contact with GLN 478 (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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475A MET* 2.8 34.6 + - - +
477A GLN* 1.3 82.0 - - + +
479A LEU* 1.3 74.6 + - - +
481A ALA* 3.2 2.6 + - - +
482A LYS* 2.8 46.6 + - + +
641A LYS* 4.3 16.1 + - - +
478F GLN* 3.9 19.5 - - + +
481F ALA* 5.4 9.4 - - + +
482F LYS* 3.7 26.9 - - + +
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Residues in contact with LEU 479 (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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475A MET* 2.8 58.0 + - + +
476A SER* 3.1 9.4 + - - +
478A GLN* 1.3 97.9 - - - +
480A LYS* 1.3 61.7 + - - +
482A LYS* 3.3 21.1 + - + +
483A LEU 3.2 16.1 + - - -
636A MET* 4.7 5.8 - - + -
640A GLU* 3.0 53.8 - - + +
641A LYS* 4.1 17.9 - - + +
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Residues in contact with LYS 480 (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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476A SER 2.9 15.6 + - - +
477A GLN* 4.6 2.9 - - - +
479A LEU* 1.3 76.3 - - - +
481A ALA* 1.3 62.2 + - - +
483A LEU* 3.3 53.9 - - + +
484A ASP* 3.6 12.8 + - - +
522A GLU* 4.7 6.3 + - - -
525A GLY* 3.7 16.8 + - - +
526A ARG 4.9 1.8 - - - -
527A GLU* 2.9 68.2 - - + +
640A GLU* 4.4 3.4 - - - -
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Residues in contact with ALA 481 (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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477A GLN 3.0 21.9 + - - +
478A GLN 3.4 0.2 - - - +
479A LEU 3.2 0.2 - - - -
480A LYS* 1.3 78.0 - - - +
482A LYS* 1.3 65.4 + - - +
484A ASP* 3.1 27.0 + - - +
485A PHE* 3.9 1.9 + - - +
527A GLU* 5.9 0.2 - - - -
478F GLN* 3.9 6.7 - - - +
479F LEU* 5.7 0.7 - - + -
482F LYS* 2.6 39.7 + - + +
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Residues in contact with LYS 482 (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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478A GLN* 2.8 36.8 + - + +
479A LEU* 3.3 23.8 + - + +
481A ALA* 1.3 77.6 - - - +
483A LEU* 1.3 53.2 + - - +
484A ASP 3.0 0.2 - - - -
485A PHE* 2.7 49.4 + - + +
640A GLU 5.5 2.0 + - - -
641A LYS* 5.0 14.3 - - - +
644A VAL* 5.0 23.2 - - + +
645A ARG* 5.7 4.8 - - - +
482F LYS* 3.4 19.2 - - + +
485F PHE* 4.0 43.9 - - + +
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Residues in contact with LEU 483 (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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479A LEU 3.2 9.1 + - - +
480A LYS* 3.3 40.2 - - - +
482A LYS* 1.3 77.5 - - - +
484A ASP* 1.3 72.1 + - - +
485A PHE* 3.3 1.8 - - - -
486A PHE* 3.0 28.8 - - + +
487A LYS* 4.1 1.9 + - - +
521A VAL* 3.1 33.9 - - + +
522A GLU* 3.0 37.7 - - - +
524A CYS 3.7 14.8 - - - +
525A GLY* 4.3 6.3 - - - -
640A GLU* 4.2 4.5 - - - +
644A VAL* 6.3 2.9 - - + -
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Residues in contact with ASP 484 (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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480A LYS* 3.6 17.2 + - - +
481A ALA* 3.1 18.6 + - - +
482A LYS 2.9 1.2 + - - -
483A LEU* 1.3 87.0 - - - +
485A PHE* 1.3 62.4 + - - +
486A PHE 3.0 2.7 - - - -
487A LYS* 3.0 27.0 + - + +
488A THR* 3.8 6.9 + - - -
527A GLU* 5.4 1.9 - - - +
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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