Contacts of the helix formed by residues 653 - 661 (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 GLU 653 (chain E).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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510E LEU* 3.2 47.2 - - + +
514E TRP* 3.3 47.5 + - + -
649E LYS* 2.8 27.4 + - + +
650E ARG* 4.1 13.5 + - - -
651E GLN 3.7 0.6 - - - +
652E LYS* 1.3 88.1 - - - +
654E LEU* 1.3 53.9 + - - +
655E TRP 3.3 2.0 - - - -
656E ASN* 2.6 25.3 - - - +
657E LEU* 3.0 16.5 - - - +
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Residues in contact with LEU 654 (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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496D LYS* 4.3 0.7 + - - -
651D GLN 5.6 2.9 - - - +
654D LEU* 3.3 56.6 - - + +
658D LEU* 3.8 18.8 - - + +
493E ASP* 6.0 1.3 - - - +
496E LYS* 5.1 12.6 - - - +
514E TRP* 3.6 30.5 - - + -
651E GLN* 4.6 10.1 - - - +
652E LYS 2.8 0.4 + - - -
653E GLU* 1.3 76.7 - - - +
655E TRP* 1.3 62.3 + - - +
656E ASN 3.2 3.0 + - - -
657E LEU* 3.8 19.3 - - + -
658E LEU* 3.5 23.6 + - - +
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Residues in contact with TRP 655 (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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492D ILE* 5.1 5.6 - - + -
495D GLU* 3.2 40.2 - - + -
496D LYS* 2.9 57.3 + - + +
499D GLU* 3.0 37.3 + - + -
500D GLN* 5.8 1.8 - - + -
652E LYS* 2.6 45.1 + - + +
654E LEU* 1.3 80.1 - - - +
656E ASN* 1.3 57.0 + - + +
658E LEU* 4.4 2.9 - - - +
659E LYS* 4.4 16.3 + - - +
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Residues in contact with ASN 656 (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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509E LYS* 6.0 1.8 - - - +
510E LEU* 4.3 18.1 - - - +
652E LYS 4.1 0.6 + - - +
653E GLU* 2.6 34.7 - - - +
655E TRP* 1.3 79.2 - - - +
657E LEU* 1.3 66.5 + - - +
658E LEU 3.0 4.9 - - - -
659E LYS* 2.9 6.3 + - - +
660E ILE* 2.6 49.2 + - + +
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Residues in contact with LEU 657 (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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658D LEU* 3.3 45.6 - - + +
507E SER* 6.4 2.7 - - - -
510E LEU* 5.2 7.6 - - + -
514E TRP* 4.4 12.6 - - + -
653E GLU* 3.0 27.3 + - + +
654E LEU* 3.8 15.0 + - + -
656E ASN* 1.3 105.4 + - - +
658E LEU* 1.3 57.3 + - - +
659E LYS 3.3 0.4 - - - -
660E ILE* 3.5 10.3 - - + -
661E ALA* 3.4 23.6 - - - +
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Residues in contact with LEU 658 (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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496D LYS* 4.0 20.4 - - - +
500D GLN* 3.7 18.8 - - + +
504D GLY 4.9 2.7 - - - +
505D ILE* 5.0 5.6 - - + -
654D LEU* 4.2 8.7 - - + -
657D LEU* 2.8 69.8 - - + +
658D LEU* 4.0 7.0 - - + +
661D ALA* 4.4 8.7 - - + -
654E LEU 3.5 14.6 + - - +
655E TRP 4.9 3.6 - - - +
656E ASN 3.0 1.4 - - - -
657E LEU* 1.3 79.8 - - - +
659E LYS* 1.3 58.2 + - - +
661E ALA* 5.5 0.2 - - - -
662E CYS* 3.0 21.2 - - - -
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Residues in contact with LYS 659 (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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499D GLU* 3.8 27.3 + - - -
500D GLN* 3.5 35.0 - - - +
502D GLU 5.8 0.2 - - - +
503D PHE 4.8 8.5 - - - +
504D GLY* 5.0 2.5 - - - -
655E TRP* 4.4 15.3 - - - +
656E ASN* 2.9 6.3 + - - +
658E LEU* 1.3 78.7 - - - +
660E ILE* 1.3 64.0 + - - +
661E ALA 3.4 1.3 - - - -
662E CYS* 3.8 7.5 - - + +
663E SER* 3.2 28.8 + - - +
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Residues in contact with ILE 660 (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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656E ASN* 2.6 36.3 + - + +
657E LEU* 3.5 20.0 - - + +
659E LYS* 1.3 73.1 - - - +
661E ALA* 1.3 64.5 + - + +
662E CYS 3.2 2.9 + - - -
663E SER* 4.1 8.8 + - - -
664E LYS* 3.7 17.0 - - - +
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Residues in contact with ALA 661 (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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658D LEU* 5.1 1.1 - - + -
661D ALA* 3.0 19.7 - - + +
662D CYS* 4.0 24.4 - - - -
665D VAL* 3.5 16.0 - - - +
657E LEU 3.4 18.5 + - - +
659E LYS 3.4 0.2 - - - -
660E ILE* 1.3 83.0 - - + +
662E CYS* 1.3 61.7 + - - +
664E LYS* 4.4 15.0 - - - +
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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