Contacts of the helix formed by residues 508 - 518 (chain E) in PDB entry 4CYM
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 TYR 508 (chain E).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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471E ALA 3.8 9.0 - - - -
472E VAL 3.4 7.9 + - - -
473E CYS 3.2 28.8 + - - -
474E GLY* 3.4 20.9 - - - -
503E ALA* 3.2 10.6 + - + +
506E LYS* 3.2 54.7 + - + -
507E GLY* 1.3 77.9 - - - +
509E GLN* 1.3 65.1 + - - +
510E SER* 3.1 3.9 + - - -
511E VAL* 3.1 14.7 + - + +
512E THR* 2.9 23.5 + - - -
544E CYS* 3.7 0.2 - - - -
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Residues in contact with GLN 509 (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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58B ILE 4.7 2.6 + - - -
59B GLY* 4.4 4.3 - - - -
60B VAL* 2.9 57.4 + - - +
62B PHE* 4.1 4.2 - - - -
95B TYR* 4.8 3.5 + - - -
507E GLY 3.3 6.9 + - - -
508E TYR* 1.3 72.1 - - - +
510E SER* 1.3 65.0 + - - +
512E THR* 3.2 2.4 + - - -
513E LEU* 2.9 35.8 + - + +
543E ASP* 3.0 57.7 + - - +
544E CYS* 3.5 9.4 - - - -
547E ALA* 4.1 6.5 - - + -
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Residues in contact with SER 510 (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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91B MET* 3.2 41.1 - - - +
95B TYR* 5.4 4.3 - - - -
476E ALA* 4.7 10.0 - - - +
508E TYR* 3.1 2.1 + - - -
509E GLN* 1.3 80.1 + - - +
511E VAL* 1.3 65.2 + - - +
513E LEU* 3.5 2.4 + - - -
514E LEU* 3.0 18.9 + - - +
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Residues in contact with VAL 511 (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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471E ALA* 4.3 9.2 - - + +
474E GLY* 4.0 34.3 - - - +
476E ALA* 4.8 7.2 - - + -
479E ILE* 3.7 28.0 - - + -
503E ALA* 3.5 20.4 - - + -
508E TYR* 3.1 18.3 + - + +
510E SER* 1.3 76.1 - - - +
512E THR* 1.3 68.7 + - - +
514E LEU* 3.0 8.4 + - - +
515E LEU* 2.8 32.4 + - + +
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Residues in contact with THR 512 (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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500E LEU* 3.8 15.3 - - + +
503E ALA* 3.6 15.5 - - - +
504E CYS* 3.7 24.4 - - - -
508E TYR 2.9 14.1 + - - -
509E GLN* 3.4 12.1 - - - -
511E VAL* 1.3 77.8 - - - +
513E LEU* 1.3 62.5 + - - +
515E LEU* 3.4 2.8 + - - +
516E LEU* 3.1 38.4 + - + +
544E CYS* 3.6 16.0 - - - +
547E ALA* 4.3 13.9 - - + -
548E LEU* 4.4 5.4 - - + -
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Residues in contact with LEU 513 (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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60B VAL* 3.9 10.3 - - + -
62B PHE* 4.9 1.3 - - + -
80B TRP* 4.8 10.5 - - + -
91B MET* 4.2 7.4 - - + -
94B VAL* 3.9 10.8 - - + +
95B TYR* 3.9 23.8 - - + -
509E GLN* 2.9 42.3 + - - +
510E SER* 3.8 5.2 - - - +
512E THR* 1.3 73.1 - - - +
514E LEU* 1.3 60.7 + - - +
516E LEU* 3.1 8.9 + - + +
517E HIS* 2.7 29.8 + - - +
547E ALA* 3.6 27.1 - - + +
551E TYR* 3.9 25.6 - - + -
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Residues in contact with LEU 514 (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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91B MET* 4.1 10.9 - - + +
93B ARG* 4.0 16.2 - - - +
94B VAL* 4.0 14.6 - - + -
476E ALA* 3.7 33.4 - - + +
479E ILE* 3.8 17.7 - - + -
480E ASP* 3.7 20.2 - - - +
510E SER 3.0 14.4 + - - +
511E VAL* 3.0 9.1 + - - +
513E LEU* 1.3 75.5 - - - +
515E LEU* 1.3 58.4 + - + +
517E HIS* 3.1 8.9 - - + +
518E TYR* 2.9 60.2 + - + -
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Residues in contact with LEU 515 (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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467E LEU* 4.7 12.6 - - + -
471E ALA* 4.6 1.8 - - + -
479E ILE* 4.4 24.9 - - + -
489E VAL* 4.4 10.7 - - + +
499E PRO* 3.8 20.0 - - + +
500E LEU* 3.6 39.3 - - + +
503E ALA* 4.2 1.6 - - + -
511E VAL* 2.8 38.0 + - + +
512E THR 3.6 3.8 - - - +
514E LEU* 1.3 73.1 - - - +
516E LEU* 1.3 65.1 + - - +
518E TYR* 2.9 17.7 + - + +
519E LYS 3.1 0.3 + - - -
520E ALA* 3.0 29.0 + - + +
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Residues in contact with LEU 516 (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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500E LEU* 4.0 20.2 - - + -
512E THR* 3.1 34.2 + - + +
513E LEU* 3.6 13.7 - - + +
515E LEU* 1.3 74.4 - - - +
517E HIS* 1.3 59.6 + - - +
519E LYS* 2.9 20.4 + - - +
520E ALA 4.0 20.7 + - - +
522E ALA* 4.5 9.2 - - + -
547E ALA 4.2 6.3 - - - +
548E LEU* 4.2 13.7 - - + -
551E TYR* 3.5 50.2 + - + -
552E ASP* 4.5 10.1 - - - +
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Residues in contact with HIS 517 (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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93B ARG* 4.6 15.1 + - + -
94B VAL* 3.7 45.3 + - + +
97B LYS* 4.0 45.8 + - + +
513E LEU 2.7 13.2 + - - +
514E LEU* 3.1 16.8 - - + +
516E LEU* 1.3 78.5 - - - +
518E TYR* 1.3 79.2 - + - +
519E LYS* 3.4 9.2 + - - +
551E TYR* 3.2 13.3 + - - +
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Residues in contact with TYR 518 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
93B ARG* 3.5 9.4 + - - -
479E ILE* 4.2 9.4 - - + -
480E ASP* 2.5 33.2 + - - +
483E VAL* 3.6 36.1 - - + -
489E VAL* 3.6 27.7 - - + +
514E LEU* 2.9 49.8 + - + -
515E LEU* 2.9 14.5 + - + +
517E HIS* 1.3 87.5 - + - +
519E LYS* 1.3 72.1 + - - +
520E ALA 3.4 0.7 + - - -
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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