Contacts of the helix formed by residues 477 - 488 (chain F) in PDB entry 4P0S
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 GLY 477 (chain F).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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469F VAL* 3.8 2.3 - - - +
470F LYS* 3.9 19.7 - - - -
471F VAL* 4.7 1.6 - - - -
475F GLY 3.0 0.8 + - - -
476F ARG* 1.3 73.5 - - - +
478F LEU* 1.3 66.6 + - - +
479F ALA* 3.1 7.0 - - - +
480F LEU* 3.0 15.3 + - - +
481F VAL* 2.9 25.6 + - - +
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Residues in contact with LEU 478 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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481E GLN* 5.6 1.3 - - + +
543E LEU* 3.9 19.5 - - + -
550E LEU* 3.7 34.1 - - + -
471F VAL* 3.7 25.1 - - + -
474F ALA 4.5 2.9 - - - +
475F GLY* 2.8 35.2 + - - +
476F ARG 3.4 0.2 - - - -
477F GLY* 1.3 78.2 - - - +
479F ALA* 1.3 51.1 + - - +
481F VAL* 3.0 16.0 + - + +
482F TRP* 2.7 37.3 + - - +
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Residues in contact with ALA 479 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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475F GLY 4.1 2.2 + - - +
477F GLY 3.1 4.2 - - - +
478F LEU* 1.3 76.2 - - - +
480F LEU* 1.3 62.8 + - - +
482F TRP* 3.6 7.6 + - - +
483F ARG* 3.2 21.7 + - - +
501F VAL* 5.0 4.9 - - - +
505F PRO 6.1 0.7 - - - -
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Residues in contact with LEU 480 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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469F VAL* 3.5 33.0 - - + -
477F GLY* 3.0 14.0 + - - +
479F ALA* 1.3 77.0 - - - +
481F VAL* 1.3 58.7 + - - +
483F ARG* 3.1 40.4 + - - +
484F ARG* 2.9 40.2 + - - +
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Residues in contact with VAL 481 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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478E GLN 5.3 0.4 - - - +
481E GLN* 3.5 47.1 - - + +
469F VAL* 3.7 19.7 - - + +
471F VAL* 5.7 0.7 - - + -
477F GLY 2.9 19.6 + - - +
478F LEU* 3.2 19.1 - - + +
480F LEU* 1.3 76.6 - - - +
482F TRP* 1.3 54.8 + - - +
484F ARG* 3.2 4.2 + - - +
485F GLN* 2.7 62.0 + - + +
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Residues in contact with TRP 482 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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478F LEU 2.7 18.9 + - - +
479F ALA* 4.1 7.0 - - - +
481F VAL* 1.3 74.3 - - - +
483F ARG* 1.3 59.9 + - - +
485F GLN* 3.4 28.7 - - - +
486F ILE* 3.3 37.8 + - + +
500F VAL* 6.0 2.2 - - + -
501F VAL* 4.0 25.9 - - + +
504F TYR* 2.8 27.3 + - + -
505F PRO 3.9 15.9 - - - -
506F SER* 3.6 4.4 - - - +
507F PRO* 3.5 50.5 - - + -
510F LEU* 4.4 24.5 - - + -
557F MET* 4.8 18.6 - - + -
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Residues in contact with ARG 483 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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479F ALA 3.2 14.1 + - - +
480F LEU* 3.1 36.8 - - - +
481F VAL 3.1 0.4 - - - -
482F TRP* 1.3 77.0 - - - +
484F ARG* 1.3 72.2 + - - +
486F ILE* 3.2 24.4 + - - +
487F GLN* 3.1 30.4 + - - +
494F LEU* 3.2 27.7 - - - +
497F ALA* 3.9 21.3 - - + +
498F SER* 3.7 23.1 - - - +
501F VAL* 3.6 19.2 - - + +
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Residues in contact with ARG 484 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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481E GLN* 4.5 4.5 + - - +
465F TRP* 6.0 1.2 - - - -
466F ALA* 3.6 29.1 + - - +
467F GLY 2.5 32.3 + - - -
468F GLY* 4.2 1.6 - - - -
469F VAL* 3.3 28.2 - - + +
480F LEU* 2.9 25.3 + - - +
481F VAL* 4.0 4.3 - - - +
483F ARG* 1.3 88.9 - - - +
485F GLN* 1.3 63.8 + - - +
486F ILE 3.1 1.8 - - - -
487F GLN* 3.2 33.6 + - + +
488F GLN* 3.1 28.5 + - - +
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Residues in contact with GLN 485 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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474E VAL* 5.6 1.7 - - - +
478E GLN* 3.6 45.3 + - + +
481E GLN* 5.5 1.3 - - + -
481F VAL* 2.7 48.4 + - + +
482F TRP* 3.4 34.4 - - + +
483F ARG 3.2 0.2 - - - -
484F ARG* 1.3 71.2 - - - +
486F ILE* 1.4 58.9 - - + +
488F GLN* 3.2 30.7 - - - +
489F LEU* 3.7 8.7 - - - +
507F PRO* 5.5 0.3 - - - +
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Residues in contact with ILE 486 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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482F TRP* 3.3 38.8 - - + +
483F ARG 3.2 10.5 - - - +
484F ARG 3.1 0.2 - - - -
485F GLN* 1.4 74.8 - - + +
487F GLN* 1.3 61.7 + - - +
488F GLN 3.2 1.1 + - - -
489F LEU* 3.7 18.4 + - + +
492F VAL* 3.3 16.4 - - + +
497F ALA* 3.9 24.2 - - + +
500F VAL* 4.5 27.4 - - + -
501F VAL* 3.7 17.5 - - + -
510F LEU* 6.3 1.3 - - + -
549F LEU* 6.6 0.2 - - + -
553F ILE* 5.1 16.4 - - + -
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Residues in contact with GLN 487 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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483F ARG* 3.1 28.4 + - - +
484F ARG* 3.2 22.9 + - + +
486F ILE* 1.3 78.1 - - - +
488F GLN* 1.3 60.8 + - - +
489F LEU 3.1 17.5 - - - +
492F VAL* 3.6 23.4 + - - +
493F SER* 3.7 2.6 - - - +
494F LEU* 3.4 30.3 - - - +
497F ALA* 3.7 19.1 - - + -
53T T 5.6 2.4 + - - -
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Residues in contact with GLN 488 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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473E GLU* 5.6 1.7 - - - +
474E VAL* 4.8 13.4 - - + +
477E ARG* 2.0 56.9 + - + +
465F TRP* 5.1 2.0 - - - -
484F ARG* 3.1 26.9 + - - +
485F GLN* 3.2 23.8 - - - +
486F ILE 3.2 1.0 - - - -
487F GLN* 1.3 80.0 - - - +
489F LEU* 1.3 62.9 + - + +
490F ASN* 4.1 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