Contacts of the helix formed by residues 477 - 488 (chain H) 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 H).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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551G THR 5.2 1.0 + - - -
469H VAL* 3.9 3.4 - - - +
470H LYS* 4.0 18.8 - - - -
471H VAL* 4.8 1.6 - - - -
475H GLY 3.0 0.8 + - - -
476H ARG* 1.3 74.1 - - - +
478H LEU* 1.3 66.5 + - - +
479H ALA* 3.0 6.2 - - - +
480H LEU* 3.0 23.5 + - - +
481H VAL* 3.0 17.3 + - - +
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Residues in contact with LEU 478 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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482G VAL* 5.2 3.6 - - + -
539G THR* 3.7 28.7 - - + +
542G GLN* 3.9 29.6 - - + +
543G LEU* 3.5 31.7 - - + +
550G LEU* 4.8 9.4 - - + -
471H VAL* 3.7 12.8 - - + -
474H ALA 4.5 0.9 - - - +
475H GLY* 2.8 35.9 + - - +
477H GLY* 1.3 79.8 - - - +
479H ALA* 1.3 50.6 + - - +
481H VAL* 2.9 14.6 + - + +
482H TRP* 2.6 36.8 + - - +
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Residues in contact with ALA 479 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
550G LEU* 4.3 13.3 - - + +
551G THR 4.0 26.4 - - - +
475H GLY 4.1 1.6 + - - -
477H GLY 4.8 2.2 - - - +
478H LEU* 1.3 76.4 - - - +
480H LEU* 1.3 63.9 + - - +
482H TRP* 3.5 6.9 + - - +
483H ARG* 3.1 22.7 + - - +
501H VAL* 5.0 4.9 - - - +
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Residues in contact with LEU 480 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
469H VAL* 3.4 32.8 - - + -
477H GLY* 3.0 14.9 + - - +
479H ALA* 1.3 79.0 - - - +
481H VAL* 1.3 58.6 + - - +
483H ARG* 3.1 41.2 + - - +
484H ARG* 2.8 39.2 + - - +
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Residues in contact with VAL 481 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
478G GLN 4.7 0.4 - - - +
481G GLN* 2.9 45.3 - - + +
482G VAL* 3.9 17.3 - - + +
543G LEU* 4.9 8.3 - - + -
469H VAL* 3.8 9.6 - - + +
471H VAL* 5.8 1.1 - - + -
477H GLY 3.0 17.5 + - - +
478H LEU* 2.9 18.7 + - + +
480H LEU* 1.3 77.1 - - - +
482H TRP* 1.3 55.7 + - - +
484H ARG* 3.1 2.1 + - - +
485H GLN* 2.7 58.3 + - + +
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Residues in contact with TRP 482 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
543G LEU* 4.5 3.6 - - + -
544G TYR* 5.9 1.3 - + - -
550G LEU* 4.2 10.8 - - + -
478H LEU 2.6 18.3 + - - +
479H ALA* 4.0 5.4 - - - +
480H LEU 3.3 0.2 - - - -
481H VAL* 1.3 74.6 - - - +
483H ARG* 1.3 60.6 + - - +
485H GLN* 3.2 35.6 - - + +
486H ILE* 3.2 35.1 - - + +
500H VAL* 6.1 3.1 - - + -
501H VAL* 4.1 25.4 - - + +
504H TYR* 2.9 25.9 + - + -
505H PRO 3.9 16.4 - - - -
506H SER* 3.6 5.0 - - - +
507H PRO* 3.6 47.6 - - + -
510H LEU* 4.5 23.3 - - + -
557H MET* 4.8 18.4 - - + -
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Residues in contact with ARG 483 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
479H ALA 3.1 14.1 + - - +
480H LEU* 3.1 38.1 - - - +
481H VAL 3.1 0.4 - - - -
482H TRP* 1.3 78.1 - - - +
484H ARG* 1.3 73.1 + - - +
486H ILE* 3.1 26.0 + - - +
487H GLN* 3.1 30.5 + - - -
494H LEU* 3.2 25.3 - - - +
497H ALA* 3.9 21.3 - - - +
498H SER* 3.7 23.3 - - - +
501H VAL* 3.5 20.2 - - + +
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Residues in contact with ARG 484 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
481G GLN* 3.5 20.5 + - + +
465H TRP* 5.9 0.8 - - - -
466H ALA* 3.6 30.0 + - - +
467H GLY 2.5 29.5 + - - -
468H GLY* 4.3 1.4 - - - -
469H VAL* 3.3 28.4 - - - +
480H LEU* 2.8 24.2 + - - +
481H VAL* 4.0 3.4 - - - +
483H ARG* 1.3 88.3 - - - +
485H GLN* 1.3 65.2 + - - +
486H ILE 3.0 2.0 - - - -
487H GLN* 3.1 33.7 + - + +
488H GLN* 3.2 20.6 + - - +
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Residues in contact with GLN 485 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
478G GLN* 2.9 51.6 + - + +
479G LEU* 4.9 1.2 - - - +
481G GLN* 3.7 10.1 - - + +
482G VAL* 5.9 1.4 - - - +
543G LEU* 3.8 16.9 - - - +
544G TYR* 3.9 14.4 + - - -
481H VAL* 2.7 45.4 + - + +
482H TRP* 3.2 35.8 - - + +
483H ARG 3.2 0.2 - - - -
484H ARG* 1.3 72.0 - - - +
486H ILE* 1.4 58.6 + - + +
488H GLN* 3.2 23.9 - - - +
489H LEU* 3.7 8.8 - - - +
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Residues in contact with ILE 486 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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482H TRP* 3.2 41.5 - - + +
483H ARG 3.1 10.5 - - - +
484H ARG 3.0 0.2 - - - -
485H GLN* 1.4 77.7 - - + +
487H GLN* 1.3 60.9 + - - +
488H GLN 3.2 1.0 + - - -
489H LEU* 3.8 12.6 + - - +
492H VAL* 3.3 19.5 - - + +
496H MET 5.4 0.2 - - - -
497H ALA* 3.8 25.1 - - + +
500H VAL* 4.5 25.6 - - + -
501H VAL* 3.6 18.6 - - + -
510H LEU* 6.4 0.9 - - + -
553H ILE* 5.4 13.5 - - + -
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Residues in contact with GLN 487 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
483H ARG* 3.1 27.8 + - - +
484H ARG* 3.1 23.2 + - + +
486H ILE* 1.3 76.7 - - - +
488H GLN* 1.3 60.8 + - - +
489H LEU 3.1 17.9 - - - +
492H VAL* 3.6 22.6 + - - +
493H SER* 3.6 2.4 - - - +
494H LEU* 3.3 31.6 - - - +
497H ALA* 3.6 19.7 - - + -
52P A 4.7 5.0 + - - -
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Residues in contact with GLN 488 (chain H).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
474G VAL* 5.3 1.9 - - - +
477G ARG* 3.3 70.5 + - + +
478G GLN* 4.7 1.6 - - + +
481G GLN* 2.7 46.1 + - + +
465H TRP* 4.6 11.6 - - - -
484H ARG* 3.2 13.7 + - - +
485H GLN* 3.2 20.6 - - - +
486H ILE 3.2 0.6 - - - -
487H GLN* 1.3 79.0 - - - +
489H LEU* 1.3 64.6 + - + +
490H ASN* 4.1 3.1 + - - +
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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