Contacts of the helix formed by residues 477 - 488 (chain D) 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 D).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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551C THR 4.2 5.3 + - - -
469D VAL* 3.9 3.8 - - - +
470D LYS* 4.0 19.3 - - - -
471D VAL* 4.8 1.3 - - - -
475D GLY 3.0 0.8 + - - -
476D ARG* 1.3 73.0 - - - +
478D LEU* 1.3 65.8 + - - +
479D ALA* 3.1 4.1 - - - +
480D LEU* 3.0 15.7 + - - +
481D VAL* 3.0 24.5 + - - +
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Residues in contact with LEU 478 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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482C VAL* 5.9 2.5 - - + -
539C THR* 4.4 11.0 - - + +
542C GLN* 3.9 35.9 - - + +
543C LEU* 3.2 35.8 - - + +
550C LEU* 3.9 14.1 - - + -
471D VAL* 3.9 22.4 - - + -
474D ALA 4.6 0.2 - - - +
475D GLY* 2.8 36.1 + - - +
477D GLY* 1.3 78.4 - - - +
479D ALA* 1.3 50.5 + - - +
481D VAL* 2.9 12.7 + - + +
482D TRP* 2.6 36.2 + - - +
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Residues in contact with ALA 479 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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550C LEU* 3.7 29.2 - - + +
551C THR 4.1 11.0 - - - +
475D GLY 4.2 1.6 + - - -
477D GLY 4.8 1.3 - - - +
478D LEU* 1.3 76.7 - - - +
480D LEU* 1.3 64.6 + - - +
482D TRP* 3.5 6.1 + - - +
483D ARG* 3.1 22.7 + - - +
501D VAL* 4.9 5.4 - - + +
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Residues in contact with LEU 480 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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469D VAL* 3.5 33.2 - - + -
477D GLY* 3.0 14.3 + - - +
479D ALA* 1.3 76.9 - - - +
481D VAL* 1.3 64.6 + - - +
483D ARG* 3.1 40.7 + - - +
484D ARG* 2.8 32.8 + - - +
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Residues in contact with VAL 481 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
478C GLN 4.8 0.7 - - - +
481C GLN* 3.4 39.2 - - + +
482C VAL* 4.6 9.4 - - + +
543C LEU* 4.4 10.1 - - + -
469D VAL* 3.8 13.2 - - + +
471D VAL* 5.8 1.6 - - + -
477D GLY 3.0 13.3 + - - +
478D LEU* 2.9 18.9 + - + +
480D LEU* 1.3 75.8 - - - +
482D TRP* 1.3 58.3 + - - +
483D ARG 3.0 0.2 + - - -
484D ARG* 3.1 2.7 + - - +
485D GLN* 2.7 62.3 + - + +
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Residues in contact with TRP 482 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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543C LEU* 5.0 3.1 - - + -
544C TYR* 6.1 1.8 - + - -
550C LEU* 4.2 11.2 - - + -
478D LEU 2.6 17.0 + - - +
479D ALA* 3.9 5.6 - - - +
480D LEU 3.3 0.2 - - - -
481D VAL* 1.3 75.6 - - - +
483D ARG* 1.3 62.0 + - - +
485D GLN* 3.4 35.8 - - - +
486D ILE* 3.3 34.1 - - + +
500D VAL* 6.0 2.9 - - + -
501D VAL* 3.9 26.5 - - + +
504D TYR* 2.8 27.0 + - + -
505D PRO 3.9 15.7 - - - -
506D SER* 3.6 5.0 - - - +
507D PRO* 3.6 48.7 - - + -
510D LEU* 4.4 24.5 - - + -
557D MET* 4.9 16.2 - - + -
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Residues in contact with ARG 483 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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479D ALA 3.1 13.5 + - - +
480D LEU* 3.1 37.8 + - - +
481D VAL 3.0 0.6 - - - -
482D TRP* 1.3 78.9 - - - +
484D ARG* 1.3 72.0 + - - +
486D ILE* 3.1 25.3 + - - +
487D GLN* 3.0 31.7 + - - +
494D LEU* 3.1 28.6 - - - +
497D ALA* 4.0 21.2 - - + +
498D SER* 3.5 25.1 - - - +
501D VAL* 3.6 19.7 - - + +
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Residues in contact with ARG 484 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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481C GLN* 3.3 26.3 + - + +
466D ALA* 3.6 29.3 + - - +
467D GLY 2.5 30.1 + - - -
469D VAL* 3.4 27.2 - - + +
480D LEU* 2.8 24.3 + - - +
481D VAL* 4.0 3.8 - - - +
483D ARG* 1.3 88.4 - - - +
485D GLN* 1.3 64.9 + - - +
486D ILE 3.0 2.5 - - - -
487D GLN* 3.1 35.3 + - + +
488D GLN* 3.1 23.7 + - - +
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Residues in contact with GLN 485 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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478C GLN* 3.7 41.3 + - + +
479C LEU* 5.7 0.2 - - - +
481C GLN* 4.5 3.1 - - + +
543C LEU* 3.5 26.2 - - - +
544C TYR* 3.6 21.0 + - - -
481D VAL* 2.7 38.7 + - + +
482D TRP* 3.4 30.4 - - + +
484D ARG* 1.3 77.4 - - - +
486D ILE* 1.3 59.6 + - + +
488D GLN* 3.1 31.2 - - - +
489D LEU* 3.7 7.4 - - - +
557D MET* 6.0 1.2 - - - +
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Residues in contact with ILE 486 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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482D TRP* 3.3 40.2 - - + +
483D ARG 3.1 11.4 + - - +
484D ARG 3.0 0.8 - - - -
485D GLN* 1.3 79.3 - - + +
487D GLN* 1.3 62.1 + - - +
488D GLN 3.1 2.7 + - - -
489D LEU* 3.6 17.5 + - - +
492D VAL* 3.3 16.0 - - + +
496D MET 5.5 0.2 - - - -
497D ALA* 3.9 23.8 - - + +
500D VAL* 4.4 26.0 - - + -
501D VAL* 3.6 20.9 - - + -
510D LEU* 6.3 1.1 - - + -
553D ILE* 5.3 14.4 - - + -
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Residues in contact with GLN 487 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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483D ARG* 3.0 28.3 + - - +
484D ARG* 3.1 24.9 + - + +
486D ILE* 1.3 78.6 - - - +
488D GLN* 1.3 65.1 + - - +
489D LEU 3.1 12.7 + - - +
492D VAL* 3.5 21.6 + - - +
493D SER* 3.7 2.8 - - - +
494D LEU* 3.4 29.7 - - - +
497D ALA* 3.7 19.1 - - + -
52X A 4.3 5.2 + - - +
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Residues in contact with GLN 488 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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474C VAL* 4.3 8.4 - - + +
477C ARG* 3.4 67.0 + - + +
478C GLN* 4.5 5.8 - - + +
481C GLN* 3.2 33.5 + - - +
465D TRP* 4.7 6.6 - - - -
484D ARG* 3.1 21.0 + - - +
485D GLN* 3.1 23.6 - - - +
486D ILE 3.1 0.8 - - - -
487D GLN* 1.3 80.4 - - - +
489D LEU* 1.3 64.2 + - + +
490D ASN* 4.0 3.8 + - - +
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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