Contacts of the helix formed by residues 474 - 489 (chain B) in PDB entry 4HPF
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 CYS 474 (chain B).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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449B ILE* 3.6 19.3 - - + +
450B LEU 3.9 10.1 - - - -
451B GLN 4.4 0.2 - - - -
452B SER* 3.8 26.7 - - - -
455B LYS* 4.0 19.2 - - - +
472B ILE 4.3 0.6 + - - -
473B ILE* 1.3 78.9 - - - +
475B PHE* 1.3 65.7 + - - +
476B ALA* 4.1 2.9 - - - -
477B GLU* 2.9 41.0 + - + +
478B LEU* 3.1 17.1 + - - +
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Residues in contact with PHE 475 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
448B GLN* 3.1 36.2 - - + +
449B ILE 4.6 1.8 + - - -
473B ILE* 3.8 22.1 - - + -
474B CYS* 1.3 71.0 - - - +
476B ALA* 1.3 55.5 + - - +
478B LEU* 3.0 6.5 + - - +
479B LYS* 2.7 58.0 + - + +
906B LEU* 3.1 36.3 - - + -
907B ASP* 4.5 18.8 - - - -
909B LEU* 3.9 15.7 - - + -
910B LEU* 5.1 8.7 - - + -
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Residues in contact with ALA 476 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
450B LEU 3.9 21.0 + - - +
451B GLN* 5.6 0.9 - - - -
474B CYS* 3.2 3.3 - - - -
475B PHE* 1.3 77.7 - - - +
477B GLU* 1.3 62.9 + - - +
479B LYS* 3.8 11.2 - - - +
480B LEU* 3.2 31.5 + - + +
729B MET* 6.2 0.2 - - - -
730B GLY* 4.9 10.8 - - - +
733B ASN* 3.8 13.9 + - - +
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Residues in contact with GLU 477 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
452B SER* 4.5 4.6 - - - -
455B LYS* 3.2 40.9 + - - +
474B CYS* 2.9 24.5 + - - +
476B ALA* 1.3 80.8 - - - +
478B LEU* 1.3 70.2 + - - +
481B GLY* 3.3 19.8 + - - -
733B ASN* 3.4 33.3 - - + +
924B GLN* 3.9 12.3 + - - -
928B THR* 4.1 23.5 - - + +
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Residues in contact with LEU 478 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
473B ILE* 5.2 2.7 - - + -
474B CYS 3.6 14.6 - - - +
475B PHE* 3.0 6.2 + - - +
477B GLU* 1.3 95.1 - - - +
479B LYS* 1.3 66.1 + - - +
480B LEU 3.3 0.4 - - - -
481B GLY* 3.0 8.7 + - - -
482B PHE* 3.0 28.2 + - + -
906B LEU* 4.1 13.9 - - + -
909B LEU* 3.3 34.5 - - + -
920B LEU* 5.4 7.6 - - + -
923B LEU* 4.4 17.7 - - + -
924B GLN* 4.7 18.4 - - + +
927B VAL* 3.7 6.6 - - + +
928B THR* 4.4 12.1 - - + -
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Residues in contact with LYS 479 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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475B PHE* 2.7 48.6 + - + +
476B ALA* 3.8 8.6 - - - +
478B LEU* 1.3 72.9 - - - +
480B LEU* 1.3 61.2 + - - +
481B GLY 3.5 0.2 + - - -
482B PHE* 3.7 0.7 + - - -
483B ILE* 3.6 25.4 + - - +
864B GLU* 4.6 17.7 - - - +
866B LYS* 6.3 2.5 - - - -
901B PHE* 3.8 14.6 - - + -
903B GLY* 4.0 24.2 - - - +
906B LEU* 3.5 24.5 - - + -
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Residues in contact with LEU 480 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
476B ALA* 3.2 16.8 + - + +
479B LYS* 1.3 77.8 - - + +
481B GLY* 1.3 61.0 + - - +
483B ILE* 3.5 17.8 + - + +
484B ALA* 3.0 27.4 + - - +
729B MET* 5.1 7.4 - - + -
730B GLY 2.7 38.4 - - - +
731B LEU* 4.2 5.2 - - + -
733B ASN* 3.9 16.9 - - + +
734B PHE* 3.8 30.1 - - + +
800B LEU* 4.3 20.6 - - + -
864B GLU* 5.9 1.6 - - - +
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Residues in contact with GLY 481 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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477B GLU 3.3 10.2 + - - -
478B LEU 3.0 4.4 + - - -
480B LEU* 1.3 75.5 - - - +
482B PHE* 1.3 66.0 + - - +
484B ALA* 2.9 17.5 + - - +
485B GLN* 3.0 15.2 + - - +
733B ASN 4.3 5.4 + - - -
737B PRO* 4.6 1.8 - - - -
927B VAL* 3.2 31.2 - - - -
928B THR* 5.3 0.4 - - - -
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Residues in contact with PHE 482 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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478B LEU* 3.0 30.5 + - + -
479B LYS 4.0 1.6 - - - +
481B GLY* 1.3 73.9 - - - +
483B ILE* 1.3 63.1 + - - +
485B GLN* 3.3 6.9 + - - +
486B GLY 3.1 16.5 + - - -
493B CYS* 3.2 15.9 - - - +
496B LEU* 3.8 32.1 - - + -
497B THR* 3.7 26.7 - - - -
500B PHE* 4.3 3.6 - + - -
901B PHE* 3.6 29.4 - + + -
905B PHE* 3.8 25.1 - + - -
906B LEU* 4.2 13.2 - - + -
923B LEU* 3.5 26.2 - - + -
927B VAL* 3.5 19.8 - - + +
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Residues in contact with ILE 483 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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479B LYS 3.6 16.3 + - - +
480B LEU* 3.5 15.9 + - + +
481B GLY 3.1 0.4 - - - -
482B PHE* 1.3 76.3 - - - +
484B ALA* 1.3 68.2 + - - +
486B GLY* 3.0 12.3 + - - -
487B CYS* 3.1 10.8 + - - -
493B CYS* 4.3 0.9 - - - -
734B PHE* 3.9 20.4 - - + -
798B ALA* 4.2 7.4 - - + -
800B LEU* 4.1 22.4 - - + -
862B LEU* 3.9 21.9 - - + +
864B GLU* 4.1 36.3 - - + +
901B PHE* 3.9 20.2 - - + -
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Residues in contact with ALA 484 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
480B LEU 3.0 13.8 + - - +
481B GLY 2.9 9.7 + - - +
483B ILE* 1.3 74.7 - - - +
485B GLN* 1.3 54.7 + - - +
487B CYS* 2.7 27.5 + - - +
488B LEU 3.0 9.2 + - - -
734B PHE* 3.8 26.0 - - + +
737B PRO* 3.7 28.7 - - + -
738B LEU* 3.3 15.0 - - + +
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Residues in contact with GLN 485 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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481B GLY 3.0 5.7 + - - +
482B PHE 3.6 7.6 - - - +
483B ILE 3.2 0.2 - - - -
484B ALA* 1.3 79.0 - - - +
486B GLY* 1.3 56.6 + - - +
488B LEU* 3.1 23.0 + - - +
489B VAL* 2.9 30.7 + - - +
492B LEU* 3.6 24.9 - - + +
493B CYS 5.0 0.2 - - - +
496B LEU* 3.8 24.5 - - + -
737B PRO* 3.8 18.8 + - - +
743B TYR* 4.9 1.9 + - - -
926B LEU 3.6 18.4 + - - +
927B VAL* 3.0 29.8 + - - +
929B GLY* 4.8 4.8 - - - +
963B LEU* 5.5 2.8 + - - +
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Residues in contact with GLY 486 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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482B PHE 3.1 6.9 + - - -
483B ILE 3.0 10.1 + - - -
485B GLN* 1.3 76.4 - - - +
487B CYS* 1.3 61.1 + - - +
489B VAL 3.3 20.2 - - - +
490B PRO* 3.9 6.6 - - - +
491B GLY 4.7 1.7 + - - -
492B LEU 4.8 0.2 - - - -
493B CYS* 3.8 24.1 - - - +
796B MET* 4.1 12.2 - - - +
862B LEU* 4.3 8.7 - - - -
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Residues in contact with CYS 487 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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483B ILE* 3.1 16.9 + - - -
484B ALA 2.7 17.5 + - - +
486B GLY* 1.3 72.0 - - - +
488B LEU* 1.3 62.9 + - - +
490B PRO* 5.3 1.4 - - - +
716B ILE* 3.7 39.5 - - + +
734B PHE* 4.3 9.2 - - - -
738B LEU* 4.2 2.9 - - + -
749B LYS* 4.5 10.9 + - - +
796B MET* 3.9 31.8 - - + +
798B ALA* 4.1 23.1 - - - -
862B LEU* 4.8 2.9 - - - -
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Residues in contact with LEU 488 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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484B ALA 3.0 5.3 + - - -
485B GLN* 3.1 33.6 + - - +
487B CYS* 1.3 80.0 - - - +
489B VAL* 1.3 67.6 - - + +
490B PRO* 3.8 6.5 - - - +
716B ILE* 5.5 2.2 - - + -
737B PRO 3.7 21.1 - - - +
738B LEU* 3.4 32.1 - - + +
743B TYR* 3.5 43.3 - - + +
748B LEU* 6.5 0.2 - - + -
749B LYS* 5.1 13.0 + - + -
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Residues in contact with VAL 489 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
485B GLN 2.9 5.9 + - - +
486B GLY* 3.3 9.7 - - - +
488B LEU* 1.3 86.7 - - + +
490B PRO* 1.3 73.1 - - + +
491B GLY 3.2 0.7 + - - -
492B LEU* 3.0 38.6 + - + +
743B TYR* 4.8 4.0 - - - +
963B LEU 3.4 24.5 - - - +
964B GLY* 4.1 6.5 - - - -
965B LEU* 3.7 33.7 - - + +
1034B PHE* 4.1 7.2 - - + -
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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
------------------------------------------------------------
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