Contacts of the helix formed by residues 473 - 488 (chain C) in PDB entry 5HP1
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 THR 473 (chain C).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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446C ALA* 3.4 9.6 - - - -
451C LYS* 4.5 13.7 - - - +
472C THR* 1.3 83.9 + - - +
474C ASN* 1.3 68.2 + - - +
475C GLN* 3.6 6.1 + - - -
476C LYS* 3.2 20.1 + - + +
477C THR* 2.9 23.9 + - - +
19E G 3.4 38.3 + - - +
20E C 2.8 24.6 + - - +
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Residues in contact with ASN 474 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
445C ALA* 3.8 6.8 - - - +
446C ALA* 2.8 36.8 + - - +
473C THR* 1.3 72.3 - - - +
475C GLN* 1.3 67.1 + - + +
477C THR* 2.5 21.6 + - - -
478C GLU* 2.9 33.0 + - - +
17E T 5.2 0.8 + - - +
18E T 3.8 19.8 + - - +
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Residues in contact with GLN 475 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
473C THR* 3.1 4.8 + - - +
474C ASN* 1.3 81.8 - - + +
476C LYS* 1.3 63.5 + - - +
478C GLU* 3.3 11.6 + - - +
479C LEU* 3.0 26.2 + - - +
501C TYR* 3.5 43.4 - - + +
16E T 5.3 3.0 + - - +
17E T 4.3 22.4 + - - +
18E T 5.0 0.9 + - - -
19E G 3.2 48.6 + - - +
20E C 3.4 28.0 + - - +
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Residues in contact with LYS 476 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
451C LYS* 6.3 0.9 - - - +
469C LEU* 5.7 0.4 - - - -
471C ASN 4.8 7.2 + - - +
472C THR* 3.3 28.0 - - - +
473C THR* 3.2 21.9 + - - +
475C GLN* 1.3 78.0 - - - +
477C THR* 1.3 57.4 + - - +
479C LEU* 3.2 11.7 + - + +
480C GLN* 2.7 30.4 + - - +
517C LEU* 3.9 11.6 - - + +
20E C 3.5 21.1 - - - +
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Residues in contact with THR 477 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
444C GLY* 3.2 15.4 - - - -
445C ALA 3.3 29.4 + - - +
454C LYS 3.6 11.2 - - - +
455C ALA* 3.8 2.3 - - - +
469C LEU* 3.7 18.2 - - + -
472C THR* 3.8 17.0 - - + +
473C THR 2.9 13.8 + - - +
474C ASN* 2.5 26.5 + - - -
476C LYS* 1.3 75.8 - - - +
478C GLU* 1.3 52.7 + - - +
480C GLN* 3.0 8.7 + - - +
481C ALA* 2.8 34.8 + - - +
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Residues in contact with GLU 478 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
442C VAL* 5.2 0.5 - - - +
443C ASP* 4.8 1.8 - - - +
444C GLY* 4.1 13.1 - - - +
474C ASN* 2.9 31.1 + - - +
475C GLN* 3.5 14.9 - - - +
477C THR* 1.3 77.9 + - - +
479C LEU* 1.3 61.2 + - - +
481C ALA* 3.6 3.3 + - - +
482C ILE* 3.4 26.0 + - - +
497C THR* 5.4 0.5 + - - -
499C SER* 2.6 46.6 + - - +
501C TYR* 4.2 3.7 - - + +
502C ALA* 4.7 3.1 - - + -
606C MG 3.8 22.0 - - - -
17E T 4.1 16.1 + - - -
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Residues in contact with LEU 479 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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475C GLN 3.0 16.0 + - - +
476C LYS* 3.6 10.5 - - + +
478C GLU* 1.3 74.2 - - - +
480C GLN* 1.3 63.4 + - - +
482C ILE* 3.3 5.1 + - - +
483C TYR* 3.0 18.0 + - - +
501C TYR* 3.9 26.2 - - + +
502C ALA* 3.8 31.0 - - + +
505C ILE* 4.6 9.4 - - + -
506C ILE* 5.0 7.4 - - + -
515C SER* 5.2 1.8 - - - +
517C LEU* 3.7 18.4 - - + -
518C VAL* 3.9 26.5 - - + -
521C ILE* 3.6 24.0 - - + +
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Residues in contact with GLN 480 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
455C ALA* 3.7 11.0 - - + -
467C VAL* 5.8 2.2 - - + +
469C LEU* 3.6 33.5 - - + +
476C LYS* 2.7 17.6 + - - +
477C THR* 3.0 12.7 + - - +
479C LEU* 1.3 74.6 - - - +
481C ALA* 1.3 63.5 + - - +
483C TYR* 3.0 34.3 + - - +
484C LEU* 2.9 34.6 + - + +
517C LEU* 3.5 23.5 - - - +
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Residues in contact with ALA 481 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
442C VAL* 3.6 14.1 - - + +
443C ASP* 3.2 42.0 - - - +
444C GLY 4.2 0.2 - - - +
455C ALA* 3.7 6.8 - - - +
456C GLY 3.6 11.4 - - - +
457C TYR* 4.7 0.3 - - - -
477C THR 2.8 15.8 + - - +
478C GLU 3.9 5.2 - - - +
479C LEU 3.3 0.2 - - - -
480C GLN* 1.3 73.4 - - - +
482C ILE* 1.3 61.5 + - - +
484C LEU* 3.3 9.2 + - - +
485C ALA 3.1 17.8 + - - -
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Residues in contact with ILE 482 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
442C VAL* 3.8 22.2 - - + -
478C GLU 3.4 9.1 + - - +
479C LEU* 3.3 8.6 + - - +
480C GLN 3.3 1.0 - - - -
481C ALA* 1.3 75.2 - - - +
483C TYR* 1.3 62.9 + - - +
485C ALA* 3.2 4.3 + - - +
486C LEU* 3.1 38.1 + - + +
495C ILE* 4.6 14.4 - - + -
497C THR* 4.3 19.1 - - + -
502C ALA* 3.6 32.3 - - + -
503C LEU* 5.2 0.4 - - + -
506C ILE* 3.9 26.5 - - + -
521C ILE* 4.9 3.8 - - + -
533C LEU* 4.8 8.1 - - + -
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Residues in contact with TYR 483 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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479C LEU 3.0 13.8 + - - +
480C GLN* 3.0 30.3 + - - +
482C ILE* 1.3 76.5 - - - +
484C LEU* 1.3 62.7 + - + +
486C LEU* 3.1 4.3 + - + +
487C GLN* 2.9 63.2 + - + +
517C LEU* 3.9 13.0 - - + -
520C GLN* 3.3 46.1 + - + +
521C ILE* 3.9 22.4 - - + +
524C GLN* 3.5 27.3 + - + -
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Residues in contact with LEU 484 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
455C ALA* 3.5 43.1 - - + +
456C GLY* 3.9 9.2 - - - +
457C TYR* 3.8 15.0 - - + -
465C LYS* 4.2 15.5 - - + +
467C VAL* 4.0 28.0 - - + -
480C GLN* 2.9 26.9 + - + +
481C ALA* 3.3 6.7 + - - +
483C TYR* 1.3 75.5 - - + +
485C ALA* 1.3 63.4 + - - +
487C GLN* 3.3 18.5 + - + +
488C ASP* 3.1 29.6 + - - +
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Residues in contact with ALA 485 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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440C PHE* 3.7 31.3 - - + -
442C VAL* 3.6 28.9 - - + -
457C TYR* 4.0 2.1 - - - -
481C ALA 3.1 5.5 + - - -
482C ILE* 3.2 8.9 + - - +
484C LEU* 1.3 76.3 - - - +
486C LEU* 1.3 59.4 + - - +
488C ASP 3.9 0.7 - - - -
489C SER* 2.9 30.7 + - - -
493C VAL* 4.7 0.2 - - - +
495C ILE* 4.0 14.6 - - + -
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Residues in contact with LEU 486 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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482C ILE* 3.1 27.8 + - + +
483C TYR* 3.1 7.8 + - - +
485C ALA* 1.3 74.1 - - - +
487C GLN* 1.3 65.8 + - - +
489C SER* 3.2 3.4 + - - -
493C VAL* 4.4 2.5 - - + -
495C ILE* 3.8 21.3 - - + -
521C ILE* 3.8 30.1 - - + -
524C GLN* 3.5 24.9 - - + +
525C LEU* 4.0 29.2 - - + -
528C LYS* 2.8 47.1 + - + -
531C VAL* 4.4 5.6 - - + -
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Residues in contact with GLN 487 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
465C LYS* 5.9 0.7 + - - -
483C TYR* 2.9 66.7 + - + +
484C LEU* 3.3 20.2 + - + +
486C LEU* 1.3 77.9 - - - +
488C ASP* 1.3 69.1 + - - +
489C SER 3.7 3.3 + - - +
524C GLN* 3.9 16.1 - - - +
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Residues in contact with ASP 488 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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440C PHE* 3.8 7.0 - - + -
457C TYR* 2.5 37.6 + - + +
463C ARG* 3.5 25.2 + - - +
465C LYS* 2.7 30.7 + - - +
484C LEU* 3.1 13.7 + - - +
485C ALA 3.9 0.9 - - - -
487C GLN* 1.3 88.7 - - - +
489C SER* 1.3 60.4 + - - +
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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