Contacts of the helix formed by residues 470 - 487 (chain C) in PDB entry 3QHE
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 470 (chain C).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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414C ARG* 3.6 10.2 + - - -
466C MET 2.9 2.8 + - - -
467C ASN* 3.5 9.7 + - - -
468C GLU 3.6 0.6 - - - -
469C LEU* 1.3 79.3 - - - +
471C GLY* 1.3 65.1 + - - +
472C LEU* 3.3 2.9 - - - -
473C GLN* 3.4 12.5 + - - +
474C ALA* 3.2 17.5 + - - +
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Residues in contact with GLY 471 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
410C LEU* 3.8 25.6 - - - -
466C MET* 2.8 28.9 + - - -
467C ASN* 4.9 0.2 - - - +
469C LEU 3.4 1.0 - - - -
470C GLY* 1.3 69.7 - - - +
472C LEU* 1.3 64.6 + - - +
474C ALA* 3.3 1.7 + - - +
475C ILE* 2.9 36.0 + - - +
508C LEU* 4.5 0.7 - - - -
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Residues in contact with LEU 472 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
466C MET 4.7 0.8 + - - -
467C ASN* 4.9 4.5 + - - +
470C GLY* 3.3 0.9 - - - -
471C GLY* 1.3 75.1 - - - +
473C GLN* 1.3 61.9 + - - +
476C ALA* 3.0 30.1 + - - +
505C LEU* 3.5 30.0 - - + +
508C LEU* 3.9 29.5 - - + +
509C THR* 4.1 26.2 - - + -
515C ASN* 4.0 33.2 - - + +
518C THR* 3.8 26.7 - - + -
519C LEU* 4.2 15.3 - - + +
522C MET* 4.9 1.6 - - - -
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Residues in contact with GLN 473 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
414C ARG* 6.1 0.4 - - - +
470C GLY* 3.4 12.1 + - - +
471C GLY 3.3 1.0 - - - -
472C LEU* 1.3 87.4 - - + +
474C ALA* 1.3 51.8 + - - +
476C ALA* 3.2 2.4 + - - +
477C GLU* 2.7 65.0 + - + +
518C THR* 4.4 14.3 - - + +
522C MET* 4.1 19.9 - - + +
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Residues in contact with ALA 474 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
410C LEU* 4.1 9.6 - - + -
413C ILE* 3.6 28.4 - - + +
414C ARG* 4.1 26.0 - - + +
417C CYS* 4.6 2.9 - - - -
470C GLY 3.2 10.8 + - - +
471C GLY 3.7 6.1 - - - +
473C GLN* 1.3 76.6 - - - +
475C ILE* 1.3 62.9 + - - +
477C GLU* 3.4 13.6 + - - +
478C LEU* 3.1 19.1 + - - +
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Residues in contact with ILE 475 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
410C LEU* 4.7 0.2 - - + -
413C ILE* 4.1 9.2 - - + -
450C VAL* 5.2 5.4 - - + -
453C LEU* 2.9 50.0 - - + -
466C MET* 3.6 15.9 - - + -
471C GLY* 2.9 24.8 + - - +
472C LEU 3.8 3.4 - - - +
474C ALA* 1.3 75.8 - - - +
476C ALA* 1.3 58.0 + - - +
478C LEU* 3.4 6.7 + - + +
479C LEU* 3.0 26.0 + - - +
501C ALA* 3.7 39.1 - - + +
504C ALA* 4.3 3.6 - - + -
505C LEU* 3.9 9.6 - - + -
508C LEU* 4.0 7.4 - - + -
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Residues in contact with ALA 476 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
472C LEU 3.0 18.5 + - - +
473C GLN 3.7 0.2 - - - +
475C ILE* 1.3 76.0 - - - +
477C GLU* 1.3 59.7 + - - +
479C LEU* 3.3 1.4 + - - +
480C GLN* 2.8 30.5 + - - +
505C LEU* 3.9 11.6 - - + +
519C LEU* 3.7 17.0 - - + -
522C MET* 3.6 22.2 - - + -
525C CYS* 3.4 21.7 - - - -
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Residues in contact with GLU 477 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
414C ARG* 5.1 6.4 + - - +
417C CYS* 4.1 5.8 - - - -
421C TRP* 3.6 42.4 + - + +
473C GLN* 2.7 49.3 + - - +
474C ALA* 3.7 18.8 + - - +
476C ALA* 1.3 72.4 - - - +
478C LEU* 1.3 58.5 + - - +
480C GLN* 3.3 8.3 + - - +
481C VAL* 2.9 33.1 + - - +
522C MET* 3.8 15.9 - - + +
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Residues in contact with LEU 478 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
413C ILE* 4.2 17.7 - - + +
416C TYR* 3.7 36.1 - - + -
417C CYS* 3.7 17.0 - - - -
441C PRO* 5.7 0.2 - - + -
446C ILE* 3.7 14.4 - - + -
450C VAL* 3.5 33.7 - - + -
474C ALA 3.1 16.1 + - - +
475C ILE* 3.6 7.0 - - + +
477C GLU* 1.3 76.1 - - - +
479C LEU* 1.3 66.9 + - - +
481C VAL* 3.4 5.0 - - + +
482C ASP* 3.0 27.0 + - + +
497C LEU* 4.1 15.7 - - + -
501C ALA* 5.6 2.2 - - + -
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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
----------------------------------------------------------
475C ILE 3.0 14.0 + - - +
476C ALA 3.3 8.3 + - - +
478C LEU* 1.3 77.0 - - - +
480C GLN* 1.3 67.7 + - - +
482C ASP* 3.9 4.0 - - - +
483C CYS* 3.1 38.8 + - - -
497C LEU* 5.3 4.5 - - - -
498C ARG* 4.4 15.2 - - + +
501C ALA* 4.2 21.5 - - + +
502C GLY* 4.4 7.9 - - - +
505C LEU* 3.8 20.2 - - + -
525C CYS* 4.5 6.3 - - - -
528C ALA* 4.5 6.3 - - + -
529C LEU* 3.7 32.5 - - + +
532C GLN* 5.3 2.7 - - + -
544C ILE* 5.1 3.6 - - + -
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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
----------------------------------------------------------
476C ALA 2.8 16.8 + - - +
477C GLU* 3.6 7.4 - - - +
479C LEU* 1.3 81.8 - - - +
481C VAL* 1.3 58.5 + - - +
483C CYS* 3.1 5.0 + - - +
484C GLU* 2.6 63.5 + - + +
522C MET* 4.3 12.5 - - - +
524C GLY* 3.5 25.7 + - - +
525C CYS* 3.3 27.6 + - - +
527C ARG* 5.3 0.2 - - - +
528C ALA* 4.4 6.0 - - + +
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Residues in contact with VAL 481 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
416C TYR* 5.3 0.4 - - + -
417C CYS* 4.4 9.6 - - - -
420C CYS* 3.6 40.8 - - + -
421C TRP* 3.9 22.0 - - + +
424C GLN* 3.8 20.9 - - - +
477C GLU 2.9 18.8 + - - +
478C LEU* 3.4 20.2 - - + +
480C GLN* 1.3 73.4 - - - +
482C ASP* 1.3 61.6 + - - +
484C GLU* 3.3 9.2 + - - +
485C MET* 2.9 38.3 + - - +
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Residues in contact with ASP 482 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
416C TYR* 5.2 3.1 + - + -
441C PRO* 3.6 25.3 - - + +
478C LEU* 3.0 22.3 + - + +
479C LEU* 3.9 3.6 - - - +
481C VAL* 1.3 80.8 - - + +
483C CYS* 1.3 60.1 + - - +
485C MET* 3.5 6.0 + - - +
486C TYR* 3.1 38.8 + - - +
494C SER* 3.3 11.4 + - - +
497C LEU* 4.8 14.8 - - + -
498C ARG* 2.7 45.2 + - + +
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Residues in contact with CYS 483 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
479C LEU* 3.1 36.2 + - - -
480C GLN 3.6 7.0 - - - +
482C ASP* 1.3 76.5 - - - +
484C GLU* 1.3 58.8 + - - +
487C GLY* 2.9 28.3 + - - -
498C ARG* 3.6 23.1 - - - +
528C ALA* 3.6 15.9 - - + -
532C GLN* 3.2 38.1 - - - +
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Residues in contact with GLU 484 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
424C GLN* 3.0 33.5 + - - +
480C GLN* 2.6 54.8 + - + +
481C VAL* 3.7 10.1 - - - +
482C ASP 3.2 0.2 - - - -
483C CYS* 1.3 80.1 - - + +
485C MET* 1.3 64.0 + - - +
487C GLY* 4.4 1.7 + - - -
524C GLY 4.5 2.8 - - - +
527C ARG* 4.3 14.9 + - - +
528C ALA* 5.5 2.5 - - + -
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Residues in contact with MET 485 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
416C TYR* 4.7 1.3 - - - +
420C CYS* 3.6 33.0 - - + -
423C TRP* 4.5 9.5 - - + -
424C GLN* 3.6 24.5 - - + +
437C PRO* 3.6 29.5 - - + +
439C PRO* 3.1 47.1 - - + +
481C VAL* 2.9 23.3 + - - +
482C ASP* 4.8 2.5 - - - -
484C GLU* 1.3 79.1 - - - +
486C TYR* 1.3 80.1 + - + +
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Residues in contact with TYR 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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416C TYR* 5.0 0.2 - - - -
437C PRO* 3.3 34.7 + - + +
439C PRO 2.7 32.3 + - - -
440C ALA* 3.5 12.8 - - + +
441C PRO* 4.1 16.4 - - + -
482C ASP* 3.1 27.6 + - - +
485C MET* 1.3 93.2 - - + +
487C GLY* 1.3 66.7 + - - +
488C LEU 3.7 7.6 + - - +
489C THR* 4.1 15.7 - - + -
494C SER* 5.4 2.2 - - - +
498C ARG* 3.8 9.0 - - - +
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Residues in contact with GLY 487 (chain C).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
483C CYS 2.9 20.4 + - - -
484C GLU 4.4 1.6 + - - -
485C MET 3.8 0.8 - - - -
486C TYR* 1.3 79.3 - - - +
488C LEU* 1.3 62.0 + - - -
489C THR 3.4 0.9 + - - -
498C ARG* 2.8 30.4 + - - -
532C GLN* 5.1 2.5 - - - -
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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
------------------------------------------------------------
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