Contacts of the helix formed by residues 445 - 457 (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 GLN 445 (chain C).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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412C GLN* 3.3 19.7 + - - +
441C PRO 3.2 2.4 + - - -
442C VAL 3.4 16.8 + - - -
443C GLU* 3.7 6.8 + - - +
444C HIS* 1.3 87.6 - - - +
446C ILE* 1.3 63.4 + - - +
447C CYS 3.5 2.2 - - - -
448C PRO* 3.3 20.5 - - + +
449C ALA 3.9 2.4 + - - -
493C TYR* 3.9 6.7 - - - -
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Residues in contact with ILE 446 (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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412C GLN* 4.1 21.3 - - + +
413C ILE* 4.4 7.2 - - + -
416C TYR* 3.5 40.2 - - + -
441C PRO* 3.4 22.4 + - + +
444C HIS* 3.5 19.7 - - + +
445C GLN* 1.3 75.5 - - - +
447C CYS* 1.3 66.9 - - - +
449C ALA* 3.0 14.9 + - - +
450C VAL* 3.1 11.2 + - + +
478C LEU* 3.7 36.6 - - + -
493C TYR* 3.3 3.6 + - - -
497C LEU* 3.9 10.3 - - + -
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Residues in contact with CYS 447 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
446C ILE* 1.3 76.7 - - - +
448C PRO* 1.4 61.6 - - + +
450C VAL* 3.1 5.1 + - - +
451C CYS* 2.8 26.4 + - - +
493C TYR* 2.9 40.1 + - + +
496C THR* 4.1 9.4 - - - -
497C LEU* 3.8 38.3 - - + +
500C TYR* 4.0 17.5 - - - -
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Residues in contact with PRO 448 (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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445C GLN* 3.3 28.9 - - + +
447C CYS* 1.4 93.7 - - + +
449C ALA* 1.3 59.7 + - - +
451C CYS* 3.2 8.9 + - + +
452C VAL* 3.1 31.0 + - + +
493C TYR* 3.7 6.3 - - + +
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Residues in contact with ALA 449 (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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409C LEU* 4.1 22.2 - - + +
412C GLN* 3.6 34.2 - - + +
413C ILE* 4.1 17.7 - - + -
445C GLN 3.9 1.4 + - - -
446C ILE* 3.0 12.0 + - - +
448C PRO* 1.3 79.4 - - - +
450C VAL* 1.3 60.7 + - - +
452C VAL* 3.5 2.8 + - - +
453C LEU* 3.2 26.3 + - - +
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Residues in contact with VAL 450 (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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413C ILE* 4.6 4.7 - - + -
446C ILE* 3.1 19.4 + - + +
447C CYS* 3.6 6.3 - - - +
449C ALA* 1.3 71.7 - - - +
451C CYS* 1.3 55.9 + - - +
453C LEU* 3.3 11.9 + - + +
454C MET* 2.7 33.6 + - - +
475C ILE* 5.2 5.4 - - + -
478C LEU* 3.5 29.8 - - + -
497C LEU* 3.9 14.1 - - + +
500C TYR* 3.7 8.5 - - + -
501C ALA* 3.4 38.8 - - + +
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Residues in contact with CYS 451 (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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447C CYS 2.8 14.0 + - - +
448C PRO* 3.2 14.1 + - + +
450C VAL* 1.3 75.6 - - - +
452C VAL* 1.3 60.3 + - + +
454C MET* 3.0 7.7 + - - +
455C LYS* 2.8 60.6 + - - +
500C TYR* 3.6 39.2 - - + -
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Residues in contact with VAL 452 (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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405C ARG* 3.4 35.7 - - - +
409C LEU* 3.9 24.5 - - + -
448C PRO* 3.1 17.9 + - + +
449C ALA 4.0 3.6 - - - +
451C CYS* 1.3 76.4 - - + +
453C LEU* 1.3 57.7 + - - +
455C LYS* 3.2 14.4 + - + +
456C LEU* 2.9 35.9 + - + +
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Residues in contact with LEU 453 (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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406C VAL* 6.0 1.8 - - + -
409C LEU* 4.4 21.2 - - + +
410C LEU* 3.7 29.2 - - + -
413C ILE* 4.7 8.5 - - + -
449C ALA 3.2 19.5 + - - +
450C VAL* 3.4 10.5 - - + +
452C VAL* 1.3 77.9 - - - +
454C MET* 1.3 62.6 + - - +
456C LEU* 3.5 6.8 + - - +
457C SER* 2.9 21.8 + - - -
466C MET* 3.5 21.1 - - + +
475C ILE* 2.9 38.4 - - + -
504C ALA* 3.9 8.1 - - + -
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Residues in contact with MET 454 (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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450C VAL 2.7 17.2 + - - +
451C CYS* 3.0 20.8 + - - +
453C LEU* 1.3 72.9 - - - +
455C LYS* 1.3 81.5 + - + +
457C SER* 2.6 24.4 + - - -
458C PHE* 3.5 19.4 - - + -
500C TYR* 3.5 56.1 - - + +
503C MET* 3.3 39.5 - - + -
504C ALA* 4.0 7.0 - - - +
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Residues in contact with LYS 455 (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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451C CYS* 2.8 41.2 + - - +
452C VAL* 3.6 15.3 - - + +
454C MET* 1.3 91.1 - - + +
456C LEU* 1.3 63.0 + - + +
458C PHE* 3.3 25.0 + - - +
459C ASP* 4.5 1.2 + - - +
500C TYR* 5.9 0.4 + - - -
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Residues in contact with LEU 456 (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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405C ARG* 4.1 23.8 - - - +
406C VAL* 4.1 17.0 - - + -
409C LEU* 4.2 11.0 - - + -
452C VAL* 2.9 35.7 + - + +
453C LEU* 4.0 5.4 - - + +
455C LYS* 1.3 73.1 - - + +
457C SER* 1.3 55.7 + - - +
458C PHE 3.0 5.6 - - - -
459C ASP* 2.9 21.5 + - + +
462C HIS* 3.3 62.3 - - + +
466C MET* 4.9 4.9 - - - -
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Residues in contact with SER 457 (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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453C LEU 2.9 16.1 + - - -
454C MET 2.6 17.3 + - - -
456C LEU* 1.3 76.4 - - - +
458C PHE* 1.3 55.6 + - - +
459C ASP 3.1 1.3 - - - -
463C ARG* 3.0 34.7 + - - +
466C MET* 4.3 15.7 - - - -
504C ALA* 3.5 21.8 - - - -
507C ASN* 2.7 35.9 + - - +
508C LEU* 4.8 2.2 - - - -
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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
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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