Contacts of the helix formed by residues 459 - 469 (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 ASP 459 (chain C).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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455C LYS 5.3 0.7 - - - +
456C LEU* 2.9 14.6 + - - +
457C SER 3.1 0.4 - - - -
458C PHE* 1.3 79.3 - - + +
460C GLU* 1.3 69.4 + - - +
461C GLU* 3.2 13.4 + - - +
462C HIS* 2.8 44.2 + - + -
463C ARG* 2.8 28.8 + - - +
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Residues in contact with GLU 460 (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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629A LEU* 4.2 11.9 - - + +
672A HIS* 3.9 33.4 - - + +
673A SER* 3.8 22.1 + - - -
674A LEU 5.6 0.5 + - - -
458C PHE 4.6 2.3 - - - +
459C ASP* 1.3 83.7 - - - +
461C GLU* 1.3 64.2 + - + +
463C ARG* 3.3 30.1 + - - +
464C HIS* 3.0 29.5 + - - +
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Residues in contact with GLU 461 (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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627A ASN* 5.2 13.2 + - - +
459C ASP* 3.2 14.2 + - - +
460C GLU* 1.3 87.1 - - + +
462C HIS* 1.3 65.4 + - + +
464C HIS* 3.4 8.4 + - - +
465C ALA* 3.3 18.2 + - - +
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Residues in contact with HIS 462 (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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402C ARG 5.5 7.9 - - - -
403C GLU* 6.1 1.2 - - - -
405C ARG* 5.4 9.9 - - + -
406C VAL* 4.0 12.4 - - + +
456C LEU* 3.3 64.9 - - + +
459C ASP* 2.8 35.7 + - + +
461C GLU* 1.3 77.7 - - + +
463C ARG* 1.3 64.2 + - - +
465C ALA* 3.4 7.6 + - - +
466C MET* 3.0 28.6 + - - +
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Residues in contact with ARG 463 (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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672A HIS* 4.5 9.3 + - - +
457C SER* 3.0 39.7 + - - +
458C PHE* 3.3 23.4 + - - +
459C ASP 2.8 10.3 + - - +
460C GLU* 3.3 37.3 + - - +
462C HIS* 1.3 75.1 - - - +
464C HIS* 1.3 57.0 + - - +
466C MET* 3.1 7.6 + - - +
467C ASN* 2.9 37.8 + - - +
507C ASN 3.5 24.7 + - - -
508C LEU* 4.0 20.4 - - + +
386D TYR* 3.2 36.3 + - - -
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Residues in contact with HIS 464 (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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460C GLU 3.0 13.4 + - - +
461C GLU* 3.5 13.0 - - - +
463C ARG* 1.3 76.5 - - - +
465C ALA* 1.3 64.3 + - - +
467C ASN* 3.1 10.0 + - - +
468C GLU* 3.0 58.9 + - + +
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Residues in contact with ALA 465 (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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403C GLU* 3.6 31.6 - - + -
406C VAL* 4.4 13.9 - - + -
461C GLU 3.3 9.9 + - - +
462C HIS* 3.7 10.3 - - - +
463C ARG 3.3 0.2 - - - -
464C HIS* 1.3 80.6 - - - +
466C MET* 1.3 61.9 + - - +
468C GLU* 3.2 17.9 + - - +
469C LEU* 3.3 23.3 + - + +
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Residues in contact with MET 466 (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* 3.7 24.9 - - + -
410C LEU* 5.3 1.1 - - + -
453C LEU* 3.5 43.7 - - + +
456C LEU* 4.9 4.9 - - - -
457C SER* 4.3 18.6 - - - -
462C HIS 3.0 19.4 + - - +
463C ARG 3.4 7.4 - - - +
465C ALA* 1.3 74.6 - - - +
467C ASN* 1.3 57.8 + - - +
469C LEU* 3.1 2.8 + - - -
470C GLY 2.9 9.7 + - - -
471C GLY* 2.8 36.0 + - - +
475C ILE* 3.6 5.2 - - + -
508C LEU* 2.9 46.9 - - + -
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Residues in contact with ASN 467 (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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463C ARG* 2.9 24.2 + - - +
464C HIS* 3.1 12.1 + - - +
466C MET* 1.3 78.2 - - - +
468C GLU* 1.3 66.3 + - - +
469C LEU 3.3 0.5 + - - -
470C GLY* 3.5 9.4 + - - +
471C GLY 4.9 0.9 - - - +
472C LEU* 4.9 5.7 + - - +
508C LEU* 3.7 14.2 + - - +
512C ASP* 3.7 18.5 + - - -
515C ASN* 3.0 26.2 + - - +
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Residues in contact with GLU 468 (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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464C HIS* 3.0 57.3 + - + +
465C ALA* 3.2 10.5 + - - +
467C ASN* 1.3 81.0 - - - +
469C LEU* 1.3 70.0 + - + +
470C GLY 3.6 0.6 + - - -
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Residues in contact with LEU 469 (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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403C GLU* 4.2 9.0 - - + +
406C VAL* 4.0 10.1 - - + -
407C LEU* 3.9 51.4 - - + +
410C LEU* 3.8 13.3 - - + +
414C ARG* 2.7 36.5 + - - +
465C ALA* 3.4 19.5 - - + +
466C MET 3.1 2.4 + - - +
468C GLU* 1.3 89.3 - - + +
470C GLY* 1.3 52.8 + - - +
471C GLY 3.4 0.7 - - - -
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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