Contacts of the helix formed by residues 522 - 532 (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 MET 522 (chain C).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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472C LEU* 4.9 0.7 - - - -
473C GLN* 3.9 23.8 - - + +
476C ALA* 3.6 34.8 - - + -
477C GLU* 3.8 30.3 - - + +
480C GLN* 4.3 10.8 - - - +
518C THR* 3.3 20.2 - - + +
519C LEU* 3.3 15.5 - - - +
520C CYS 3.0 2.8 - - - -
521C SER* 1.3 77.9 - - - +
523C LYS* 1.3 59.3 - - - +
524C GLY 3.3 2.7 - - - -
525C CYS* 2.9 23.6 + - + +
526C MET* 3.0 12.8 + - - +
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Residues in contact with LYS 523 (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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520C CYS 4.0 5.6 - - - +
521C SER* 3.1 20.2 + - - +
522C MET* 1.3 73.6 - - - +
524C GLY* 1.3 58.3 + - - +
526C MET* 3.3 8.5 + - - +
527C ARG* 2.9 44.4 + - - +
562C THR* 3.3 35.9 - - + +
565C GLU* 5.4 5.9 + - - -
566C VAL* 4.5 6.2 - - + +
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Residues in contact with GLY 524 (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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480C GLN* 3.5 27.9 - - - +
484C GLU* 4.5 1.6 - - - +
522C MET 3.2 1.0 + - - -
523C LYS* 1.3 77.0 - - - +
525C CYS* 1.3 60.8 + - - +
527C ARG* 3.5 26.2 + - - +
528C ALA* 3.1 22.5 + - - +
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Residues in contact with CYS 525 (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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476C ALA* 3.4 39.0 - - - +
479C LEU* 4.5 11.2 - - - -
480C GLN* 3.3 26.2 + - + +
505C LEU* 4.9 0.7 - - - -
519C LEU* 4.0 12.1 - - + -
522C MET* 2.9 22.0 + - + +
524C GLY* 1.3 74.3 - - - +
526C MET* 1.3 59.4 + - - +
528C ALA* 3.1 3.6 + - - +
529C LEU* 2.8 45.1 + - - +
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Residues in contact with MET 526 (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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519C LEU* 3.6 15.3 - - - +
520C CYS* 3.6 24.9 - - - +
522C MET 3.0 16.8 + - - +
523C LYS* 3.6 8.1 - - - +
525C CYS* 1.3 73.3 - - - +
527C ARG* 1.3 65.1 + - - +
529C LEU* 3.4 13.1 + - - +
530C VAL* 3.1 28.8 + - - +
548C LEU* 4.0 11.4 - - + -
551C LEU* 3.7 24.5 - - + -
562C THR* 4.2 5.8 - - + -
563C LEU* 3.5 34.3 - - + -
566C VAL* 3.9 25.6 - - + -
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Residues in contact with ARG 527 (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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484C GLU* 4.3 12.7 + - - +
523C LYS* 2.9 25.8 + - - +
524C GLY* 3.7 27.1 + - - +
526C MET* 1.3 75.8 - - - +
528C ALA* 1.3 56.5 + - - +
530C VAL* 3.5 4.9 + - - +
531C ALA* 3.1 28.6 + - - +
566C VAL* 4.0 21.8 - - + -
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Residues in contact with ALA 528 (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* 4.5 2.7 - - + -
480C GLN* 4.4 11.9 - - + +
483C CYS* 3.6 30.5 - - + -
484C GLU* 5.5 3.1 - - + +
524C GLY 3.1 13.4 + - - +
525C CYS* 3.1 11.1 + - - +
527C ARG* 1.3 74.5 - - - +
529C LEU* 1.3 65.0 + - - +
531C ALA* 3.2 6.4 + - - +
532C GLN* 3.1 31.5 + - - +
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Residues in contact with LEU 529 (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* 3.7 26.2 - - + -
505C LEU* 5.1 1.3 - - + -
519C LEU* 4.8 5.8 - - + -
525C CYS* 2.8 34.6 + - - +
526C MET* 3.4 26.0 + - - +
528C ALA* 1.3 71.6 - - - +
530C VAL* 1.3 63.6 + - - +
532C GLN* 3.1 15.0 + - - +
533C LEU 3.6 0.3 + - - -
544C ILE* 3.1 51.5 - - + +
547C VAL* 4.1 31.0 - - + -
548C LEU* 4.7 11.0 - - + -
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Residues in contact with VAL 530 (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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526C MET 3.1 16.4 + - - +
527C ARG* 3.8 5.4 - - - +
529C LEU* 1.3 75.9 - - - +
531C ALA* 1.3 63.2 + - - +
533C LEU* 3.1 28.1 + - + +
534C LYS* 4.5 2.1 + - - +
548C LEU* 4.7 11.4 - - + -
566C VAL* 3.5 40.6 - - + +
567C GLY 4.2 2.2 - - - +
568C SER* 3.9 16.2 - - - +
571C ALA* 3.8 24.9 - - + +
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Residues in contact with ALA 531 (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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488C LEU* 3.7 15.0 - - + +
527C ARG 3.1 17.2 + - - +
528C ALA* 3.2 9.1 + - - +
530C VAL* 1.3 77.8 - - - +
532C GLN* 1.3 69.3 + - - +
533C LEU 3.2 1.2 + - - -
534C LYS* 3.2 18.2 + - - +
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Residues in contact with GLN 532 (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* 5.3 1.6 - - + -
483C CYS* 3.2 36.2 - - - +
487C GLY* 4.9 2.4 + - - -
488C LEU* 3.5 19.1 - - - +
498C ARG* 2.8 25.2 + - + +
528C ALA 3.1 23.1 + - - +
529C LEU* 3.1 10.2 + - - +
531C ALA* 1.3 76.3 - - - +
533C LEU* 1.3 63.7 + - - +
534C LYS 3.0 2.5 - - - -
535C SER* 3.0 21.4 + - - -
540C LEU* 3.7 21.5 - - + +
541C GLN* 4.1 5.0 - - - +
544C ILE* 3.7 26.7 - - + -
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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