Contacts of the helix formed by residues 512 - 522 (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 512 (chain C).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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467C ASN* 3.7 13.3 + - - -
508C LEU 3.5 18.1 - - - +
509C THR 2.9 5.4 + - - +
510C PHE 3.8 4.3 - - - +
511C GLY* 1.3 77.0 - - - +
513C VAL* 1.3 61.8 + - - +
514C ALA* 3.2 10.7 + - - +
515C ASN* 2.8 47.6 + - + -
516C LYS* 3.1 29.4 + - - +
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Residues in contact with VAL 513 (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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511C GLY 3.9 4.0 + - - +
512C ASP* 1.3 73.0 + - - +
514C ALA* 1.3 63.3 + - - +
516C LYS* 3.5 8.8 + - - +
517C ALA* 3.1 24.0 + - + +
556C ASP* 6.0 2.0 - - + +
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Residues in contact with ALA 514 (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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512C ASP* 3.2 7.7 + - - +
513C VAL* 1.3 79.5 - - - +
515C ASN* 1.3 62.4 + - - +
517C ALA* 3.3 6.3 + - - +
518C THR* 2.8 36.5 + - - +
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Residues in contact with ASN 515 (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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467C ASN* 3.0 30.2 + - - +
472C LEU* 4.0 23.7 - - + +
508C LEU* 2.8 36.7 + - - +
509C THR* 4.2 4.6 - - - +
512C ASP* 2.8 31.2 + - + +
514C ALA* 1.3 76.2 - - - +
516C LYS* 1.3 56.4 + - - +
518C THR* 3.4 6.1 + - - -
519C LEU* 2.8 32.4 + - - +
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Residues in contact with LYS 516 (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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509C THR* 3.3 31.4 - - - +
511C GLY* 4.0 4.4 - - - +
512C ASP 3.1 22.3 + - - +
513C VAL* 3.8 7.2 - - - +
515C ASN* 1.3 76.1 - - - +
517C ALA* 1.3 62.2 + - - +
519C LEU 3.4 0.2 + - - -
520C CYS* 3.1 31.4 + - - -
550C ASN* 3.2 23.9 + - - +
551C LEU* 3.7 21.2 - - + +
553C TRP* 3.0 34.8 + - - +
554C ARG* 4.9 6.4 - - - +
555C ALA* 5.8 2.5 - - - +
559C SER* 4.7 2.5 - - - +
384D GLU* 2.6 26.9 + - - -
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Residues in contact with ALA 517 (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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513C VAL* 3.1 19.7 + - + +
514C ALA* 3.6 6.1 - - - +
516C LYS* 1.3 76.5 - - - +
518C THR* 1.3 63.7 + - - +
520C CYS* 3.3 3.5 + - - +
521C SER* 2.9 24.9 + - - -
556C ASP* 4.1 18.4 - - - +
559C SER* 4.2 11.0 - - - -
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Residues in contact with THR 518 (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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472C LEU* 3.8 19.7 - - + -
473C GLN* 4.4 19.5 - - + +
514C ALA* 2.8 25.5 + - - +
515C ASN* 3.7 6.8 + - - -
517C ALA* 1.3 72.6 - - - +
519C LEU* 1.3 63.3 + - - +
521C SER* 2.8 25.4 + - - +
522C MET* 3.3 15.9 - - + +
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Residues in contact with LEU 519 (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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472C LEU* 4.2 11.4 - - + +
476C ALA* 3.7 29.4 - - + -
505C LEU* 4.3 15.7 - - + -
509C THR* 4.0 12.1 - - + -
515C ASN 2.8 20.6 + - - +
518C THR* 1.3 72.6 - - - +
520C CYS* 1.3 60.6 + - - +
522C MET* 3.2 23.2 + - - +
525C CYS* 4.0 15.7 - - + -
526C MET* 3.6 10.0 - - - +
529C LEU* 4.8 4.3 - - + -
547C VAL* 3.7 29.6 - - + -
551C LEU* 3.9 24.2 - - + -
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Residues in contact with CYS 520 (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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516C LYS 3.1 20.8 + - - +
517C ALA 3.8 1.8 - - - +
519C LEU* 1.3 72.2 - - - +
521C SER* 1.3 62.2 + - - +
522C MET 3.0 7.4 + - - -
523C LYS* 4.0 1.6 - - - +
526C MET* 3.6 19.1 - - - +
551C LEU* 4.0 31.6 - - - -
559C SER* 3.7 38.1 - - - +
562C THR* 3.4 29.1 + - - +
563C LEU* 4.3 7.2 - - - -
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Residues in contact with SER 521 (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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517C ALA 2.9 14.3 + - - -
518C THR* 2.8 24.1 + - - +
520C CYS* 1.3 75.1 - - - +
522C MET* 1.3 59.4 + - - +
523C LYS* 3.1 21.7 + - - +
562C THR* 5.6 0.4 - - - -
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Residues in contact with MET 522 (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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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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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