Contacts of the helix formed by residues 556 - 566 (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 556 (chain C).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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513C VAL* 6.0 2.5 - - + +
517C ALA* 4.1 17.4 - - - +
554C ARG 3.7 2.4 + - - -
555C ALA* 1.3 77.1 - - - +
557C VAL* 1.3 65.9 + - - +
558C ASN* 3.1 16.7 + - - +
559C SER* 2.7 44.6 + - - -
560C LYS* 3.0 21.1 + - - +
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Residues in contact with VAL 557 (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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556C ASP* 1.3 76.4 - - + +
558C ASN* 1.3 71.3 + - - +
560C LYS* 3.4 9.7 + - + +
561C LYS* 3.2 23.1 + - + +
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Residues in contact with ASN 558 (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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556C ASP* 3.1 12.2 + - - +
557C VAL* 1.3 81.6 - - - +
559C SER* 1.3 57.9 + - - +
561C LYS* 3.2 11.2 + - - +
562C THR* 3.0 32.7 + - - +
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Residues in contact with SER 559 (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* 4.3 2.7 + - - +
517C ALA* 4.2 11.1 + - - -
520C CYS* 3.7 35.4 - - - +
551C LEU 4.8 0.4 - - - -
555C ALA* 3.8 16.8 - - - -
556C ASP* 2.7 34.9 + - - -
558C ASN* 1.3 73.1 - - - +
560C LYS* 1.3 55.8 + - - +
562C THR* 3.3 2.2 + - - +
563C LEU* 2.8 36.7 + - - +
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Residues in contact with LYS 560 (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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555C ALA* 3.3 26.9 + - + +
556C ASP 3.0 19.2 + - - +
557C VAL* 3.8 8.7 - - + +
559C SER* 1.3 75.1 - - - +
561C LYS* 1.3 63.0 + - - +
563C LEU* 3.5 4.8 + - - +
564C ARG* 3.1 24.3 + - - +
597C ALA 5.5 0.8 + - - -
598C HIS* 3.6 61.9 + - + +
602C ASN* 5.4 1.6 + - - -
381D GLU* 4.7 6.0 + - - -
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Residues in contact with LYS 561 (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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557C VAL* 3.2 11.7 + - + +
558C ASN* 3.2 13.4 + - - +
560C LYS* 1.3 79.5 - - - +
562C THR* 1.3 58.2 + - - +
564C ARG* 3.2 11.0 + - - +
565C GLU* 2.8 68.5 + - + +
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Residues in contact with THR 562 (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* 3.4 29.6 + - + +
521C SER* 5.6 0.3 - - - -
523C LYS* 3.3 36.1 - - + +
526C MET* 4.2 14.6 - - + -
558C ASN* 3.0 17.7 + - - +
559C SER* 3.3 6.5 + - - -
561C LYS* 1.3 73.6 - - - +
563C LEU* 1.3 67.5 + - - +
565C GLU* 3.2 8.4 + - - -
566C VAL* 3.0 30.4 + - + +
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Residues in contact with LEU 563 (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* 4.3 5.8 - - - -
526C MET* 3.5 25.4 - - + -
548C LEU* 4.3 12.3 - - + +
551C LEU* 3.6 36.8 - - + +
552C SER* 3.8 14.8 - - - -
555C ALA* 4.2 0.9 - - + -
559C SER 2.8 27.4 + - - +
560C LYS* 3.7 4.7 - - - +
562C THR* 1.3 74.4 - - - +
564C ARG* 1.3 60.5 + - - +
566C VAL* 3.4 4.6 - - - +
568C SER* 2.8 42.3 + - - +
595C LEU* 3.9 17.3 - - + -
598C HIS* 4.0 13.7 - - + -
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Residues in contact with ARG 564 (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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560C LYS 3.1 14.6 + - - +
561C LYS* 3.4 13.0 - - - +
563C LEU* 1.3 76.0 - - - +
565C GLU* 1.3 74.2 + - - +
567C GLY* 3.0 20.6 + - - -
568C SER 4.4 0.6 + - - +
569C VAL* 5.3 6.2 + - - -
595C LEU* 5.4 0.4 - - - +
599C CYS* 4.3 10.8 - - - -
601C GLU* 3.1 43.6 - - - +
602C ASN* 3.7 23.8 + - - +
605C ASP* 4.9 10.1 + - - +
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Residues in contact with GLU 565 (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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523C LYS* 5.4 6.1 + - - -
561C LYS* 2.8 65.9 + - + +
562C THR* 3.2 7.1 + - - +
564C ARG* 1.3 88.8 + - + +
566C VAL* 1.3 60.1 + - + +
567C GLY* 3.1 1.9 + - - -
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Residues in contact with VAL 566 (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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523C LYS* 4.5 6.5 - - + +
526C MET* 3.9 33.7 - - + +
527C ARG* 4.0 25.4 - - + +
530C VAL* 3.5 31.7 - - + +
562C THR* 3.0 29.2 + - + +
563C LEU* 3.4 14.8 - - - +
565C GLU* 1.3 77.9 - - + +
567C GLY* 1.3 59.4 + - - +
568C SER* 3.6 11.7 - - - +
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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