Contacts of the helix formed by residues 451 - 460 (chain C) in PDB entry 6RKU
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 THR 451 (chain C).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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378C HIS* 4.9 3.4 - - + -
411C VAL* 4.3 8.5 - - - +
436C TRP* 5.7 10.8 - - + -
437C LEU* 4.9 8.2 - - + +
441C PHE* 4.2 21.8 - - + +
450C LEU* 1.3 79.5 + - - +
452C GLU* 1.3 72.1 + - + +
453C GLN* 3.3 13.7 - - + +
454C GLN* 3.2 27.6 + - - -
455C ALA* 2.9 29.1 + - - +
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Residues in contact with GLU 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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407C LYS* 4.3 16.7 + - + +
411C VAL* 4.5 16.0 - - + +
451C THR* 1.3 79.3 - - + +
453C GLN* 1.3 58.5 + - - +
455C ALA* 3.2 6.8 + - - +
456C GLN* 2.9 30.4 + - - +
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Residues in contact with GLN 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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375C ASP* 6.4 0.2 - - - +
378C HIS* 5.6 5.4 + - + -
379C ILE* 3.7 29.1 - - + +
436C TRP* 4.1 25.0 - - - -
451C THR* 3.3 10.2 - - + +
452C GLU* 1.3 79.1 - - - +
454C GLN* 1.3 64.0 + - + +
456C GLN* 3.3 10.6 + - - +
457C ALA* 2.9 22.7 + - + +
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Residues in contact with GLN 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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378C HIS* 3.0 41.9 + - + +
379C ILE* 5.1 7.2 - - + -
382C ALA* 3.5 27.0 - - + +
441C PHE* 6.2 1.2 - - - +
448C TYR* 3.3 18.1 + - - -
449C TYR 5.0 0.4 + - - -
450C LEU* 3.2 36.4 - - + +
451C THR* 3.2 25.1 + - - +
453C GLN* 1.3 78.6 - - + +
455C ALA* 1.3 58.5 + - - +
457C ALA* 3.2 8.0 + - - +
458C ILE* 2.9 33.8 + - - +
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Residues in contact with ALA 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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407C LYS* 3.7 28.0 - - + +
410C LEU* 4.8 12.0 - - + +
411C VAL* 4.3 10.3 - - + -
450C LEU* 5.3 4.4 - - + +
451C THR 2.9 18.4 + - - +
452C GLU 3.6 4.3 - - - +
454C GLN* 1.3 76.7 - - - +
456C GLN* 1.3 57.6 + - - +
458C ILE* 3.2 11.9 + - + +
459C LEU* 2.9 35.2 + - - +
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Residues in contact with GLN 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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464A GLN* 5.5 5.2 - - - +
407C LYS* 3.8 26.3 + - - +
452C GLU 2.9 16.2 + - - +
453C GLN* 3.7 7.7 - - - +
455C ALA* 1.3 75.6 - - - +
457C ALA* 1.3 64.6 + - - +
459C LEU* 3.3 5.9 + - + +
460C ASP* 2.9 44.3 + - - +
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Residues in contact with ALA 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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379C ILE* 4.2 26.9 - - + +
382C ALA* 6.3 0.9 - - + -
383C LEU* 5.3 9.9 - - + +
453C GLN 2.9 14.4 + - - +
454C GLN* 3.5 11.4 - - - +
456C GLN* 1.3 76.6 - - - +
458C ILE* 1.3 63.1 + - + +
460C ASP* 3.1 24.1 + - - +
461C LEU* 3.7 7.8 + - - +
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Residues in contact with ILE 458 (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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463A LEU* 3.7 9.2 - - + +
382C ALA* 4.2 14.1 - - + +
383C LEU* 5.0 4.0 - - - +
386C ALA* 3.6 35.0 - - + -
393C ILE* 5.0 17.7 - - + -
397C ILE* 6.4 0.2 - - + -
410C LEU* 5.0 13.7 - - + -
450C LEU* 4.2 28.9 - - + -
454C GLN* 2.9 24.0 + - + +
455C ALA* 3.2 9.4 + - - +
457C ALA* 1.3 78.0 - - + +
459C LEU* 1.3 63.3 + - + +
461C LEU* 3.2 33.3 + - + +
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Residues in contact with LEU 459 (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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462A ARG* 4.7 1.6 - - - +
463A LEU* 3.8 30.5 + - + +
464A GLN* 4.0 30.8 - - + +
397C ILE* 4.2 27.8 - - + -
403C PRO* 4.4 14.1 - - + +
406C ALA* 5.3 5.6 - - + -
407C LYS* 4.3 35.9 - - + +
410C LEU* 4.4 15.5 - - + -
455C ALA 2.9 20.9 + - - +
456C GLN* 3.3 5.8 + - - +
458C ILE* 1.3 76.5 - - + +
460C ASP* 1.3 58.4 + - - +
461C LEU 3.2 4.4 + - - +
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Residues in contact with ASP 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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462A ARG* 4.6 23.3 + - - +
464A GLN* 3.4 23.0 + - - -
456C GLN* 2.9 39.7 + - - +
457C ALA* 3.1 13.0 + - - +
459C LEU* 1.3 75.7 - - - +
461C LEU* 1.3 61.9 + - - +
462C ARG* 5.0 3.3 - - - +
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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