Contacts of the helix formed by residues 451 - 458 (chain L) in PDB entry 6Y5D
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 GLN 451 (chain L).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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342L ASN 5.7 0.8 + - - -
392L LYS* 4.6 26.3 - - - +
406L ARG* 3.2 7.9 + - - -
450L PRO* 1.3 92.3 - - + +
452L ASP* 1.3 66.5 + - - +
453L SER* 3.8 17.0 - - - +
454L GLN* 3.0 31.4 + - + +
455L TRP* 3.3 6.9 - - - -
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Residues in contact with ASP 452 (chain L).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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391L GLY* 3.2 14.0 - - - -
392L LYS* 3.7 6.1 + - - +
393L SER* 3.2 32.9 + - - -
396L CYS* 3.6 23.1 - - - +
402L GLU* 5.2 2.4 - - + +
404L CYS* 4.2 3.9 - - + +
406L ARG* 2.8 33.4 + - - +
450L PRO 3.8 0.8 + - - +
451L GLN* 1.3 74.5 + - - +
453L SER* 1.3 56.3 + - - +
454L GLN 3.1 0.2 - - - -
455L TRP* 2.9 27.5 + - - +
456L ASP* 3.5 1.9 + - - -
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Residues in contact with SER 453 (chain L).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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451L GLN* 3.8 14.1 - - - +
452L ASP* 1.3 79.0 - - - +
454L GLN* 1.3 61.0 + - - +
455L TRP 3.1 2.0 + - - -
456L ASP* 3.9 15.6 + - - +
459L ASP* 4.7 4.9 - - - +
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Residues in contact with GLN 454 (chain L).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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448L GLN 4.7 2.4 + - - -
449L ASN* 3.3 38.4 + - + +
450L PRO* 3.3 6.5 - - - +
451L GLN* 3.0 46.6 + - + +
453L SER* 1.3 79.8 - - - +
455L TRP* 1.3 69.4 + - + +
456L ASP 3.7 1.1 - - - -
459L ASP* 5.8 1.1 - - - -
463L CYS* 3.0 19.4 - - - -
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Residues in contact with TRP 455 (chain L).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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404L CYS* 3.0 15.7 - - + -
405L CYS* 2.6 43.7 + - - +
406L ARG* 3.3 54.6 - - + +
409L CYS* 3.6 14.1 - - + -
442L PHE* 4.4 1.3 - + - -
445L VAL* 3.8 16.8 - - + -
446L CYS* 3.8 31.6 - - - -
449L ASN* 2.7 29.4 + - + +
451L GLN 3.3 8.5 - - - -
452L ASP 2.9 10.9 + - - +
454L GLN* 1.3 84.2 - - + +
456L ASP* 1.3 62.8 + - - +
463L CYS* 3.7 14.4 - - + -
467L CYS* 3.4 35.2 - - - -
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Residues in contact with ASP 456 (chain L).
Click here for Legend to table.
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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401L GLU 5.6 1.4 - - - +
403L LYS 4.2 7.8 - - - +
404L CYS* 4.5 0.7 - - - +
405L CYS* 3.8 0.9 - - - -
452L ASP 3.5 5.3 + - - -
453L SER* 3.9 11.3 + - - +
454L GLN 3.7 1.2 - - - -
455L TRP* 1.3 78.0 - - - +
457L ARG* 1.3 80.3 + - - +
458L LYS* 3.0 31.5 + - - +
459L ASP* 2.8 45.2 + - - +
460L LEU 3.7 0.3 + - - -
463L CYS* 4.6 0.4 - - - -
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Residues in contact with ARG 457 (chain L).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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162L ALA* 4.4 1.9 - - - +
166L ARG* 3.2 54.0 + - - +
400L LYS* 5.2 3.1 - - - +
403L LYS* 3.2 45.9 + - + +
404L CYS 4.5 0.9 - - - -
405L CYS* 4.1 3.4 - - - -
455L TRP 3.1 5.0 + - - -
456L ASP* 1.3 79.3 + - - +
458L LYS* 1.3 77.2 + - - +
459L ASP 3.0 1.3 + - - -
460L LEU* 3.1 19.8 + - - +
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Residues in contact with LYS 458 (chain L).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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162L ALA* 3.4 19.0 - - - +
456L ASP* 3.0 24.1 + - - +
457L ARG* 1.3 93.1 - - - +
459L ASP* 1.3 90.5 + - - +
460L LEU 3.3 1.3 - - - -
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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