Contacts of the helix formed by residues 250 - 254 (chain F) in PDB entry 5UQ9
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 LEU 250 (chain F).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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455E TYR* 3.3 26.7 - - - +
457E LEU* 4.7 11.4 - - + -
465E ILE* 5.5 2.2 - - + -
467E THR* 3.7 13.0 - - + +
469E TRP* 3.6 25.6 - - + -
239F ILE 6.0 0.2 - - - +
242F PHE* 3.7 39.3 + - + +
244F ASP* 3.8 28.7 - - + +
248F LYS 3.9 0.8 + - - -
249F HIS* 1.3 74.0 - - - +
251F LEU* 1.3 68.9 + - - +
253F LYS* 2.9 27.6 + - + +
254F ILE* 3.4 7.9 - - + +
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Residues in contact with LEU 251 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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441E SER* 3.4 42.4 + - - +
442E LEU* 3.7 23.3 - - + +
445E ALA* 3.9 6.1 - - + -
469E TRP* 5.4 1.0 - - - -
202F TYR* 3.8 21.3 - - + +
213F GLN* 4.6 5.8 - - - +
239F ILE* 4.2 18.1 + - + +
240F LEU* 3.7 29.2 - - + -
249F HIS* 4.6 0.6 - - - +
250F LEU* 1.3 78.3 - - - +
252F PRO* 1.3 67.8 - - + +
253F LYS 3.0 1.4 + - - -
254F ILE* 3.0 29.1 + - + +
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Residues in contact with PRO 252 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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458E LEU* 4.3 15.2 - - - +
202F TYR* 5.8 0.2 - - - +
213F GLN* 3.9 22.0 - - + +
249F HIS* 3.7 27.1 - - + +
250F LEU 3.6 2.9 - - - -
251F LEU* 1.3 93.4 - - + +
253F LYS* 1.3 59.4 + - + +
254F ILE 3.4 3.1 - - - +
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Residues in contact with LYS 253 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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457E LEU* 3.4 21.3 - - + +
458E LEU* 2.7 34.6 + - - +
244F ASP* 3.2 29.6 + - - +
246F ASP* 5.4 7.3 - - - +
248F LYS* 3.7 35.8 - - - +
249F HIS 3.6 21.5 - - - +
250F LEU* 2.9 13.2 + - + +
252F PRO* 1.3 79.4 - - + +
254F ILE* 1.3 56.6 + - - +
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Residues in contact with ILE 254 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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437E MET* 6.0 0.5 - - - +
441E SER* 3.3 26.1 - - - +
444E GLN* 4.1 11.2 - - + -
445E ALA* 3.6 32.5 - - + -
455E TYR* 3.7 37.0 - - + -
456E GLU 3.7 4.9 - - - +
458E LEU* 4.3 4.9 - - - +
469E TRP* 4.1 12.1 - - + -
250F LEU* 3.4 14.1 - - + +
251F LEU* 3.0 24.5 + - + +
252F PRO 4.4 3.6 - - - +
253F LYS* 1.3 79.1 - - - +
255F ARG* 1.3 77.0 + - - +
256F ASP* 3.5 2.8 + - - +
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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