Contacts of the helix formed by residues 323 - 328 (chain F) in PDB entry 1TKK
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 323 (chain F).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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132F THR* 4.1 0.4 - - - -
133F ASP 3.4 18.8 - - - +
134F TYR* 4.0 15.0 - - + -
135F THR* 2.7 42.3 + - - -
321F ASP* 3.4 7.0 + - - +
322F PHE* 1.3 73.2 - - - +
324F ALA* 1.3 67.8 + - - +
325F PRO* 3.4 4.0 - - - -
326F LEU* 3.2 24.6 + - + +
327F MET* 3.2 16.7 + - + +
2480F ALA* 2.8 27.5 + - - +
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Residues in contact with ALA 324 (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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296F SER* 3.7 8.7 - - - +
297F MET 3.5 23.6 - - - +
298F ILE* 4.1 11.1 - - + +
299F GLU 3.4 19.3 - - - +
304F ILE* 4.1 1.9 - - + +
323F ASP* 1.3 81.6 + - - +
325F PRO* 1.3 70.3 - - + +
327F MET* 3.2 28.5 + - - +
328F LEU* 3.6 10.6 - - - +
2480F ALA* 4.2 2.2 - - + -
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Residues in contact with PRO 325 (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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299F GLU 3.6 6.3 - - - +
300F THR 3.7 1.1 - - - -
301F LYS* 3.7 30.1 - - + +
304F ILE* 3.4 33.0 - - + -
322F PHE 3.9 0.2 - - - +
323F ASP 3.4 4.5 - - - -
324F ALA* 1.3 94.6 - - + +
326F LEU* 1.3 59.9 + - - +
328F LEU* 3.4 26.4 + - + +
330F THR 5.1 1.7 - - - +
331F ASP* 5.9 2.4 - - - +
339F TYR* 3.4 27.4 - - + +
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Residues in contact with LEU 326 (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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16F THR* 4.8 2.8 + - - -
132F THR* 5.1 0.2 - - + -
134F TYR* 3.6 26.1 + - + +
154F GLN* 5.9 1.6 - - - +
156F PHE* 3.5 34.1 - - + -
323F ASP* 3.5 13.9 - - - +
324F ALA 3.2 0.6 - - - -
325F PRO* 1.3 78.2 - - - +
327F MET* 1.3 63.2 + - - +
328F LEU 3.4 5.7 + - - +
339F TYR* 3.6 53.2 - - + -
341F GLY 5.1 0.2 - - - +
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Residues in contact with MET 327 (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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15F LEU* 3.5 16.0 - - + +
16F THR* 3.0 32.1 + - - -
17F LYS 4.6 3.6 + - - +
19F PHE* 3.5 48.9 - - + -
134F TYR* 3.9 18.4 - - + +
135F THR* 3.9 12.1 - - - +
137F SER* 5.8 0.2 - - - +
298F ILE* 4.2 12.8 - - + -
323F ASP* 3.2 41.5 - - + +
324F ALA* 3.2 9.1 + - - +
326F LEU* 1.3 77.8 - - - +
328F LEU* 1.3 59.3 + - + +
2480F ALA* 4.4 3.4 - - + -
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Residues in contact with LEU 328 (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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13F VAL* 4.0 14.8 - - + +
14F PRO 3.7 3.4 - - - +
15F LEU* 3.7 29.8 - - + -
16F THR* 3.9 1.8 + - - -
29F ALA* 3.8 18.6 - - + -
298F ILE* 4.6 5.6 - - + -
299F GLU 4.0 17.5 - - - +
300F THR* 4.1 25.1 - - + -
324F ALA 3.6 16.2 - - - +
325F PRO* 3.6 13.2 - - + +
326F LEU 3.2 7.8 - - - +
327F MET* 1.3 78.3 - - + +
329F LYS* 1.3 66.9 + - - +
330F THR* 3.1 19.3 + - - +
332F VAL* 6.3 0.4 - - + -
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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