Contacts of the helix formed by residues 323 - 328 (chain A) 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 A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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132A THR* 4.4 0.7 - - - +
133A ASP 3.6 18.2 - - - +
134A TYR* 4.1 17.5 - - + -
135A THR* 2.8 34.4 + - - -
321A ASP* 3.2 7.3 - - - +
322A PHE* 1.3 71.7 + - - +
324A ALA* 1.3 70.2 + - - +
325A PRO* 3.3 4.3 - - - -
326A LEU* 2.9 27.4 + - + +
327A MET* 3.1 20.6 + - + +
2470A ALA* 2.6 26.3 + - - -
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Residues in contact with ALA 324 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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296A SER* 4.1 6.0 + - - +
297A MET 3.6 21.8 - - - +
298A ILE* 4.0 9.5 - - + +
299A GLU 3.5 17.9 - - - +
304A ILE* 4.7 0.4 - - + -
322A PHE* 3.6 0.4 - - - +
323A ASP* 1.3 80.5 + - - +
325A PRO* 1.3 68.5 - - + +
327A MET* 3.0 31.3 + - - +
328A LEU* 3.6 10.7 - - - +
2470A ALA* 4.0 10.7 - - + +
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Residues in contact with PRO 325 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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299A GLU 3.6 11.2 - - - +
300A THR 3.6 7.4 - - - +
301A LYS* 3.9 19.3 - - + +
304A ILE* 3.2 35.2 - - + -
322A PHE 4.0 0.7 - - - +
323A ASP 3.3 4.5 - - - -
324A ALA* 1.3 91.4 - - + +
326A LEU* 1.3 60.5 + - + +
328A LEU* 3.3 26.4 + - + +
330A THR 5.1 1.7 - - - +
331A ASP* 6.0 2.2 - - - -
339A TYR* 3.7 22.2 - - + +
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Residues in contact with LEU 326 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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16A THR* 4.9 3.1 + - - -
132A THR* 5.3 0.2 - - + -
134A TYR* 3.5 28.2 + - + +
154A GLN* 5.6 2.7 - - - +
156A PHE* 3.4 34.1 - - + -
323A ASP* 2.9 18.2 + - - +
325A PRO* 1.3 75.4 - - + +
327A MET* 1.3 60.7 + - - +
328A LEU 3.2 7.0 + - - +
339A TYR* 3.7 52.9 - - + -
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Residues in contact with MET 327 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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15A LEU* 3.3 18.8 - - + +
16A THR* 2.8 31.8 + - - -
17A LYS 4.5 5.0 + - - +
19A PHE* 3.8 40.8 - - + -
134A TYR* 3.9 20.4 - - + +
135A THR* 4.0 11.4 - - - +
137A SER* 5.6 0.4 - - - +
298A ILE* 4.3 8.5 - - - -
323A ASP* 3.1 37.7 - - + +
324A ALA* 3.0 20.7 + - - +
326A LEU* 1.3 77.6 - - - +
328A LEU* 1.3 57.9 - - + +
2470A ALA* 4.5 2.2 - - + -
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Residues in contact with LEU 328 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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13A VAL* 3.9 20.2 - - + +
14A PRO 3.8 2.5 - - - -
15A LEU* 3.2 33.0 - - + -
16A THR* 4.0 4.7 + - - -
29A ALA* 3.8 14.4 - - + -
298A ILE* 4.5 3.8 - - + -
299A GLU 4.1 5.4 - - - +
300A THR* 4.0 36.8 - - + +
324A ALA 3.6 15.9 - - - +
325A PRO* 3.5 14.8 - - + +
326A LEU 3.2 8.7 - - - +
327A MET* 1.3 79.1 - - - +
329A LYS* 1.3 65.4 + - - +
330A THR 3.4 16.6 + - - +
332A VAL* 6.0 0.7 - - + -
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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