Contacts of the helix formed by residues 294 - 306 (chain A) in PDB entry 1TFZ
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 294 (chain A).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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198A TYR 4.7 0.2 - - - +
199A GLY* 5.7 0.2 - - - -
292A SER* 3.1 8.8 + - - -
293A GLU* 1.3 90.4 - - + +
295A ILE* 1.3 62.2 + - - +
296A PHE* 3.4 14.2 + - - +
297A ARG* 3.1 40.9 + - + +
298A THR* 3.0 19.2 + - - -
300A ARG* 5.0 2.6 + - - -
376A GLN* 3.6 4.9 - - - +
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Residues in contact with ILE 295 (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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292A SER* 3.3 9.3 + - - -
294A ASP* 1.3 72.8 + - - +
296A PHE* 1.3 75.0 + - + +
298A THR* 3.8 1.8 - - - -
299A LEU* 3.1 37.3 + - + +
346A ILE* 4.0 17.1 - - + +
357A LEU* 3.6 58.1 - - + +
358A GLN* 4.2 2.2 - - - +
359A ILE* 4.8 0.4 - - + -
374A ILE* 3.7 26.0 - - + +
375A ILE* 4.4 1.6 - - - -
376A GLN* 2.9 29.5 + - + +
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Residues in contact with PHE 296 (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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294A ASP* 3.2 10.8 + - - +
295A ILE* 1.3 79.8 - - + +
297A ARG* 1.3 58.0 + - - +
299A LEU 3.5 0.3 + - - -
300A ARG* 3.1 39.1 + - - +
333A LEU* 5.7 2.2 - - + -
337A GLN* 3.5 37.9 - - + -
340A GLU* 3.3 42.4 - - + +
341A CYS* 3.6 25.4 - - - -
344A LEU* 3.3 13.3 - - + +
346A ILE* 3.5 21.1 - - + -
357A LEU* 4.0 16.2 - - + -
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Residues in contact with ARG 297 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
197A ASP* 3.0 39.2 + - - +
198A TYR* 3.8 6.7 + - - +
199A GLY* 3.5 22.3 - - - +
201A ARG* 4.3 1.2 - - - +
293A GLU* 2.9 29.5 + - - +
294A ASP* 3.1 29.3 + - - +
296A PHE* 1.3 76.9 - - - +
298A THR* 1.3 64.7 + - - +
300A ARG* 3.3 24.3 + - - +
301A GLU* 3.0 39.1 + - + +
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Residues in contact with THR 298 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
198A TYR* 2.5 28.9 + - + +
199A GLY* 3.5 3.5 - - - -
200A ILE* 3.8 24.0 - - + -
292A SER* 2.7 27.0 + - - -
294A ASP 3.0 5.9 + - - -
295A ILE* 4.0 4.7 - - - -
297A ARG* 1.3 77.2 - - - +
299A LEU* 1.3 57.6 + - + +
301A GLU* 3.9 0.9 - - - +
302A MET* 2.9 48.1 + - + +
374A ILE* 3.9 13.5 - - + -
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Residues in contact with LEU 299 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
295A ILE* 3.1 34.9 + - + +
296A PHE 4.0 3.4 - - - +
297A ARG 3.2 0.2 - - - -
298A THR* 1.3 78.9 - - + +
300A ARG* 1.3 59.7 + - - +
302A MET* 4.5 0.7 - - - +
303A ARG* 2.9 39.5 + - - +
313A PHE* 3.5 35.7 - - + -
344A LEU* 4.0 22.4 - - + +
346A ILE* 4.2 10.3 - - + -
359A ILE* 3.6 37.7 - - + -
374A ILE* 4.0 16.6 - - + -
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Residues in contact with ARG 300 (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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294A ASP* 5.0 2.6 + - - -
296A PHE* 3.1 30.4 + - - +
297A ARG* 3.3 31.7 + - - +
299A LEU* 1.3 75.8 - - - +
301A GLU* 1.3 67.4 + - - +
303A ARG* 3.9 3.2 - - - +
304A LYS* 3.1 44.7 + - - +
340A GLU* 3.2 25.1 + - - -
344A LEU* 3.7 21.3 - - + +
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Residues in contact with GLU 301 (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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197A ASP 5.5 0.2 - - - +
198A TYR* 3.5 38.1 - - + -
297A ARG* 3.0 31.0 + - + +
300A ARG* 1.3 80.0 + - - +
302A MET* 1.3 61.1 + - - +
304A LYS* 3.4 31.5 + - - +
305A ARG* 2.8 52.7 + - - +
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Residues in contact with MET 302 (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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46A GLY 3.5 23.3 - - - +
47A LEU* 3.5 28.9 - - + -
198A TYR* 4.2 9.2 - - + -
200A ILE* 4.6 2.2 - - - -
298A THR* 2.9 43.7 + - + +
299A LEU* 4.2 0.9 - - - +
301A GLU* 1.3 73.0 - - - +
303A ARG* 1.3 64.6 + - - +
305A ARG* 3.1 13.8 + - - +
306A SER* 3.1 13.7 + - - -
311A PHE* 4.2 22.5 + - + +
313A PHE* 3.7 32.5 - - + -
361A THR* 4.4 7.9 - - + -
374A ILE* 4.0 15.7 - - + -
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Residues in contact with ARG 303 (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 LEU* 2.9 28.9 + - + +
300A ARG* 4.0 3.1 - - - +
302A MET* 1.3 73.7 - - - +
304A LYS* 1.3 64.2 + - - +
305A ARG 3.3 0.3 + - - -
306A SER* 3.5 20.8 + - - -
307A SER 5.1 0.3 + - - -
313A PHE* 4.0 34.5 - - + +
314A MET 4.8 4.0 + - - -
316A SER* 3.9 16.9 + - - +
343A GLU 4.8 4.2 + - - -
344A LEU* 2.9 49.3 + - + +
345A GLY* 4.1 0.4 - - - -
359A ILE* 3.6 14.7 - - - +
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Residues in contact with LYS 304 (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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300A ARG* 3.1 36.9 + - - +
301A GLU* 3.4 26.8 + - - +
303A ARG* 1.3 76.4 - - - +
305A ARG* 1.3 78.5 + - + +
306A SER 3.5 0.4 + - - -
307A SER 5.1 1.6 + - - -
308A ILE* 3.8 15.8 - - + +
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Residues in contact with ARG 305 (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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45A TRP* 3.2 58.8 - - + +
46A GLY* 4.9 1.8 - - - -
196A LEU* 5.2 2.0 - - - +
198A TYR* 2.9 38.6 + - - -
301A GLU* 2.8 60.6 + - - +
302A MET* 3.1 8.9 + - - +
304A LYS* 1.3 91.5 - - + +
306A SER* 1.3 56.2 + - - +
307A SER 3.4 2.0 - - - -
308A ILE* 3.1 15.7 + - + -
310A GLY* 2.7 37.2 + - - -
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Residues in contact with SER 306 (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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302A MET 3.1 10.4 + - - -
303A ARG* 3.5 21.0 + - - +
304A LYS 3.5 0.2 - - - -
305A ARG* 1.3 77.3 - - - +
307A SER* 1.3 63.4 + - - +
308A ILE 3.5 0.5 + - - -
309A GLY 4.1 1.0 + - - -
310A GLY 3.6 14.6 + - - +
311A PHE 2.7 28.6 + - - +
312A ASP* 3.4 24.2 - - - +
313A PHE* 4.1 5.5 + - - -
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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