Contacts of the helix formed by residues 298 - 310 (chain A) in PDB entry 1T0R
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 ILE 298 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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199A GLY 3.0 27.8 - - - +
200A PHE* 3.9 28.3 - - + +
203A MET* 4.3 9.2 - - + -
269A PHE* 5.5 0.9 - - + -
293A PHE* 4.1 16.4 - - + -
294A MET* 3.2 43.6 + - + +
297A TRP* 1.3 89.3 - - - +
299A VAL* 1.3 68.7 + - + +
301A GLN* 3.1 8.3 + - - +
302A PHE* 3.1 53.2 + - + -
320A PHE* 5.6 1.3 - - + -
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Residues in contact with VAL 299 (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 MET* 2.6 38.1 + - + +
295A LEU* 4.0 14.4 - - + +
298A ILE* 1.3 70.3 - - + +
300A ALA* 1.3 66.9 + - - +
302A PHE* 3.1 13.3 + - - +
303A GLU* 3.2 26.0 + - - +
317A TRP* 3.7 22.4 - - + +
320A PHE* 4.7 14.8 - - + -
321A MET* 3.7 32.8 - - + -
324A LEU* 4.6 4.9 - - + -
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Residues in contact with ALA 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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295A LEU 3.7 15.8 + - - +
296A GLU* 4.4 5.2 - - - +
298A ILE 3.5 0.4 - - - -
299A VAL* 1.3 77.8 - - - +
301A GLN* 1.3 72.7 + - - +
303A GLU* 3.4 17.6 + - - +
304A ARG* 3.1 21.5 + - - +
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Residues in contact with GLN 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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198A THR 6.1 0.7 - - - +
199A GLY* 6.1 1.3 - - - +
203A MET* 5.3 4.3 - - - -
296A GLU 3.0 23.3 + - - +
297A TRP* 3.0 45.7 + - - +
298A ILE* 3.1 10.9 + - - +
299A VAL 3.2 0.2 - - - -
300A ALA* 1.3 76.3 + - - +
302A PHE* 1.3 60.2 + - - +
304A ARG* 3.3 6.8 + - - +
305A GLN* 2.8 40.2 + - + +
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Residues in contact with PHE 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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194A PHE* 4.7 14.4 - + - -
195A ALA* 3.5 12.8 - - - -
199A GLY* 3.4 31.0 - - - -
200A PHE* 3.4 27.1 - + - -
262A ILE* 3.5 33.0 - - + -
298A ILE* 3.1 46.5 + - + -
299A VAL* 3.1 8.0 + - - +
301A GLN* 1.3 76.4 - - - +
303A GLU* 1.3 57.4 + - - +
305A GLN* 3.6 5.4 - - + +
306A LEU* 2.8 40.7 + - + +
317A TRP* 3.8 26.2 - + + -
320A PHE* 5.7 1.6 - + - -
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Residues in contact with GLU 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 VAL* 3.2 21.1 + - - +
300A ALA* 3.4 20.5 - - - +
302A PHE* 1.3 75.9 - - - +
304A ARG* 1.3 54.7 + - - +
306A LEU* 3.6 8.0 - - - +
307A LEU* 2.7 36.7 + - - +
313A LYS* 4.0 26.4 + - + +
317A TRP* 3.4 30.3 + - + +
321A MET* 4.4 6.1 - - - +
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Residues in contact with ARG 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 ALA 3.1 13.2 + - - +
301A GLN* 3.5 11.2 - - - +
302A PHE 3.2 0.2 - - - -
303A GLU* 1.3 76.2 - - - +
305A GLN* 1.3 66.1 + - + +
307A LEU* 3.0 29.0 + - - +
308A ASP* 2.8 68.8 + - - +
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Residues in contact with GLN 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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194A PHE* 4.0 31.1 - - + -
198A THR* 3.7 22.7 - - + +
301A GLN* 2.8 32.3 + - + +
302A PHE* 3.6 8.7 - - + +
304A ARG* 1.3 73.5 - - + +
306A LEU* 1.3 61.9 + - - +
308A ASP* 3.7 6.5 + - - +
309A LEU* 3.1 33.0 + - - +
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Residues in contact with LEU 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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194A PHE* 4.4 11.4 - - + -
255A GLN* 5.0 0.4 - - - +
258A VAL* 4.0 20.2 - - + -
262A ILE* 4.7 7.6 - - + -
302A PHE* 2.8 40.6 + - + +
303A GLU* 3.8 7.4 - - - +
305A GLN* 1.3 70.7 - - - +
307A LEU* 1.3 62.8 + - - +
309A LEU* 3.6 3.1 + - - -
310A GLY 3.3 1.9 + - - -
311A LEU* 2.9 67.4 + - + +
312A ASP 3.9 19.5 - - - +
313A LYS* 4.3 8.1 - - + +
314A PRO* 4.1 17.7 - - + -
317A TRP* 5.2 1.8 - - + -
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Residues in contact with LEU 307 (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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303A GLU 2.7 22.1 + - - +
304A ARG* 3.0 35.0 + - - +
306A LEU* 1.3 69.1 - - - +
308A ASP* 1.3 64.4 + - - +
309A LEU 3.0 6.2 + - - -
310A GLY* 3.0 14.2 + - - -
311A LEU 4.5 5.2 - - - +
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Residues in contact with ASP 308 (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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304A ARG* 2.8 52.4 + - - +
305A GLN* 4.2 6.3 + - - +
307A LEU* 1.3 78.4 - - - +
309A LEU* 1.3 61.5 + - - +
310A GLY 3.5 0.4 + - - -
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Residues in contact with LEU 309 (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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194A PHE* 4.0 17.0 - - + -
239A GLY* 4.2 10.5 - - - +
242A LEU* 3.4 41.1 - - + -
243A LYS* 3.6 41.3 - - + +
246A VAL* 4.2 17.3 - - - +
305A GLN* 3.1 22.4 + - - +
306A LEU* 3.9 4.9 - - - +
307A LEU 3.0 1.2 - - - -
308A ASP* 1.3 82.5 - - - +
310A GLY* 1.3 59.0 + - - +
311A LEU* 3.8 11.1 + - + +
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Residues in contact with GLY 310 (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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246A VAL* 5.0 6.8 - - - +
251A LYS* 4.0 19.2 - - - +
306A LEU 3.3 0.2 + - - -
307A LEU 3.0 13.6 + - - -
308A ASP 3.5 0.8 + - - -
309A LEU* 1.3 79.4 - - - +
311A LEU* 1.3 64.2 + - - +
312A ASP* 4.7 3.5 - - - +
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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