Contacts of the helix formed by residues 318 - 330 (chain B) in PDB entry 1T8U
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 318 (chain B).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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314B ARG* 2.7 36.3 + - + +
317B SER* 1.3 80.3 + - - +
319B PRO* 1.3 67.3 - - - +
320B ALA* 4.1 6.6 + - - +
321B GLY* 3.1 32.4 + - - -
322B GLU* 3.1 10.4 + - - +
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Residues in contact with PRO 319 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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171B PHE* 4.2 9.9 - - + -
315B LEU* 3.3 27.5 - - + +
316B ILE 3.9 6.3 - - - +
317B SER 3.8 5.2 - - - +
318B ASP* 1.3 88.8 - - - +
320B ALA* 1.3 59.4 + - - +
322B GLU 3.2 1.0 + - - -
323B LEU* 2.8 36.7 + - - +
341B PHE* 3.7 43.7 - - + -
350B PRO* 4.3 12.8 - - + -
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Residues in contact with ALA 320 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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318B ASP* 3.3 6.6 + - - +
319B PRO* 1.3 82.1 - - + +
321B GLY* 1.3 63.3 + - - +
323B LEU* 3.5 5.3 + - - +
324B GLY* 3.1 19.1 + - - -
334B ARG* 5.1 1.2 + - - -
336B ILE 4.8 3.8 - - - +
337B THR* 3.7 10.3 - - - +
338B ASP* 3.5 38.6 - - + +
341B PHE* 3.8 10.7 - - + -
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Residues in contact with GLY 321 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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314B ARG* 3.6 22.0 + - - -
318B ASP* 3.1 28.3 + - - -
320B ALA* 1.3 79.5 - - - +
322B GLU* 1.3 61.7 + - - +
324B GLY* 3.2 10.6 + - - -
325B ARG* 3.6 7.4 + - - +
334B ARG* 4.6 5.4 + - - -
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Residues in contact with GLU 322 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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310B VAL* 3.1 29.4 - - + +
311B SER* 3.9 13.9 - - - +
314B ARG* 2.9 39.7 + - + +
315B LEU* 3.7 39.7 - - + +
318B ASP 3.1 8.2 + - - +
319B PRO 3.7 5.2 - - - +
321B GLY* 1.3 74.6 - - - +
323B LEU* 1.3 65.3 + - + +
325B ARG* 2.9 38.4 + - - +
326B VAL* 3.1 15.2 + - + +
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Residues in contact with LEU 323 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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168B LEU* 4.3 10.3 - - + -
171B PHE* 4.1 22.4 - - + -
172B LEU* 3.7 34.3 - - + -
315B LEU* 3.8 24.9 - - + -
319B PRO 2.8 28.0 + - - +
320B ALA 3.9 4.9 - - - +
322B GLU* 1.3 74.5 - - - +
324B GLY* 1.3 62.2 + - - +
326B VAL* 3.8 4.9 - - + -
327B GLN* 3.0 36.0 + - + +
336B ILE* 3.9 36.6 - - + +
341B PHE* 4.6 1.1 - - + -
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Residues in contact with GLY 324 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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320B ALA 3.1 12.2 + - - -
321B GLY 3.2 2.4 + - - -
322B GLU 2.9 2.0 + - - -
323B LEU* 1.3 78.0 - - - +
325B ARG* 1.3 61.6 + - - +
327B GLN* 3.8 7.4 - - - +
328B ASP* 3.2 27.2 + - - +
334B ARG* 3.1 37.6 + - - -
336B ILE 5.6 0.2 - - - -
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Residues in contact with ARG 325 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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308B LEU* 3.6 30.2 - - + +
309B PHE* 3.2 27.9 + - - +
310B VAL* 4.1 2.0 - - - +
311B SER* 4.7 1.0 - - - +
314B ARG* 3.4 29.6 - - - +
321B GLY 3.6 3.5 + - - +
322B GLU* 2.9 31.4 + - - +
324B GLY* 1.3 77.3 - - - +
326B VAL* 1.3 62.4 + - + +
328B ASP* 3.3 9.9 + - - +
329B PHE* 2.9 24.8 + - - +
334B ARG* 4.4 1.2 - - - +
400B HIS* 6.0 7.4 - - - +
402B PHE* 5.7 0.8 - - - -
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Residues in contact with VAL 326 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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168B LEU* 4.1 13.5 - - + -
172B LEU* 3.8 29.2 - - + -
239B ILE* 4.0 18.2 - - + -
308B LEU* 3.8 9.6 - - + -
310B VAL* 4.0 26.0 - - + -
322B GLU* 3.1 20.4 + - - +
323B LEU* 3.8 10.8 - - + +
324B GLY 3.3 0.2 - - - -
325B ARG* 1.3 75.5 - - + +
327B GLN* 1.3 58.4 + - - +
329B PHE* 3.2 3.1 + - - +
330B LEU* 2.9 39.4 + - + +
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Residues in contact with GLN 327 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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172B LEU* 4.8 9.4 - - + -
175B HIS* 3.3 19.5 - - + -
323B LEU* 3.0 35.0 + - + +
324B GLY* 3.8 8.8 - - - +
326B VAL* 1.3 75.3 - - - +
328B ASP* 1.3 61.9 + - - +
330B LEU* 3.2 4.0 + - - +
331B GLY 3.0 4.0 + - - -
332B LEU* 2.8 49.8 + - + +
333B LYS 4.3 0.7 - - - +
334B ARG* 3.8 12.6 - - + +
335B ILE 2.9 24.2 + - - -
336B ILE* 3.1 44.1 + - + +
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Residues in contact with ASP 328 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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324B GLY 3.2 10.6 + - - +
325B ARG* 3.5 9.6 - - - +
327B GLN* 1.3 75.3 - - - +
329B PHE* 1.3 64.8 + - - +
331B GLY* 2.9 13.9 + - - -
332B LEU 4.4 3.8 - - - +
334B ARG* 2.8 46.9 + - - +
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Residues in contact with PHE 329 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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237B LYS* 3.0 45.8 + - + +
238B LEU 3.6 16.4 - - - -
239B ILE* 3.8 16.6 - - + -
305B ARG 3.7 22.9 - - - -
306B GLN* 3.7 14.8 - - - -
307B MET 3.8 6.5 - - - -
308B LEU* 3.6 47.6 - - + -
325B ARG 2.9 13.5 + - - +
326B VAL 3.4 7.0 - - - +
328B ASP* 1.3 77.3 - - - +
330B LEU* 1.3 71.0 + - + +
331B GLY 3.4 0.5 + - - -
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Residues in contact with LEU 330 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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155B ALA* 3.5 30.1 - - + -
172B LEU* 4.1 5.6 - - + -
211B ILE* 4.6 17.2 - - + +
213B MET* 3.9 28.0 - - + -
237B LYS* 3.8 15.7 + - + +
239B ILE* 4.1 6.3 - - + -
326B VAL* 2.9 35.2 + - + +
327B GLN 3.8 3.8 - - - +
328B ASP 3.2 0.2 - - - -
329B PHE* 1.3 96.1 - - + +
331B GLY* 1.3 61.8 + - - +
332B LEU* 3.9 27.8 - - + +
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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