Contacts of the helix formed by residues 295 - 311 (chain B) in PDB entry 1T0H
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 SER 295 (chain B).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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290B SER* 4.1 5.6 - - - +
292B THR 5.1 1.1 - - - -
293B ARG 3.4 6.4 + - - -
294B SER* 1.3 77.3 + - - +
296B LEU* 1.3 58.9 + - - +
297B ALA* 3.6 9.0 + - - +
298B GLU* 2.9 28.7 + - - +
299B VAL* 3.0 29.3 + - - +
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Residues in contact with LEU 296 (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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272B LEU* 3.9 38.6 - - + +
288B GLU* 3.4 43.1 - - + +
289B ARG* 3.9 6.0 - - - +
290B SER* 3.8 23.9 - - - +
294B SER 3.9 0.4 + - - -
295B SER* 1.3 72.6 - - - +
297B ALA* 1.3 58.2 + - - +
299B VAL* 3.7 5.1 - - + +
300B GLN* 2.9 29.8 + - - +
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Residues in contact with ALA 297 (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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295B SER* 3.2 7.9 + - - +
296B LEU* 1.3 77.2 - - - +
298B GLU* 1.3 64.4 + - - +
300B GLN* 3.4 6.6 + - - +
301B SER* 3.1 22.9 + - - -
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Residues in contact with GLU 298 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
267B THR* 5.5 2.4 + - - -
268B ALA* 3.5 19.3 - - + +
293B ARG 4.6 2.1 - - - +
294B SER* 2.9 35.0 + - - -
295B SER* 2.9 20.5 + - - +
297B ALA* 1.3 75.4 - - - +
299B VAL* 1.3 61.6 + - - +
301B SER* 3.3 8.3 + - - -
302B GLU* 3.0 24.6 + - + +
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Residues in contact with VAL 299 (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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268B ALA* 4.5 3.4 - - + -
269B ASP 3.2 31.4 - - - +
270B ILE* 4.3 6.7 - - + +
272B LEU* 4.3 10.8 - - + +
273B ALA* 3.9 37.7 - - + +
294B SER* 3.8 13.0 - - - +
295B SER 3.0 21.0 + - - +
296B LEU* 3.7 8.3 - - + +
298B GLU* 1.3 76.7 - - - +
300B GLN* 1.3 58.6 + - - +
302B GLU* 3.0 8.6 + - - +
303B ILE* 2.9 29.6 + - + +
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Residues in contact with GLN 300 (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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273B ALA* 5.7 2.6 - - - +
296B LEU 2.9 18.0 + - - +
297B ALA* 3.8 7.2 - - - +
299B VAL* 1.3 78.4 - - - +
301B SER* 1.3 62.6 + - - +
303B ILE* 3.2 19.0 + - - +
304B GLU* 3.0 63.1 + - - +
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Residues in contact with SER 301 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
297B ALA 3.1 14.2 + - - -
298B GLU* 3.6 11.0 - - - -
299B VAL 3.3 0.2 - - - -
300B GLN* 1.3 74.5 - - - +
302B GLU* 1.3 64.8 + - - +
304B GLU* 3.4 13.3 + - - +
305B ARG* 3.0 27.4 + - - +
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Residues in contact with GLU 302 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
265B ARG 4.3 0.5 - - - +
266B VAL* 3.9 18.4 - - + +
267B THR 4.8 1.9 + - - -
268B ALA* 3.9 22.6 - - + +
270B ILE* 4.5 11.9 - - + -
298B GLU* 3.0 21.8 + - + +
299B VAL 3.0 6.9 + - - +
301B SER* 1.3 77.5 + - - +
303B ILE* 1.3 65.4 + - - +
305B ARG* 2.9 48.0 + - - +
306B ILE* 3.0 30.5 + - + +
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Residues in contact with ILE 303 (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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270B ILE* 4.0 16.4 - - + -
273B ALA* 3.8 30.1 - - + -
299B VAL* 2.9 19.4 + - + +
300B GLN* 3.7 23.3 - - - +
302B GLU* 1.3 74.6 - - - +
304B GLU* 1.3 63.5 + - + +
306B ILE* 3.1 6.7 + - + +
307B PHE* 3.0 52.3 + - + -
332B THR* 5.8 0.2 - - - -
333B SER* 4.0 10.3 - - - +
334B LEU* 3.7 33.9 - - + -
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Residues in contact with GLU 304 (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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300B GLN* 3.0 47.3 + - - +
301B SER* 3.6 13.5 - - - +
303B ILE* 1.3 77.4 - - + +
305B ARG* 1.3 56.7 + - - +
307B PHE* 3.4 8.7 + - - +
308B GLU* 3.0 28.3 + - - +
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Residues in contact with ARG 305 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
264B THR* 2.9 23.7 + - - +
265B ARG 3.0 26.9 + - - -
266B VAL* 4.0 8.7 - - - +
301B SER 3.0 14.3 + - - +
302B GLU* 2.9 42.4 + - - +
304B GLU* 1.3 77.5 - - - +
306B ILE* 1.3 58.8 + - - +
308B GLU* 3.3 7.6 + - + +
309B LEU* 2.9 46.1 + - + +
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Residues in contact with ILE 306 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
224B PRO* 4.6 5.2 - - + -
228B PRO* 4.4 15.5 - - + -
266B VAL* 4.5 14.8 - - + -
270B ILE* 4.6 7.2 - - + -
302B GLU* 3.0 25.8 + - + +
303B ILE* 3.1 13.7 + - + +
305B ARG* 1.3 77.1 - - + +
307B PHE* 1.3 66.1 + - - +
309B LEU* 3.3 13.4 + - + +
310B ALA* 3.2 21.7 + - + +
316B VAL* 4.7 4.3 - - + +
318B LEU* 4.0 39.9 - - + -
334B LEU* 3.9 31.2 - - + -
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Residues in contact with PHE 307 (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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222B VAL* 3.9 16.8 - - + -
223B VAL* 3.3 31.6 - - - -
224B PRO* 3.5 40.2 - - + -
225B SER 5.4 1.0 + - - -
303B ILE* 3.0 46.3 + - + +
304B GLU* 3.6 11.0 - - - +
306B ILE* 1.3 76.1 - - - +
308B GLU* 1.3 63.0 + - - +
310B ALA* 3.1 12.8 + - - +
311B ARG* 3.1 12.3 + - - +
333B SER* 3.7 15.9 - - - -
334B LEU* 4.2 3.6 - - + -
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Residues in contact with GLU 308 (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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304B GLU 3.0 17.0 + - - +
305B ARG* 3.7 8.1 - - - +
307B PHE* 1.3 75.1 - - - +
309B LEU* 1.3 64.0 + - - +
311B ARG* 3.1 65.4 + - - +
312B THR* 4.6 2.1 + - - +
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Residues in contact with LEU 309 (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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262B SER* 4.2 28.9 + - - +
264B THR* 3.8 31.4 - - + -
305B ARG* 2.9 35.8 + - + +
306B ILE* 3.3 15.7 + - - +
308B GLU* 1.3 76.8 - - + +
310B ALA* 1.3 59.4 + - - +
311B ARG 3.7 0.2 + - - -
312B THR* 4.4 9.4 + - - -
314B GLN* 4.6 9.9 - - - +
316B VAL* 3.8 18.1 - - + +
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Residues in contact with ALA 310 (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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224B PRO* 4.0 4.5 - - + -
225B SER* 3.7 18.2 - - - +
226B MSE 3.7 35.1 - - + +
306B ILE* 3.2 9.6 + - + +
307B PHE 3.1 9.7 + - - +
309B LEU* 1.3 76.7 - - - +
311B ARG* 1.3 64.6 + - - +
312B THR 3.2 2.7 - - - -
313B LEU* 3.0 17.3 + - - -
314B GLN 4.7 0.7 - - - -
316B VAL* 3.7 13.9 - - + -
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Residues in contact with ARG 311 (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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59A PRO* 6.2 0.3 - - - +
60A VAL* 4.4 16.9 + - - +
61A ALA 5.7 3.6 - - - +
225B SER* 4.7 9.6 - - - -
307B PHE 3.1 9.3 + - - +
308B GLU* 3.1 50.9 + - - +
310B ALA* 1.3 77.4 - - - +
312B THR* 1.3 81.3 + - + +
313B LEU* 3.3 9.4 + - - +
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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