Contacts of the helix formed by residues 244 - 260 (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 244 (chain B).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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243B ARG* 1.3 69.2 - - - +
245B PRO* 1.3 64.5 - - - +
246B VAL* 2.9 16.5 + - - +
247B THR* 3.0 16.9 + - + +
248B ARG 2.8 31.2 + - - -
313B GLU* 2.9 15.7 + - - +
384B ARG* 2.8 41.1 + - - -
391B ASN* 5.4 0.5 + - - -
404B TRP* 3.2 33.7 - - + +
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Residues in contact with PRO 245 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
243B ARG 2.8 7.3 - - - +
244B ASP* 1.3 87.5 - - - +
246B VAL* 1.3 56.4 + - + +
248B ARG* 3.8 8.2 + - + +
249B ALA* 3.0 29.6 + - - +
289B GLY* 3.6 18.6 - - - +
291B TYR* 3.8 14.1 - - + +
387B TYR* 3.5 38.5 + - + -
391B ASN* 3.4 25.6 - - - +
404B TRP* 3.7 15.7 - - + -
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Residues in contact with VAL 246 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
244B ASP* 2.9 13.7 + - - +
245B PRO* 1.3 75.9 - - - +
247B THR* 1.3 63.0 + - + +
249B ALA* 3.3 5.4 + - - +
250B ILE* 3.0 48.9 + - + +
380B VAL* 4.2 22.0 - - + -
383B LEU* 4.1 15.3 - - + -
384B ARG* 3.6 43.7 - - + +
387B TYR* 3.9 21.5 - - + -
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Residues in contact with THR 247 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
243B ARG* 2.9 35.1 + - - +
244B ASP* 3.0 29.9 + - + +
246B VAL* 1.3 75.0 - - + +
248B ARG* 1.3 59.8 + - - +
250B ILE* 3.8 8.9 - - + -
251B SER* 2.8 31.0 + - - -
313B GLU* 4.5 1.0 + - - -
372B HIS* 3.8 6.3 - - - +
384B ARG* 4.3 10.5 - - - +
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Residues in contact with ARG 248 (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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160B VAL* 3.9 11.2 - - + -
161B LYS* 2.9 37.0 + - - +
162B LYS* 3.9 6.5 - - + +
243B ARG* 3.8 17.7 - - + +
244B ASP 2.8 16.5 + - - +
245B PRO 3.8 4.0 + - - +
247B THR* 1.3 78.0 + - - +
249B ALA* 1.3 60.1 + - - +
251B SER* 3.3 3.8 + - - -
252B ASP* 2.9 70.4 + - - +
285B ALA* 2.8 32.9 + - - +
288B ILE* 3.6 27.5 - - - +
289B GLY* 4.1 7.6 - - - +
291B TYR* 3.4 26.2 - - - +
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Residues in contact with ALA 249 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
245B PRO 3.0 19.5 + - - +
246B VAL* 3.6 6.5 - - - +
247B THR 3.3 0.2 - - - -
248B ARG* 1.3 81.3 - - - +
250B ILE* 1.3 56.8 + - - +
252B ASP* 3.3 3.1 + - - +
253B TYR* 2.9 28.2 + - - +
266B PHE* 3.7 19.0 - - + -
285B ALA* 3.4 31.8 - - + +
286B ILE* 5.0 2.7 - - + -
383B LEU* 5.2 2.9 - - + -
387B TYR* 4.6 6.5 - - + +
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Residues in contact with ILE 250 (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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246B VAL* 3.0 32.5 + - + +
247B THR* 3.9 7.4 - - + +
249B ALA* 1.3 73.2 - - - +
251B SER* 1.3 56.9 + - - +
253B TYR* 3.4 2.4 + - + +
254B THR* 2.8 39.8 + - - +
266B PHE* 3.7 28.0 - - + -
372B HIS* 3.7 31.6 - - + +
373B PRO* 4.5 4.0 - - + +
375B ILE* 3.6 37.9 - - + -
380B VAL* 4.8 4.9 - - + -
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Residues in contact with SER 251 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
162B LYS* 3.2 25.7 - - - -
243B ARG* 3.4 12.8 + - - -
247B THR 2.8 18.4 + - - -
248B ARG 3.5 4.9 - - - -
250B ILE* 1.3 74.9 - - - +
252B ASP* 1.3 65.6 + - - +
254B THR* 3.2 4.7 + - - -
255B GLN* 2.9 23.4 + - - +
370B ARG* 5.1 1.0 + - - -
372B HIS* 3.7 11.6 - - - -
603B A3P 2.7 26.5 + - - -
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Residues in contact with ASP 252 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
161B LYS* 2.9 21.6 + - - +
162B LYS* 3.7 9.5 - - - +
248B ARG* 2.9 51.5 + - - +
249B ALA 3.4 5.8 - - - +
251B SER* 1.3 74.7 - - - +
253B TYR* 1.3 62.6 + - - +
255B GLN* 3.1 10.8 + - - +
256B THR 3.2 1.2 + - - -
284B SER* 4.9 0.5 + - - -
285B ALA* 4.1 4.6 - - + -
288B ILE* 3.5 15.4 - - - +
701B NA 2.4 48.6 - - - -
1C SGN 2.8 12.3 + - - +
2C IDS 3.5 0.2 - - - +
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Residues in contact with TYR 253 (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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249B ALA 2.9 16.5 + - - +
250B ILE* 3.6 6.3 - - + +
252B ASP* 1.3 77.4 - - - +
254B THR* 1.3 58.8 + - - +
256B THR* 3.2 4.7 + - - -
257B LEU* 2.8 57.0 + - + +
263B ILE* 3.4 28.0 + - + +
264B PRO 2.7 29.4 + - - -
265B THR* 3.3 9.4 - - - -
266B PHE* 3.5 42.4 - + + -
269B LEU* 4.0 6.3 - - + -
283B TRP* 4.1 13.0 - + + -
373B PRO* 4.4 12.1 - - + -
1C SGN 3.6 19.7 + - - +
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Residues in contact with THR 254 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
250B ILE 2.8 21.6 + - - -
251B SER* 3.5 7.9 - - - -
253B TYR* 1.3 77.7 - - - +
255B GLN* 1.3 64.5 + - - +
257B LEU* 3.2 13.4 + - + +
258B SER* 3.0 22.3 + - - -
370B ARG* 3.9 23.6 - - + -
371B THR 3.8 21.8 - - - +
372B HIS* 4.0 7.3 - - + -
373B PRO* 3.2 25.1 - - + +
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Residues in contact with GLN 255 (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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161B LYS* 4.4 0.6 - - - +
162B LYS* 2.7 39.1 + - - +
251B SER 2.9 12.1 + - - +
252B ASP* 3.1 10.5 + - - +
254B THR* 1.3 77.0 - - - +
256B THR* 1.3 61.9 + - - +
258B SER* 2.5 22.7 + - - -
259B LYS* 3.5 7.0 + - - +
368B LYS* 5.3 0.2 + - - -
370B ARG* 3.0 27.0 + - - +
701B NA 4.3 1.8 - - - -
2C IDS 2.6 34.1 + - - +
3C SGN 3.5 17.5 + - - -
4C UAP 3.0 32.0 + - - +
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Residues in contact with THR 256 (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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252B ASP 3.2 1.6 + - - -
253B TYR 3.2 7.5 + - - -
255B GLN* 1.3 77.0 - - - +
257B LEU* 1.3 53.1 + - - +
259B LYS* 2.9 13.9 + - + +
260B ARG* 2.7 62.9 + - + +
263B ILE* 4.0 14.8 - - + -
701B NA 2.3 28.5 - - - -
1C SGN 2.8 32.7 + - - +
2C IDS 4.1 1.2 + - - -
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Residues in contact with LEU 257 (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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253B TYR* 2.8 39.8 + - + +
254B THR* 3.3 15.5 - - + +
255B GLN 3.2 0.2 - - - -
256B THR* 1.3 77.1 - - - +
258B SER* 1.3 61.1 + - - +
260B ARG 3.7 4.7 - - - +
261B PRO* 3.1 49.7 - - + +
263B ILE* 3.9 22.4 - - + +
373B PRO* 4.7 16.8 - - + -
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Residues in contact with SER 258 (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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254B THR* 3.0 12.1 + - - -
255B GLN 2.5 20.8 + - - -
257B LEU* 1.3 76.2 - - - +
259B LYS* 1.3 64.7 + - - +
261B PRO* 5.0 3.0 - - - +
370B ARG* 3.7 28.0 + - - -
4C UAP 5.1 0.2 + - - -
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Residues in contact with LYS 259 (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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255B GLN* 3.8 12.8 - - - -
256B THR* 2.9 8.5 + - - +
258B SER* 1.3 90.4 - - - +
260B ARG* 1.3 66.7 + - + +
261B PRO* 3.7 8.6 - - - +
2C IDS 2.6 35.4 + - - -
3C SGN 2.9 31.2 + - - +
4C UAP 2.9 28.7 + - - +
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Residues in contact with ARG 260 (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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256B THR* 2.7 27.7 + - + +
257B LEU* 3.2 7.6 - - - +
259B LYS* 1.3 82.1 - - + +
261B PRO* 1.3 65.8 - - - +
262B ASP 3.2 4.2 + - - -
263B ILE* 3.4 48.1 - - + +
1C SGN 3.5 22.0 + - - -
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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
------------------------------------------------------------
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