Contacts of the helix formed by residues 281 - 302 (chain B) in PDB entry 3RT0
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 GLY 281 (chain B).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
279B GLY 3.5 5.6 + - - -
280B GLU* 1.3 76.4 - - - +
282B ARG* 1.3 66.2 + - - -
283B GLN 3.4 2.5 - - - -
284B VAL* 3.2 12.4 + - - +
285B GLN* 3.1 22.1 + - - +
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Residues in contact with ARG 282 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
370A ASP* 6.3 0.6 - - - +
182B TYR* 4.7 1.0 + - - -
218B LYS 3.8 8.1 - - - +
219B MET 3.3 23.3 - - - +
220B LEU 2.7 45.5 + - - -
221B MET 3.1 23.6 + - - +
281B GLY* 1.3 68.7 - - - -
283B GLN* 1.3 66.9 + - - +
285B GLN* 3.2 10.1 + - - +
286B TRP* 3.0 30.8 + - - -
338B HIS* 4.2 5.1 + - - -
417B PHE* 3.7 32.4 - - + -
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Residues in contact with GLN 283 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
281B GLY 3.4 0.8 - - - -
282B ARG* 1.3 76.9 - - - +
284B VAL* 1.3 61.3 + - + +
286B TRP* 3.4 2.9 + - - -
287B ASP* 2.8 68.6 + - - +
415B VAL* 3.1 28.8 + - - +
417B PHE* 4.0 24.8 + - + +
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Residues in contact with VAL 284 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
284A VAL* 6.1 5.2 - - + -
280B GLU* 4.0 23.6 - - + +
281B GLY* 3.2 18.5 + - - +
282B ARG 3.1 0.6 - - - -
283B GLN* 1.3 78.8 - - + +
285B GLN* 1.3 65.6 + - - +
287B ASP* 3.5 9.3 + - - +
288B LYS* 3.2 45.6 + - - +
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Residues in contact with GLN 285 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
218B LYS* 3.8 13.3 - - - +
219B MET* 3.2 38.7 - - + +
269B ILE* 4.0 15.6 - - + +
272B GLU* 2.9 27.4 + - - +
280B GLU* 3.6 20.4 - - + +
281B GLY 3.1 18.0 + - - +
282B ARG* 3.2 11.0 + - - +
284B VAL* 1.3 78.5 - - + +
286B TRP* 1.3 59.0 + - + +
288B LYS* 3.3 8.5 + - - +
289B VAL* 2.9 28.8 + - - +
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Residues in contact with TRP 286 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
215B LEU* 3.9 21.8 - - + -
219B MET* 3.0 49.9 + - + +
220B LEU* 4.1 15.0 - - + -
262B LEU* 5.2 0.2 - - + -
266B ILE* 4.7 4.3 - - + -
282B ARG* 3.0 26.2 + - - +
283B GLN* 4.0 4.5 - - - +
285B GLN* 1.3 75.5 - - + +
287B ASP* 1.3 66.1 + - - +
289B VAL* 3.0 44.9 - - + +
290B PHE* 3.0 34.4 + + - +
333B LEU* 3.5 32.1 - - + -
340B VAL* 4.0 14.6 - - + -
415B VAL* 4.0 18.6 - - + -
417B PHE* 3.4 26.5 - + + -
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Residues in contact with ASP 287 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
283B GLN* 2.8 55.9 + - - +
284B VAL* 3.7 10.1 - - - +
286B TRP* 1.3 75.5 - - - +
288B LYS* 1.3 57.1 + - + +
291B THR* 2.7 40.3 + - - +
415B VAL* 3.5 18.8 + - - +
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Residues in contact with LYS 288 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
269B ILE* 5.3 8.5 - - + -
280B GLU* 3.9 21.1 + - - +
284B VAL* 3.2 33.5 + - + +
285B GLN* 3.6 10.5 - - - +
286B TRP 3.3 0.2 - - - -
287B ASP* 1.3 75.4 - - + +
289B VAL* 1.3 65.0 + - - +
291B THR* 4.9 1.8 - - - -
292B SER* 2.8 33.8 + - - +
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Residues in contact with VAL 289 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
219B MET* 4.0 9.4 - - + -
262B LEU* 3.3 29.8 - - + -
265B GLU* 3.3 26.1 - - + +
266B ILE* 4.1 13.9 - - + -
269B ILE* 5.3 5.6 - - + +
285B GLN 2.9 21.2 + - - +
286B TRP* 3.0 40.6 - - + +
288B LYS* 1.3 74.3 - - - +
290B PHE* 1.3 56.1 + - - +
293B CYS* 3.1 26.7 + - - +
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Residues in contact with PHE 290 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
258B LEU* 5.4 0.7 - - + -
262B LEU* 3.9 26.5 - - + -
286B TRP* 3.0 48.7 + + - +
289B VAL* 1.3 78.3 - - + +
291B THR* 1.3 60.3 + - - +
293B CYS* 4.2 3.8 - - - -
294B PHE* 2.9 49.2 + + - +
331B VAL* 4.1 15.5 - - + -
333B LEU* 3.9 24.7 - - + -
340B VAL* 3.9 16.6 - - + -
342B SER* 3.3 38.8 - - - +
413B PRO* 4.0 2.0 - - + -
415B VAL* 3.6 16.8 - - + -
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Residues in contact with THR 291 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
287B ASP* 2.7 27.9 + - - +
288B LYS* 4.3 2.0 - - - -
290B PHE* 1.3 77.0 - - - +
292B SER* 1.3 59.6 + - - +
294B PHE 3.3 0.2 + - - -
295B LEU* 2.9 52.7 + - + +
412B GLU* 4.3 19.5 - - + +
413B PRO* 3.8 20.5 + - + +
415B VAL* 5.4 1.0 - - - +
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Residues in contact with SER 292 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
265B GLU* 3.5 27.3 + - - -
288B LYS* 2.8 25.0 + - - +
291B THR* 1.3 78.2 - - - +
293B CYS* 1.3 57.5 + - - +
295B LEU* 3.4 5.7 + - - +
296B THR* 2.8 36.6 + - - -
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Residues in contact with CYS 293 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
258B LEU* 3.5 31.6 - - - -
261B ALA* 4.2 5.9 - - - +
262B LEU* 3.7 41.3 - - + +
265B GLU* 4.0 8.2 + - + -
289B VAL 3.1 20.0 + - - +
290B PHE* 3.6 7.4 - - - +
291B THR 3.3 0.2 - - - -
292B SER* 1.3 76.1 - - - +
294B PHE* 1.3 69.6 + - - +
296B THR* 3.3 5.4 + - - -
297B VAL* 3.1 23.0 + - - +
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Residues in contact with PHE 294 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
258B LEU* 4.2 21.5 - - + -
290B PHE* 2.9 36.1 + + - +
293B CYS* 1.3 83.6 - - - +
295B LEU* 1.3 60.1 + - - +
297B VAL* 3.3 4.8 + - - +
298B ASP* 2.9 28.9 + - - +
329B ALA* 3.9 22.4 - - + -
331B VAL* 4.2 6.5 - - + -
342B SER* 3.3 33.2 - - - -
344B CYS* 3.6 29.6 - - + -
400B ILE* 3.9 14.7 - - + +
411B PRO 3.7 15.9 - - - +
413B PRO* 3.7 23.6 - - + -
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Residues in contact with LEU 295 (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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291B THR* 2.9 33.8 + - + +
292B SER* 3.9 5.6 - - - +
294B PHE* 1.3 77.7 - - + +
296B THR* 1.3 57.9 + - - +
298B ASP* 3.7 5.8 - - - +
299B GLY* 2.9 25.1 + - - -
305B ILE* 4.1 4.5 - - - +
411B PRO* 3.8 45.3 - - + +
412B GLU* 4.0 12.6 - - + -
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Residues in contact with THR 296 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
257B ARG* 4.2 10.8 - - - +
261B ALA* 4.6 7.0 - - + -
264B GLU* 5.4 1.8 - - - +
265B GLU* 4.2 8.8 + - - +
268B ARG* 5.4 4.9 + - - +
292B SER* 2.8 24.0 + - - -
293B CYS* 3.6 6.7 - - - -
294B PHE 3.1 0.2 - - - -
295B LEU* 1.3 75.3 - - - +
297B VAL* 1.3 67.0 + - - +
299B GLY* 3.3 1.4 + - - -
300B GLU* 3.0 44.8 + - + +
305B ILE* 3.8 18.7 - - + +
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Residues in contact with VAL 297 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
253B TYR* 4.0 20.4 - - + -
254B CYS* 4.3 16.4 - - - -
257B ARG* 4.2 9.2 - - + -
258B LEU* 3.4 41.1 - - + -
261B ALA* 4.0 11.9 - - + -
293B CYS 3.1 7.7 + - - +
294B PHE* 3.6 7.2 - - - +
296B THR* 1.3 77.2 - - - +
298B ASP* 1.3 60.4 + - - +
300B GLU* 3.1 10.7 + - - +
301B ILE* 2.9 33.0 + - + +
400B ILE* 4.2 15.0 - - + -
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Residues in contact with ASP 298 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
294B PHE 2.9 17.0 + - - +
295B LEU* 3.7 6.8 - - - +
296B THR 3.2 0.2 - - - -
297B VAL* 1.3 78.0 - - - +
299B GLY* 1.3 57.1 + - - +
301B ILE* 3.4 6.2 - - - +
302B GLU* 3.1 28.3 + - - +
400B ILE* 4.3 9.6 - - + -
401B GLY* 3.0 25.5 + - - -
406B LYS* 2.9 39.1 + - - -
411B PRO* 3.5 27.7 - - + +
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Residues in contact with GLY 299 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
295B LEU 2.9 16.9 + - - -
296B THR 3.8 1.3 - - - -
298B ASP* 1.3 77.0 + - - +
300B GLU* 1.3 63.5 + - - +
302B GLU* 3.5 7.4 + - - -
303B GLY 3.1 3.6 + - - -
304B LYS* 2.9 33.3 + - - -
305B ILE* 3.2 18.9 + - - -
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Residues in contact with GLU 300 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
253B TYR* 2.6 35.0 + - + +
257B ARG* 2.8 46.4 + - - +
296B THR* 3.0 28.6 + - - +
297B VAL* 3.1 8.5 + - - +
299B GLY* 1.3 76.3 - - - +
301B ILE* 1.3 61.6 + - - +
303B GLY* 3.3 9.5 + - - -
305B ILE* 3.6 30.6 - - + +
306B GLY 4.2 11.4 - - - +
307B ARG* 3.6 25.5 + - + -
315B LYS* 5.5 1.4 + - - -
318B GLU 3.6 2.9 - - - +
320B VAL* 4.1 2.0 - - - -
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Residues in contact with ILE 301 (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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250B VAL* 4.2 20.9 - - + -
253B TYR* 3.5 28.5 - - + -
297B VAL* 2.9 23.9 + - + +
298B ASP* 3.4 12.6 - - - +
300B GLU* 1.3 78.6 - - - +
302B GLU* 1.3 61.6 + - + +
319B ALA* 3.1 6.4 - - - -
320B VAL* 3.0 37.5 + - + -
321B ALA 5.0 3.8 - - - +
322B SER 5.6 0.2 - - - +
325B VAL 4.9 2.0 - - - +
400B ILE* 4.9 4.7 - - + -
401B GLY* 3.9 29.8 - - - +
403B ARG* 3.5 21.4 + - + +
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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
----------------------------------------------------------
298B ASP* 3.1 16.6 + - - +
299B GLY* 4.0 6.4 - - - +
300B GLU 3.4 0.2 - - - -
301B ILE* 1.3 82.9 - - + +
303B GLY* 1.3 59.9 + - - +
304B LYS* 3.7 36.1 + - + +
319B ALA* 4.2 9.4 - - - +
403B ARG* 3.8 45.2 + - + +
406B LYS* 4.0 20.8 - - - +
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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
------------------------------------------------------------
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