Contacts of the helix formed by residues 287 - 308 (chain B) in PDB entry 5TQB
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 287 (chain B).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
51A TYR* 2.7 31.1 + - - -
254B PHE* 4.2 3.4 - - - -
281B ILE* 4.4 0.6 - - - +
284B ASP* 3.5 22.1 + - - -
285B ASP 3.3 4.0 - - - -
286B LEU* 1.3 75.3 - - - +
288B VAL* 1.3 64.5 + - - +
290B VAL* 3.1 31.8 + - - +
291B TRP* 3.2 25.8 + - - -
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Residues in contact with VAL 288 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
51A TYR* 5.9 0.2 - - - -
286B LEU 3.4 3.9 + - - +
287B SER* 1.3 71.1 - - - +
289B GLU* 1.3 63.4 + - - +
291B TRP* 3.2 10.6 + - - +
292B TYR* 3.1 18.9 + - - +
332B CYS* 3.7 19.3 - - - +
335B VAL* 3.9 24.0 - - + +
336B PHE* 3.8 36.8 - - + -
339B GLU* 4.8 2.9 - - + -
341B TYR* 3.6 43.4 - - + -
346B LEU* 4.0 6.7 - - + -
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Residues in contact with GLU 289 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
48A ARG 4.8 1.6 - - - +
49A GLN* 4.6 7.5 - - - +
50A PRO* 4.2 5.5 - - - +
51A TYR* 4.1 27.6 + - + -
69A GLY* 3.8 23.6 + - - +
258B VAL* 4.3 4.8 - - + +
262B ARG* 4.2 3.5 + - - -
287B SER* 3.3 1.2 + - - -
288B VAL* 1.3 79.2 - - - +
290B VAL* 1.3 57.6 + - - +
292B TYR* 3.6 6.9 + - - +
293B LEU* 3.0 40.4 + - + +
341B TYR* 3.7 18.0 + - - +
343B ASP* 5.0 1.2 - - - +
346B LEU* 4.4 14.3 - - + +
406B EDO 2.3 31.1 + - - -
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Residues in contact with VAL 290 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
51A TYR* 5.0 1.1 - - + -
254B PHE* 3.8 22.4 - - + -
258B VAL* 4.2 16.8 - - + -
277B THR* 3.9 11.4 - - + +
280B LEU* 3.9 25.1 - - + -
281B ILE* 3.6 25.8 - - + -
287B SER* 3.1 26.3 + - - +
288B VAL 3.2 0.8 - - - -
289B GLU* 1.3 78.0 - - - +
291B TRP* 1.3 64.1 + - - +
292B TYR 3.2 0.2 - - - -
293B LEU* 4.0 6.9 - - + +
294B GLY 3.0 19.4 + - - -
328B TRP* 3.7 4.2 - - - -
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Residues in contact with TRP 291 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
204A ARG* 4.1 16.2 - - - -
281B ILE* 3.6 33.9 - - + +
285B ASP 2.9 24.7 + - - -
287B SER 3.2 28.1 + - - -
288B VAL* 3.2 3.6 + - - +
290B VAL* 1.3 76.4 - - - +
292B TYR* 1.3 58.8 + - - +
295B GLY* 2.9 25.6 + - - -
327B LYS 5.1 0.4 - - - -
328B TRP* 3.3 69.6 - + - +
331B GLN* 3.5 29.9 - - + +
332B CYS* 3.6 24.5 - - + -
335B VAL* 4.0 15.1 - - + +
403B EDO 3.7 18.8 - - - -
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Residues in contact with TYR 292 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
69A GLY 3.6 20.4 - - - -
70A ARG* 3.4 7.1 - - - -
71A ALA* 3.1 16.6 + - - +
101A PHE* 4.7 2.0 - + - -
288B VAL 3.1 12.2 + - - +
289B GLU* 3.6 7.2 - - + +
291B TRP* 1.3 77.4 - - - +
293B LEU* 1.3 72.4 + - + +
295B GLY* 3.1 1.9 + - - -
296B TYR* 2.7 39.3 + - + +
329B LEU* 4.1 14.0 - - + +
332B CYS* 4.0 6.8 - - - -
346B LEU* 3.8 46.2 - - + -
349B HIS* 2.5 41.1 + + + -
350B ALA* 4.4 5.2 - - + -
353B LEU* 4.1 13.7 - - + -
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Residues in contact with LEU 293 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
69A GLY 4.6 2.5 - - - +
101A PHE* 3.5 37.2 - - + -
258B VAL* 3.8 34.3 - - + +
261B VAL* 3.8 23.6 - - + -
262B ARG* 4.1 12.8 - - + +
265B ILE* 3.8 11.0 - - + +
277B THR* 4.4 3.6 - - + -
289B GLU* 3.0 29.1 + - + +
290B VAL* 3.4 8.7 + - + +
292B TYR* 1.3 86.4 - - + +
294B GLY* 1.3 55.9 + - - +
296B TYR* 4.5 1.8 - - + -
297B ALA* 2.8 32.7 + - - +
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Residues in contact with GLY 294 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
277B THR* 3.9 10.0 - - - +
290B VAL 3.0 12.3 + - - -
293B LEU* 1.3 74.0 - - - +
295B GLY* 1.3 64.6 + - - +
297B ALA* 3.5 2.0 + - - +
298B ARG* 2.9 49.8 + - - +
328B TRP* 3.6 16.8 - - - -
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Residues in contact with GLY 295 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
291B TRP 2.9 12.3 + - - -
292B TYR 3.6 2.9 - - - -
294B GLY* 1.3 78.0 - - - +
296B TYR* 1.3 56.1 + - - +
298B ARG 3.3 0.7 + - - -
299B TYR* 2.9 12.5 + - - +
325B SER* 2.6 34.6 + - - -
328B TRP* 3.6 21.9 - - - +
329B LEU* 4.0 11.2 - - - -
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Residues in contact with TYR 296 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
71A ALA* 3.5 27.7 - - + +
72A VAL 5.6 0.7 + - - -
100A MSE 3.7 20.4 - - - +
101A PHE* 4.2 8.7 - + - -
265B ILE* 4.1 14.6 - - + -
292B TYR* 2.7 33.1 + - + +
293B LEU* 3.8 5.8 - - - +
295B GLY* 1.3 69.8 - - - +
297B ALA* 1.3 60.6 + - - +
299B TYR* 3.1 9.9 + + - +
300B ARG* 2.9 67.5 + - + +
329B LEU* 4.4 1.0 - - - +
349B HIS* 3.8 19.9 - + - -
353B LEU* 3.6 32.5 - - + -
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Residues in contact with ALA 297 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
265B ILE* 3.8 25.7 - - + +
270B GLU* 3.7 11.1 - - + +
273B ALA* 4.2 13.5 - - + +
274B LEU* 4.1 15.7 - - + +
277B THR* 5.4 0.9 - - + -
293B LEU 2.8 19.2 + - - +
294B GLY* 3.8 7.4 - - - +
296B TYR* 1.3 77.7 - - - +
298B ARG* 1.3 57.3 + - - +
300B ARG* 4.6 3.1 - - - -
301B LEU* 3.0 27.2 + - - +
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Residues in contact with ARG 298 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
274B LEU* 3.4 54.4 + - + +
277B THR* 3.2 18.4 + - - -
278B GLU* 3.9 12.7 + - - +
294B GLY* 2.9 38.5 + - - +
295B GLY 3.7 4.0 - - - +
296B TYR 3.1 0.2 - - - -
297B ALA* 1.3 74.8 - - - +
299B TYR* 1.3 60.5 + - - +
301B LEU* 4.2 4.7 - - - -
302B GLY* 3.0 22.7 + - - -
321B THR* 3.4 21.1 - - + +
322B TRP* 3.9 0.7 - - - -
324B SER* 4.3 17.8 - - - +
325B SER* 3.8 13.9 - - - +
328B TRP* 3.2 48.5 - - - +
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Residues in contact with TYR 299 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
295B GLY 2.9 8.5 + - - +
296B TYR* 3.1 21.7 + + + +
298B ARG* 1.3 74.5 - - - +
300B ARG* 1.3 68.3 + - + +
303B GLU* 3.0 39.3 + - + +
322B TRP* 2.8 50.4 + + - +
325B SER* 3.3 12.9 + - - +
329B LEU* 5.4 0.4 - - + -
353B LEU* 3.9 33.9 - - + +
356B SER* 3.1 26.7 + - - -
357B ILE* 3.7 26.7 - - + -
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Residues in contact with ARG 300 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
74A ARG* 3.9 22.6 - - - +
100A MSE 3.9 24.6 - - - +
265B ILE* 4.2 6.8 + - + +
268B ASP* 4.3 5.1 + - - -
270B GLU* 4.0 15.9 + - + +
296B TYR* 2.9 56.9 + - + +
297B ALA 3.8 4.7 - - - +
299B TYR* 1.3 75.3 - - - +
301B LEU* 1.3 66.0 + - - +
303B GLU* 3.2 37.4 + - - +
304B LYS* 3.2 38.1 + - - +
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Residues in contact with LEU 301 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
270B GLU* 4.1 16.5 - - + +
271B GLU* 4.0 34.8 - - + +
274B LEU* 3.9 32.5 - - + -
297B ALA 3.0 18.8 + - - +
298B ARG 3.7 5.2 - - - +
300B ARG* 1.3 76.0 - - - +
302B GLY* 1.3 63.1 + - - +
304B LYS* 3.4 10.8 + - + +
305B GLU* 3.1 50.8 + - + +
321B THR* 4.1 13.2 - - + -
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Residues in contact with GLY 302 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
298B ARG 3.0 11.7 + - - -
299B TYR 3.2 0.2 + - - -
300B ARG 3.2 0.4 - - - -
301B LEU* 1.3 76.2 - - - +
303B GLU* 1.3 58.7 + - - +
305B GLU* 3.5 3.3 + - - -
306B ARG* 2.9 31.8 + - - +
318B TRP* 3.6 8.4 - - - +
321B THR* 3.9 13.7 - - - +
322B TRP* 3.6 26.5 - - - -
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Residues in contact with GLU 303 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
299B TYR* 3.0 43.9 + - + +
300B ARG* 3.2 36.5 + - - +
302B GLY* 1.3 75.3 - - - +
304B LYS* 1.3 63.1 + - + +
306B ARG* 3.3 10.3 + - - +
307B GLU* 3.0 30.4 + - + +
322B TRP* 3.7 18.9 - - + +
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Residues in contact with LYS 304 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
268B ASP* 3.3 27.4 + - - -
270B GLU* 2.4 42.4 + - - +
271B GLU* 6.0 1.3 - - - +
300B ARG* 3.2 30.1 + - - +
301B LEU* 3.7 13.2 - - + +
303B GLU* 1.3 78.4 - - + +
305B GLU* 1.3 65.0 + - + +
307B GLU* 3.1 9.4 + - - +
308B ALA* 3.0 23.8 + - - +
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Residues in contact with GLU 305 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
301B LEU* 3.1 40.2 + - + +
304B LYS* 1.3 79.0 - - + +
306B ARG* 1.3 56.5 + - - +
308B ALA* 3.4 7.1 + - - +
309B SER* 3.0 26.7 + - - -
312B ALA* 5.1 2.8 - - - +
317B ALA* 3.9 10.0 - - + +
318B TRP* 3.6 22.7 + - + +
321B THR* 2.7 32.2 + - - -
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Residues in contact with ARG 306 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
302B GLY 2.9 19.6 + - - +
303B GLU* 3.5 10.4 - - - +
304B LYS 3.1 0.2 - - - -
305B GLU* 1.3 75.3 - - - +
307B GLU* 1.3 69.4 + - - +
309B SER* 3.0 21.4 - - - -
318B TRP* 3.7 49.2 - - + +
322B TRP* 3.7 22.6 - - - -
360B GLU* 2.4 44.1 + - - +
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Residues in contact with GLU 307 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
303B GLU* 3.0 22.3 + - + +
304B LYS* 3.1 8.7 + - - +
306B ARG* 1.3 84.4 + - - +
308B ALA* 1.3 58.0 + - - +
309B SER 3.2 2.5 + - - -
310B GLY 4.4 3.5 + - - -
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Residues in contact with ALA 308 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
304B LYS 3.0 15.3 + - - +
305B GLU* 3.5 8.1 - - - +
307B GLU* 1.3 74.8 - - - +
309B SER* 1.3 52.0 + - - +
310B GLY 3.2 3.1 - - - -
311B GLN* 3.0 15.5 + - + +
312B ALA* 2.8 37.9 + - + +
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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) + - + + + + + -
------------------------------------------------------------
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