Contacts of the helix formed by residues 285 - 304 (chain C) in PDB entry 1T4P
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 THR 285 (chain C).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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283C GLY 4.0 6.0 - - - -
284C LYS* 1.3 88.7 - - + +
286C PRO* 1.3 77.2 - - + +
287C GLU* 3.6 12.4 + - - +
288C GLU* 2.8 37.6 + - + +
289C VAL* 3.4 7.6 + - - +
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Residues in contact with PRO 286 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
284C LYS 4.8 0.9 - - - +
285C THR* 1.3 85.5 - - - +
287C GLU* 1.3 57.1 + - - +
289C VAL* 3.1 11.4 + - + +
290C THR* 3.0 30.4 + - - +
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Residues in contact with GLU 287 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
285C THR* 3.0 11.3 + - - +
286C PRO* 1.3 77.2 - - - +
288C GLU* 1.3 61.5 + - - +
290C THR* 3.6 11.7 - - - +
291C ARG* 2.7 71.4 + - - +
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Residues in contact with GLU 288 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
242C PRO* 3.5 28.0 - - + +
243C ALA* 4.7 0.9 - - - -
282C LEU 4.7 0.7 - - - +
283C GLY* 4.1 8.1 - - - -
284C LYS* 3.1 50.4 + - - +
285C THR* 2.8 26.0 + - + +
287C GLU* 1.3 78.8 - - - +
289C VAL* 1.3 61.3 + - - +
291C ARG* 3.5 25.2 + - - +
292C THR* 2.9 29.0 + - - -
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Residues in contact with VAL 289 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
30C ALA* 5.7 0.7 - - + -
243C ALA* 4.2 8.3 - - + -
280C PRO* 3.1 46.9 - - + +
283C GLY* 3.4 26.2 - - - +
285C THR 4.1 4.7 - - - +
286C PRO* 3.1 11.5 + - + +
288C GLU* 1.3 76.2 - - - +
290C THR* 1.3 60.1 + - - +
292C THR* 3.4 1.9 + - - -
293C VAL* 3.0 39.0 + - + +
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Residues in contact with THR 290 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
286C PRO* 3.0 16.3 + - - +
287C GLU* 3.6 15.5 - - - +
289C VAL* 1.3 73.1 - - - +
291C ARG* 1.3 67.4 + - - +
293C VAL* 4.7 4.5 - - - +
294C ASN* 2.9 53.9 + - - +
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Residues in contact with ARG 291 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
238C PRO 4.5 0.2 + - - -
239C VAL* 2.8 47.9 + - - +
240C PHE* 3.8 14.1 - - + +
242C PRO* 4.1 11.0 - - + +
287C GLU* 2.7 55.4 + - - +
288C GLU* 3.5 29.2 + - - +
289C VAL 3.3 0.2 - - - -
290C THR* 1.3 79.7 - - - +
292C THR* 1.3 55.9 + - - +
294C ASN* 3.7 4.6 - - - +
295C THR* 2.6 37.4 + - + +
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Residues in contact with THR 292 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
233C VAL* 4.4 11.0 - - + -
240C PHE 3.9 8.7 + - - -
241C THR* 4.1 17.9 - - + +
242C PRO* 3.2 8.5 - - - +
243C ALA* 3.0 42.2 + - + +
278C VAL* 4.4 14.8 - - + -
288C GLU 2.9 16.4 + - - -
289C VAL 3.6 4.9 - - - -
290C THR 3.3 0.2 - - - -
291C ARG* 1.3 78.5 - - - +
293C VAL* 1.3 63.9 + - - +
295C THR* 3.4 2.5 + - - +
296C ALA* 3.0 22.0 + - - +
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Residues in contact with VAL 293 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
30C ALA* 3.7 33.0 - - + +
31C LEU* 4.0 13.0 - - + -
34C ALA* 3.4 31.6 - - + -
278C VAL* 4.5 12.8 - - + -
280C PRO* 5.3 0.2 - - + -
289C VAL* 3.0 36.9 + - + +
290C THR* 4.2 4.5 - - - +
292C THR* 1.3 71.8 - - - +
294C ASN* 1.3 60.4 + - - +
296C ALA* 3.2 8.1 + - - +
297C VAL* 2.9 28.5 + - + +
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Residues in contact with ASN 294 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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34C ALA* 4.5 14.4 - - - +
254C TYR* 5.6 0.7 - - - -
290C THR* 2.9 47.2 + - - +
291C ARG* 3.7 4.2 - - - +
293C VAL* 1.3 78.6 - - - +
295C THR* 1.3 59.1 + - - +
297C VAL* 3.2 8.6 + - - +
298C ALA* 2.8 28.5 + - - +
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Residues in contact with THR 295 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
236C LEU* 3.5 23.8 - - - +
240C PHE* 3.2 26.0 - - + +
241C THR* 3.8 5.0 - - + +
254C TYR* 4.3 28.1 - - + -
258C LEU* 5.1 0.2 - - - +
291C ARG* 2.6 32.2 + - + +
292C THR* 3.6 6.1 - - - +
294C ASN* 1.3 75.6 - - - +
296C ALA* 1.3 62.9 + - - +
298C ALA* 3.2 7.4 + - - +
299C LEU* 2.9 29.9 + - - +
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Residues in contact with ALA 296 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
31C LEU* 3.6 20.0 - - + -
233C VAL* 4.3 6.9 - - + +
275C ILE* 4.2 12.5 - - + +
278C VAL* 4.2 16.2 - - + -
292C THR 3.0 14.7 + - - +
293C VAL 3.4 8.7 - - - +
295C THR* 1.3 79.4 + - - +
297C VAL* 1.3 63.4 - - - +
299C LEU* 3.2 13.4 + - - +
300C THR* 3.0 25.1 + - - -
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Residues in contact with VAL 297 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
31C LEU* 4.0 23.1 - - + +
34C ALA* 4.2 22.4 - - + +
36C LEU* 4.1 21.8 - - + +
39C LYS* 4.1 18.2 - - + -
293C VAL 2.9 17.5 + - - +
294C ASN* 3.4 10.5 - - - +
296C ALA* 1.3 75.8 - - - +
298C ALA* 1.3 64.3 + - - +
300C THR* 3.0 5.4 + - - -
301C LEU* 2.9 42.5 + - + +
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Residues in contact with ALA 298 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
254C TYR* 3.4 28.0 - - + +
258C LEU* 4.4 9.1 - - + +
294C ASN 2.8 16.8 + - - +
295C THR* 3.2 8.7 + - - +
297C VAL* 1.3 74.2 - - - +
299C LEU* 1.3 58.0 + - - +
301C LEU* 3.2 9.3 + - - +
302C SER* 2.9 29.6 + - - -
306C THR* 5.6 0.9 - - - +
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Residues in contact with LEU 299 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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231C PHE* 3.8 31.2 - - + -
233C VAL* 5.0 6.1 - - + -
236C LEU* 4.6 8.1 - - + -
254C TYR* 5.2 0.4 - - + +
257C GLY* 3.5 28.9 - - - +
258C LEU* 3.3 22.9 - - + -
261C THR* 3.7 11.8 - - + +
275C ILE* 5.1 8.7 - - + -
295C THR* 2.9 29.1 + - - +
296C ALA* 3.4 13.7 - - - +
298C ALA* 1.3 75.3 - - - +
300C THR* 1.3 63.9 + - - +
302C SER* 3.2 7.5 + - - -
303C CYS* 3.0 28.9 + - - -
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Residues in contact with THR 300 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
36C LEU* 3.8 30.4 - - + +
40C LEU* 4.4 8.1 - - + -
95C VAL* 4.7 7.6 - - + -
273C LEU* 4.3 9.9 - - + -
275C ILE* 3.3 23.1 - - - +
296C ALA 3.0 14.0 + - - -
297C VAL* 3.0 10.0 + - - -
299C LEU* 1.3 76.6 - - - +
301C LEU* 1.3 61.3 + - - +
303C CYS* 3.1 16.8 + - - +
304C PHE* 3.2 38.1 - - + -
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Residues in contact with LEU 301 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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36C LEU* 4.8 2.9 - - + -
39C LYS* 3.3 50.0 - - + +
40C LEU* 3.8 22.7 - - + +
43C THR* 4.1 10.6 - - + +
297C VAL* 2.9 40.8 + - + +
298C ALA* 3.8 8.3 - - - +
300C THR* 1.3 76.8 - - - +
302C SER* 1.3 62.4 + - - +
304C PHE* 3.1 11.1 + - - +
306C THR* 3.1 36.2 + - + +
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Residues in contact with SER 302 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
258C LEU* 3.7 9.7 + - - -
261C THR* 2.7 29.1 + - - +
262C GLU* 3.2 26.8 + - - +
265C TYR* 3.6 11.6 - - - +
298C ALA 2.9 17.2 + - - -
299C LEU* 3.5 3.8 - - - -
300C THR 3.2 0.2 - - - -
301C LEU* 1.3 75.1 - - - +
303C CYS* 1.3 65.6 + - - +
304C PHE 3.2 0.3 + - - -
305C GLY 3.4 9.0 + - - -
306C THR* 3.6 18.2 - - - +
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Residues in contact with CYS 303 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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45C TYR* 5.1 0.2 + - - -
229C LEU* 3.9 20.6 - - - -
231C PHE* 6.0 0.4 - - - -
261C THR* 3.5 30.1 - - - -
264C ILE* 5.6 1.8 - - + -
265C TYR* 3.3 22.7 - - - +
270C LEU* 3.9 27.3 - - + +
273C LEU* 4.2 19.1 - - + -
275C ILE* 5.8 1.3 - - - -
299C LEU* 3.0 23.0 + - - -
300C THR 3.1 9.1 + - - +
302C SER* 1.3 76.1 - - - +
304C PHE* 1.3 63.9 + - + +
305C GLY 3.5 0.2 - - - -
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Residues in contact with PHE 304 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
8C ILE* 3.3 22.0 - - + -
40C LEU* 3.6 25.8 - - + -
43C THR* 4.0 15.1 - - + +
44C GLU* 4.8 2.9 - - - +
45C TYR* 3.3 45.4 - + + -
93C ILE* 3.9 11.7 - - + -
95C VAL* 3.4 33.9 - - + -
265C TYR* 3.6 4.7 - - - -
270C LEU* 3.7 24.5 - - + -
273C LEU* 4.3 6.5 - - + -
300C THR* 3.2 33.1 + - + -
301C LEU 3.1 11.2 + - - +
302C SER 3.1 0.6 - - - -
303C CYS* 1.3 81.8 - - + +
305C GLY* 1.3 56.2 + - - +
306C THR 3.8 1.4 + - - -
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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
------------------------------------------------------------
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