Contacts of the helix formed by residues 288 - 305 (chain B) in PDB entry 7CR3
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 TRP 288 (chain B).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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287B THR* 1.3 80.3 - - + +
289B ASN* 1.3 102.8 + - - +
290B GLY 3.4 0.2 - - - -
291B ARG* 4.5 1.9 - - - +
292B LEU* 3.1 35.9 + - + +
112G PHE* 3.9 33.9 - + + -
118G TYR* 3.6 40.1 + + + +
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Residues in contact with ASN 289 (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 ALA* 3.6 30.2 + - + +
287B THR* 4.2 1.9 - - - +
288B TRP* 1.3 125.3 - - - +
290B GLY* 1.3 57.3 + - - +
292B LEU* 3.4 5.4 + - - +
293B LEU* 3.0 36.1 + - + +
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Residues in contact with GLY 290 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
250B VAL* 4.3 13.8 - - - +
253B ALA* 4.1 12.3 - - - +
254B GLU* 5.1 2.2 - - - -
285B PRO* 4.0 11.6 - - - +
287B THR* 3.3 17.6 + - - -
289B ASN* 1.3 79.4 - - - +
291B ARG* 1.3 56.5 + - - +
293B LEU* 3.3 4.3 + - - +
294B ALA* 2.9 30.7 + - - +
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Residues in contact with ARG 291 (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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284B TYR* 4.5 12.1 - - - -
285B PRO* 2.7 43.2 + - + +
286B GLN* 4.1 11.6 - - - +
287B THR 3.2 23.8 + - - +
288B TRP* 3.9 3.2 + - - +
289B ASN 3.4 0.2 - - - -
290B GLY* 1.3 74.6 - - - +
292B LEU* 1.3 59.0 + - - +
294B ALA* 3.8 2.4 - - - +
295B ALA* 2.9 31.5 + - - +
266D ASP* 3.3 25.1 + - - +
269D TRP* 3.8 50.6 - - + +
282D ASP* 4.6 3.2 + - - -
283D LYS* 4.7 5.5 - - - +
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Residues in contact with LEU 292 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
288B TRP* 3.1 33.1 + - + +
289B ASN* 3.8 5.4 - - - +
290B GLY 3.2 0.2 - - - -
291B ARG* 1.3 77.0 - - - +
293B LEU* 1.3 67.1 + - + +
295B ALA* 3.3 12.8 + - + +
296B THR* 3.2 31.0 + - + +
108G VAL* 5.2 10.8 - - + -
112G PHE* 5.0 21.3 - - + -
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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
----------------------------------------------------------
249B LEU* 3.7 43.3 - - + +
250B VAL* 4.4 9.4 - - + +
253B ALA* 4.2 11.7 - - + -
289B ASN* 3.0 22.9 + - + +
290B GLY 3.8 3.1 - - - +
292B LEU* 1.3 81.4 - - + +
294B ALA* 1.3 61.1 + - - +
296B THR* 2.7 26.1 + - + +
297B PHE* 3.0 29.0 + - + -
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Residues in contact with ALA 294 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
246B ALA* 6.4 0.4 - - - -
250B VAL* 4.6 3.7 - - + +
270B TRP* 4.0 31.6 - - + -
285B PRO* 4.5 11.2 - - + -
290B GLY 2.9 17.2 + - - +
291B ARG* 4.0 2.5 - - - +
293B LEU* 1.3 76.5 - - - +
295B ALA* 1.3 58.3 + - - +
297B PHE* 4.5 3.8 - - - +
298B THR* 2.9 36.9 + - - +
269D TRP* 4.6 9.2 - - + -
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Residues in contact with ALA 295 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
291B ARG 2.9 20.5 + - - +
292B LEU* 3.6 10.8 - - + +
293B LEU 3.2 0.4 - - - -
294B ALA* 1.3 76.0 - - - +
296B THR* 1.3 61.6 + - + +
298B THR* 3.5 10.2 - - - +
299B LEU* 4.5 10.6 - - - +
269D TRP* 4.8 3.3 - - + -
272D LEU* 3.6 31.0 - - + +
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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
----------------------------------------------------------
292B LEU* 3.2 24.5 - - + +
293B LEU* 2.7 21.6 + - + +
295B ALA* 1.3 80.5 - - + +
297B PHE* 1.3 77.6 + - - +
298B THR 3.3 1.4 + - - -
299B LEU* 3.9 12.3 + - - +
300B ILE* 4.1 12.1 - - - +
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Residues in contact with PHE 297 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
242B CYS* 4.3 17.1 - - - -
245B LEU* 3.8 24.5 - - + -
246B ALA* 3.7 31.4 - - + -
249B LEU* 3.8 32.1 - - + -
250B VAL* 6.4 0.2 - - + -
275B LEU* 4.4 4.8 - - - +
293B LEU* 3.0 38.7 + - + +
294B ALA* 3.8 3.6 - - - +
296B THR* 1.3 91.3 + - - +
298B THR* 1.3 60.4 + - - +
299B LEU 3.4 0.2 - - - -
300B ILE* 3.9 8.2 - - + +
301B GLY* 2.9 25.5 + - - -
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Residues in contact with THR 298 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
275B LEU* 4.9 6.7 - - - +
294B ALA* 2.9 22.7 + - - +
295B ALA* 3.5 17.5 - - - +
297B PHE* 1.3 74.3 - - - +
299B LEU* 1.3 69.8 + - + +
300B ILE 3.0 2.2 - - - -
301B GLY 4.4 0.2 - - - +
302B VAL* 3.0 36.2 + - - +
272D LEU* 3.8 26.2 - - + -
273D ILE* 6.5 0.4 - - + -
276D THR* 4.5 5.8 + - + +
278D ILE* 3.7 25.3 - - - +
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Residues in contact with LEU 299 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
295B ALA 4.5 9.4 - - - +
296B THR* 3.9 8.0 + - - +
297B PHE 3.4 0.4 - - - -
298B THR* 1.3 81.8 - - + +
300B ILE* 1.3 67.3 + - + +
302B VAL* 4.4 5.2 - - + +
303B SER* 3.1 24.7 + - - -
236D TRP* 4.4 25.6 + - + +
272D LEU* 4.5 8.5 - - + -
276D THR* 4.3 12.8 - - + -
305D PHE* 3.5 38.8 - - + +
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Residues in contact with ILE 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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242B CYS* 3.7 18.8 - - - -
296B THR 4.1 13.2 - - - +
297B PHE* 3.5 10.9 + - + +
298B THR 3.0 0.4 - - - -
299B LEU* 1.3 89.8 - - + +
301B GLY* 1.3 66.6 + - - +
303B SER* 3.4 3.8 + - - -
304B PHE* 3.0 51.8 + - + -
236D TRP* 4.8 17.3 - - + -
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Residues in contact with GLY 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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242B CYS* 4.2 7.5 - - - -
275B LEU* 3.6 37.9 - - - -
297B PHE 2.9 12.6 + - - -
300B ILE* 1.3 77.4 - - - +
302B VAL* 1.3 61.0 + - - +
304B PHE* 2.9 14.4 + - - -
305B PHE* 3.0 18.8 + - - +
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Residues in contact with VAL 302 (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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274B THR 3.9 14.8 - - - +
275B LEU* 3.5 12.2 - - + +
277B THR* 3.7 29.1 - - + +
298B THR* 3.0 34.5 + - - +
299B LEU* 4.4 6.3 - - + +
301B GLY* 1.3 74.3 - - - +
303B SER* 1.3 67.5 + - - +
305B PHE 4.2 0.8 - - - -
306B ALA* 3.5 23.6 + - - +
276D THR* 4.7 16.8 - - + +
278D ILE* 4.5 6.7 - - + -
305D PHE 5.4 7.2 - - - +
309D ALA* 5.0 1.0 - - - +
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Residues in contact with SER 303 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
299B LEU 3.1 21.0 + - - -
300B ILE* 3.4 5.8 + - - -
301B GLY 3.0 0.8 - - - -
302B VAL* 1.3 85.1 - - - +
304B PHE* 1.3 62.7 + - - +
305B PHE 3.5 0.2 - - - -
306B ALA 4.0 0.2 + - - -
307B LEU* 3.4 24.4 + - - +
236D TRP* 4.5 6.7 + - - -
305D PHE 5.1 2.9 + - - -
308D PRO* 4.0 22.9 - - - +
309D ALA* 4.2 19.5 + - - +
312D LEU* 5.8 6.0 - - - +
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Residues in contact with PHE 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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235B ALA* 3.8 23.4 - - - +
236B TRP* 5.4 1.4 - - - -
238B ILE* 4.2 23.8 - - + -
239B GLY* 3.9 22.6 - - - -
242B CYS* 5.0 2.9 - - + -
300B ILE* 3.0 44.9 + - + +
301B GLY* 2.9 5.5 + - - +
303B SER* 1.3 81.3 - - - +
305B PHE* 1.3 61.9 + - - +
306B ALA 3.3 0.6 + - - -
307B LEU* 3.9 32.6 + - + +
308B PRO* 4.2 4.3 - - - +
221D LEU* 3.5 43.7 - - + -
312D LEU* 5.5 5.6 - - + -
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Residues in contact with PHE 305 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
299A LEU* 3.5 36.8 - - + -
302A VAL* 5.4 7.8 - - - +
303A SER* 5.1 3.3 + - - -
236B TRP* 5.1 13.6 + + - -
239B GLY* 3.2 36.6 - - - -
240B PHE* 4.4 3.4 - - - -
243B LEU* 4.1 19.5 - - + -
272B LEU* 5.0 5.8 - - + -
275B LEU* 3.3 55.9 - - + +
276B THR* 4.1 14.9 - - + +
301B GLY* 3.0 10.8 + - - +
304B PHE* 1.3 78.6 - - - +
306B ALA* 1.3 58.1 + - - +
307B LEU 3.5 0.9 - - - -
308B PRO* 4.1 12.3 - - - +
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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