Contacts of the helix formed by residues 288 - 305 (chain A) 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 A).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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287A THR* 1.3 81.2 - - + +
289A ASN* 1.3 102.9 + - - +
290A GLY 3.4 0.4 - - - -
291A ARG* 4.5 1.5 - - - +
292A LEU* 3.1 36.2 + - + +
112D PHE* 3.9 32.6 - + + -
115D ILE* 6.4 0.4 - - + -
118D TYR* 3.6 40.9 + + + +
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Residues in contact with ASN 289 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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253A ALA* 3.6 31.3 + - + +
287A THR* 4.2 2.1 - - - +
288A TRP* 1.3 125.6 - - - +
290A GLY* 1.3 57.4 + - - +
292A LEU* 3.4 4.9 + - - +
293A LEU* 3.0 36.8 + - + +
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Residues in contact with GLY 290 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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250A VAL* 4.3 14.0 - - - +
253A ALA* 4.1 11.1 - - - +
254A GLU* 5.1 2.5 - - - -
285A PRO* 4.0 11.6 - - - +
287A THR* 3.3 17.5 + - - -
289A ASN* 1.3 80.3 - - - +
291A ARG* 1.3 56.9 + - - +
293A LEU* 3.3 4.7 + - - +
294A ALA* 2.9 30.3 + - - +
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Residues in contact with ARG 291 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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284A TYR* 4.5 11.7 - - - -
285A PRO* 2.7 43.6 + - + +
286A GLN* 4.1 12.4 - - - +
287A THR 3.2 24.3 + - - +
288A TRP* 3.9 2.8 + - - +
289A ASN 3.4 0.2 - - - -
290A GLY* 1.3 75.1 - - - +
292A LEU* 1.3 57.8 + - - +
294A ALA* 3.8 2.2 - - - +
295A ALA* 2.9 30.8 + - - +
266B ASP* 3.3 24.9 + - - -
269B TRP* 3.8 52.5 - - + +
282B ASP* 4.6 3.0 + - - -
283B LYS* 4.7 6.3 - - - +
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Residues in contact with LEU 292 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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288A TRP* 3.1 33.1 + - + +
289A ASN* 3.8 4.9 - - - +
291A ARG* 1.3 77.9 - - - +
293A LEU* 1.3 65.9 + - + +
295A ALA* 3.3 12.9 + - + +
296A THR* 3.2 30.9 + - + +
108D VAL* 5.2 11.7 - - + -
112D PHE* 5.0 21.3 - - + -
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Residues in contact with LEU 293 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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249A LEU* 3.7 43.3 - - + +
250A VAL* 4.4 9.4 - - + +
253A ALA* 4.2 11.0 - - + -
289A ASN* 3.0 22.3 + - + +
290A GLY* 3.8 3.4 - - - +
292A LEU* 1.3 82.1 - - + +
294A ALA* 1.3 60.6 + - - +
296A THR* 2.7 24.9 + - + +
297A PHE* 3.0 31.2 + - + -
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Residues in contact with ALA 294 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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246A ALA* 6.4 0.4 - - - -
250A VAL* 4.6 3.0 - - + +
270A TRP* 4.0 32.3 - - + -
285A PRO* 4.5 10.3 - - + -
290A GLY 2.9 18.1 + - - +
291A ARG* 4.0 3.4 - - - +
293A LEU* 1.3 76.5 - - - +
295A ALA* 1.3 57.9 + - - +
297A PHE* 4.5 4.0 - - - +
298A THR* 2.9 37.3 + - - +
269B TRP* 4.6 9.0 - - + -
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Residues in contact with ALA 295 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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291A ARG 2.9 19.8 + - - +
292A LEU* 3.6 11.9 - - + +
293A LEU 3.2 0.4 - - - -
294A ALA* 1.3 75.9 - - - +
296A THR* 1.3 61.2 + - + +
298A THR* 3.5 10.9 - - - +
299A LEU* 4.5 9.9 - - - +
269B TRP* 4.8 3.5 - - + -
272B LEU* 3.6 31.3 - - + +
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Residues in contact with THR 296 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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292A LEU* 3.2 24.7 - - + +
293A LEU* 2.7 20.6 + - + +
295A ALA* 1.3 80.8 - - + +
297A PHE* 1.3 79.4 + - - +
298A THR 3.3 1.1 + - - -
299A LEU* 3.9 11.8 + - - +
300A ILE* 4.1 11.8 - - - +
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Residues in contact with PHE 297 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
242A CYS* 4.3 17.8 - - - -
245A LEU* 3.8 23.8 - - + -
246A ALA* 3.7 32.5 - - + -
249A LEU* 3.8 31.2 - - + -
250A VAL* 6.4 0.4 - - + -
275A LEU* 4.4 5.0 - - - +
293A LEU* 3.0 39.6 + - + +
294A ALA* 3.8 3.6 - - - +
296A THR* 1.3 90.3 + - - +
298A THR* 1.3 59.3 + - - +
299A LEU 3.4 0.2 - - - -
300A ILE* 3.5 9.2 + - + +
301A GLY* 2.9 25.6 + - - -
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Residues in contact with THR 298 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
275A LEU* 4.9 6.7 - - - +
294A ALA* 2.9 22.2 + - - +
295A ALA* 3.5 17.0 - - - +
297A PHE* 1.3 73.8 - - - +
299A LEU* 1.3 69.3 + - + +
300A ILE 3.0 1.8 - - - -
301A GLY 4.4 0.4 - - - +
302A VAL* 3.0 36.2 + - - +
272B LEU* 3.8 27.3 - - + +
273B ILE* 6.5 0.7 - - + -
276B THR* 4.5 5.2 + - + +
278B ILE* 3.7 25.4 - - - +
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Residues in contact with LEU 299 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
295A ALA 4.5 9.4 - - - +
296A THR* 3.9 7.7 + - - +
297A PHE 3.4 0.6 - - - -
298A THR* 1.3 83.5 - - + +
300A ILE* 1.3 67.3 + - + +
302A VAL* 4.4 4.4 - - + +
303A SER* 3.1 25.2 + - - -
236B TRP* 4.4 26.1 + - + +
272B LEU* 4.5 7.9 - - + -
276B THR* 4.3 12.3 - - + -
305B PHE* 3.5 38.8 - - + +
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Residues in contact with ILE 300 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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242A CYS* 3.7 18.2 - - - -
296A THR 4.1 13.5 - - - +
297A PHE* 3.5 10.0 + - + +
298A THR 3.0 0.6 - - - -
299A LEU* 1.3 89.5 - - + +
301A GLY* 1.3 65.9 + - - +
303A SER* 3.4 3.4 + - - -
304A PHE* 3.0 51.1 + - + -
236B TRP* 4.8 16.4 - - + -
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Residues in contact with GLY 301 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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242A CYS* 4.2 7.5 - - - -
275A LEU* 3.6 36.8 - - - -
297A PHE 2.9 12.2 + - - -
300A ILE* 1.3 76.1 - - - +
302A VAL* 1.3 63.0 + - - +
304A PHE* 2.9 14.7 + - - -
305A PHE* 3.0 19.0 + - - +
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Residues in contact with VAL 302 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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274A THR 3.9 14.1 - - - +
275A LEU* 3.5 13.6 - - + +
277A THR* 3.7 30.3 - - + +
298A THR* 3.0 35.2 + - - +
299A LEU* 4.4 5.8 - - + +
301A GLY* 1.3 72.9 - - - +
303A SER* 1.3 67.5 + - - +
304A PHE 3.4 0.2 - - - -
305A PHE 4.2 0.6 - - - -
306A ALA* 3.5 23.6 + - - +
276B THR* 4.7 17.3 - - + +
278B ILE* 4.5 6.7 - - + -
305B PHE 5.4 7.0 - - - +
309B ALA* 5.0 0.9 - - - +
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Residues in contact with SER 303 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
299A LEU 3.1 20.8 + - - -
300A ILE* 3.4 4.6 + - - -
301A GLY 3.0 1.0 - - - -
302A VAL* 1.3 83.5 - - - +
304A PHE* 1.3 64.2 + - - +
305A PHE 3.5 0.2 - - - -
306A ALA 4.0 0.4 + - - -
307A LEU* 3.4 24.3 + - - +
236B TRP* 4.5 6.7 + - - -
305B PHE 5.1 2.6 + - - -
308B PRO* 4.0 22.5 - - - +
309B ALA* 4.2 20.6 + - - +
312B LEU* 5.8 6.6 - - - +
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Residues in contact with PHE 304 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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234A THR* 6.5 0.2 - - + -
235A ALA* 3.8 23.5 - - - +
236A TRP* 5.4 1.4 - - - -
238A ILE* 4.2 22.4 - - + -
239A GLY* 3.9 22.6 - - - +
242A CYS* 5.0 2.7 - - + -
300A ILE* 3.0 45.4 + - + +
301A GLY* 2.9 4.7 + - - +
303A SER* 1.3 80.2 - - - +
305A PHE* 1.3 60.4 + - - +
306A ALA 3.3 1.3 + - - -
307A LEU* 3.9 32.0 + - + +
308A PRO* 4.2 4.9 - - - +
221B LEU* 3.5 45.3 - - + -
312B LEU* 5.5 4.9 - - + -
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Residues in contact with PHE 305 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
236A TRP* 5.1 14.2 + + - -
239A GLY* 3.2 37.7 - - - -
240A PHE* 4.4 3.1 - - - -
243A LEU* 4.1 19.3 - - + -
272A LEU* 5.0 6.1 - - + -
275A LEU* 3.3 56.3 - - + +
276A THR* 4.1 15.3 - - + +
301A GLY* 3.0 10.4 + - - +
302A VAL 4.9 0.2 - - - +
304A PHE* 1.3 77.5 - - - +
306A ALA* 1.3 57.7 + - - +
307A LEU 3.5 0.9 - - - -
308A PRO* 4.1 11.9 - - - +
299G LEU* 3.5 36.9 - - + +
302G VAL* 5.4 7.8 - - - +
303G SER* 5.1 2.9 + - - -
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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
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Atomic class I II III IV V VI VII VIII
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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