Contacts of the helix formed by residues 289 - 308 (chain A) in PDB entry 4L6V
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 289 (chain A).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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228A ASP* 5.2 3.4 - - - -
278A LYS* 3.6 57.1 - - + +
280A GLY* 4.1 15.4 + - - -
281A LEU 3.7 6.3 + - - +
282A ASN* 3.3 62.1 - - + +
283A PRO* 4.1 9.0 - - + -
287A GLY 4.7 0.2 - - - -
288A LEU* 1.3 72.4 - - - +
290A LEU* 1.3 58.5 + - - +
291A SER* 3.0 16.8 - - - +
292A ASP* 2.9 37.1 + - - +
293A THR* 3.2 12.9 + - - +
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Residues in contact with LEU 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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149A ALA* 4.1 19.7 - - + +
216A GLN* 4.1 10.4 + - - +
220A SER* 4.0 27.6 - - - -
221A MET* 3.5 18.8 - - + +
224A ASN* 3.6 39.3 - - + +
288A LEU 3.3 10.4 + - - +
289A TRP* 1.3 74.4 - - - +
291A SER* 1.3 61.9 + - - +
293A THR* 3.2 16.4 + - + +
294A ALA* 3.2 25.8 + - - +
375A PRO 4.9 7.2 - - - +
377A PRO* 6.2 0.4 - - + -
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Residues in contact with SER 291 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
221A MET* 3.4 26.5 - - - +
253A TYR* 6.0 0.4 - - - -
273A ASP 5.6 0.2 - - - -
274A PHE* 3.5 18.0 - - - +
276A THR* 2.4 43.8 + - - +
278A LYS* 4.1 9.7 + - - -
289A TRP* 3.5 16.1 - - - +
290A LEU* 1.3 79.0 - - - +
292A ASP* 1.3 60.7 + - - +
294A ALA* 4.1 0.2 - - - +
295A HIS* 3.3 15.9 + - - +
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Residues in contact with ASP 292 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
276A THR* 2.8 40.7 + - - +
277A PHE* 3.2 5.6 + - - -
278A LYS* 3.2 5.8 + - - +
279A GLY* 3.2 25.6 + - - -
280A GLY 4.5 0.7 + - - -
288A LEU* 6.0 3.0 - - + +
289A TRP* 2.9 28.4 + - - +
291A SER* 1.3 75.6 + - - +
293A THR* 1.3 55.8 + - + +
294A ALA 3.1 1.8 - - - -
295A HIS* 3.2 2.4 + - - +
296A HIS* 2.6 38.5 + - - +
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Residues in contact with THR 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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216A GLN* 2.8 33.9 + - - +
288A LEU* 4.3 25.4 - - + -
289A TRP 3.2 11.8 + - - +
290A LEU* 3.2 18.9 + - + +
292A ASP* 1.3 77.5 - - + +
294A ALA* 1.3 58.2 + - - +
296A HIS* 3.4 10.9 - - - +
297A HIS* 3.0 36.2 + - - +
375A PRO* 5.6 5.6 - - + +
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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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213A ALA* 3.9 8.6 - - - +
216A GLN* 3.3 17.5 - - + +
217A ILE* 3.8 29.2 - - + +
221A MET* 4.0 10.8 - - - -
275A LEU* 4.2 4.9 - - + -
290A LEU 3.2 14.9 + - - +
291A SER 4.1 1.6 - - - +
292A ASP 3.1 0.6 - - - -
293A THR* 1.3 78.6 + - - +
295A HIS* 1.3 65.2 + - - +
296A HIS 3.1 0.9 - - - -
297A HIS 3.5 0.5 + - - -
298A LEU* 3.1 24.8 + - - +
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Residues in contact with HIS 295 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
275A LEU* 3.6 41.6 + - + +
276A THR 3.2 18.2 + - - +
277A PHE* 3.9 26.7 - + + -
291A SER 3.3 16.7 + - - +
292A ASP 3.2 3.9 + - - +
294A ALA* 1.3 78.0 - - - +
296A HIS* 1.3 63.4 + - - +
298A LEU* 3.5 9.0 + - + +
299A ALA* 3.0 26.0 + - + +
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Residues in contact with HIS 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 ASP 2.6 22.4 + - - +
293A THR* 3.4 12.6 + - - +
295A HIS* 1.3 74.1 - - - +
297A HIS* 1.3 79.8 + + - +
299A ALA* 2.8 10.1 + - + +
300A ILE* 2.8 52.0 + - + +
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Residues in contact with HIS 297 (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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209A SER* 2.8 36.7 + - - +
212A TRP* 3.2 35.4 - + - -
213A ALA* 4.0 7.6 - - + -
216A GLN* 3.5 9.0 + - - -
293A THR* 3.0 22.4 + - + +
296A HIS* 1.3 106.0 + + - +
298A LEU* 1.3 57.9 + - - +
300A ILE* 4.2 4.3 - - + -
301A ALA* 2.8 28.8 + - - +
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Residues in contact with LEU 298 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
210A LEU* 3.6 23.8 - - + -
213A ALA* 4.0 10.4 - - + +
217A ILE* 5.7 4.7 - - + -
263A PHE* 5.8 11.4 - - + -
275A LEU* 3.9 31.0 - - + -
294A ALA 3.1 19.1 + - - +
295A HIS* 3.6 10.1 - - + +
297A HIS* 1.3 77.7 - - - +
299A ALA* 1.3 61.8 + - - +
301A ALA* 3.7 3.3 - - - +
302A VAL* 3.4 28.5 + - + +
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Residues in contact with ALA 299 (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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295A HIS* 3.0 22.8 + - + +
296A HIS* 2.8 12.4 + - + +
298A LEU* 1.3 76.5 - - - +
300A ILE* 1.3 65.0 - - + +
302A VAL* 3.6 5.9 + - - +
303A LEU* 3.2 23.0 + - - +
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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
----------------------------------------------------------
209A SER* 3.7 15.5 - - - +
296A HIS* 2.8 52.4 + - + +
297A HIS* 4.2 2.7 - - + -
299A ALA* 1.3 70.0 - - + +
301A ALA* 1.3 67.9 + - - +
303A LEU* 3.2 17.7 + - + +
304A PHE* 2.9 55.0 + - + +
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Residues in contact with ALA 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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206A GLY* 3.4 12.5 - - - +
209A SER* 3.5 5.3 + - - -
210A LEU* 3.3 42.0 - - + +
297A HIS 2.8 23.7 + - - +
298A LEU 3.7 5.4 - - - +
300A ILE* 1.3 72.4 - - - +
302A VAL* 1.3 64.8 + - - +
304A PHE* 2.9 13.7 + - - +
305A ILE* 2.9 19.7 + - + +
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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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210A LEU* 5.5 2.9 - - + -
268A TRP* 6.6 0.7 - - + -
298A LEU* 3.4 25.1 + - + +
299A ALA* 3.9 5.6 - - - +
300A ILE 3.4 0.2 - - - -
301A ALA* 1.3 79.2 - - + +
303A LEU* 1.3 63.9 + - - +
305A ILE* 3.3 8.0 + - - +
306A ILE* 3.0 34.2 + - + +
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Residues in contact with LEU 303 (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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299A ALA 3.2 11.3 + - - +
300A ILE* 3.2 22.0 + - + +
302A VAL* 1.3 81.2 - - - +
304A PHE* 1.3 65.8 + - + +
306A ILE* 3.5 12.3 - - + +
307A ALA* 3.0 30.3 + - + +
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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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201A LEU* 2.8 37.4 - - + +
205A LEU* 3.3 46.9 - - + -
206A GLY* 3.5 7.2 - - - -
209A SER* 5.4 0.4 - - - -
300A ILE* 2.9 39.6 + - + +
301A ALA 2.9 7.1 + - - +
303A LEU* 1.3 84.4 - - + +
305A ILE* 1.3 65.2 + - - +
307A ALA* 3.4 8.8 + - + +
308A GLY 3.1 15.4 + - - -
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Residues in contact with ILE 305 (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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202A ALA* 3.3 34.0 - - + +
206A GLY* 3.8 6.7 - - - -
207A LEU* 3.7 25.1 - - + -
210A LEU* 5.9 2.9 - - + -
301A ALA* 2.9 22.7 + - + +
302A VAL* 3.3 8.3 + - - +
304A PHE* 1.3 74.5 - - - +
306A ILE* 1.3 58.0 + - + +
308A GLY* 3.1 7.6 + - - -
309A HIS* 2.5 47.2 + - + -
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Residues in contact with ILE 306 (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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302A VAL* 3.0 26.9 + - + +
303A LEU* 3.5 17.9 - - + +
305A ILE* 1.3 77.2 - - + +
307A ALA* 1.3 66.9 + - - +
308A GLY 2.9 1.7 + - - -
309A HIS* 3.0 24.5 + - + +
310A MET* 5.5 0.2 - - - +
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Residues in contact with ALA 307 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
198A ASN* 4.7 0.5 - - - +
201A LEU* 3.5 26.3 - - + +
303A LEU* 3.0 23.6 + - + +
304A PHE* 3.9 14.1 - - + +
305A ILE 3.3 0.2 - - - -
306A ILE* 1.3 77.4 - - - +
308A GLY* 1.3 55.6 + - - +
309A HIS 3.2 4.9 + - - -
310A MET* 3.9 23.8 + - + +
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Residues in contact with GLY 308 (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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198A ASN* 3.2 47.0 + - - +
201A LEU* 3.9 13.2 - - - -
202A ALA* 4.1 2.0 - - - +
304A PHE 3.1 6.9 + - - -
305A ILE 3.1 7.7 + - - -
306A ILE 2.9 2.4 + - - -
307A ALA* 1.3 76.7 - - - +
309A HIS* 1.3 69.4 + - - +
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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
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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