Contacts of the helix formed by residues 293 - 312 (chain A) in PDB entry 4FE1
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 293 (chain A).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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228A ASP* 5.6 1.1 - - - -
282A ASN* 3.9 29.1 - - + +
283A GLY* 4.2 13.3 + - - -
284A GLY 5.1 1.3 + - - -
285A LEU 4.7 2.6 + - - -
286A ASN* 3.6 53.3 - - + +
287A PRO* 4.6 6.5 - - + +
291A GLY 3.7 1.0 + - - -
292A LEU* 1.3 68.8 - - - +
294A LEU* 1.3 59.6 + - - +
295A SER* 3.5 21.8 - - - +
296A ASP* 2.8 49.3 + - - +
297A THR* 3.1 13.6 + - - +
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Residues in contact with LEU 294 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
149A ALA* 3.5 24.9 - - + +
216A GLN* 4.5 5.6 - - - +
220A SER* 3.0 28.7 - - - +
221A LEU* 3.4 17.0 - - + +
224A ASN* 3.2 39.9 - - + +
292A LEU 3.1 12.2 + - - +
293A TRP* 1.3 72.8 - - - +
295A SER* 1.3 59.8 + - - +
297A THR* 2.7 29.6 + - + +
298A ALA* 3.1 6.2 + - - +
379A PRO 4.0 15.9 - - - +
381A PRO* 4.7 6.5 - - + -
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Residues in contact with SER 295 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
221A LEU* 3.3 28.7 - - - +
253A TYR* 5.9 0.4 - - - -
277A ASP 4.3 3.8 - - - -
278A PHE 3.2 23.4 - - - +
280A THR* 2.8 38.0 + - - +
282A ASN* 4.9 0.2 + - - -
293A TRP* 3.5 20.3 - - - +
294A LEU* 1.3 81.0 - - - +
296A ASP* 1.3 59.4 + - - +
298A ALA* 3.7 0.7 + - - -
299A HIS 3.5 10.9 + - - -
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Residues in contact with ASP 296 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
280A THR* 2.6 29.2 + - - +
281A PHE* 3.0 9.9 + - - -
282A ASN 3.0 15.5 + - - -
283A GLY* 2.9 30.7 + - - -
292A LEU* 5.6 2.5 - - + -
293A TRP* 2.8 33.7 + - - +
295A SER* 1.3 76.4 + - - +
297A THR* 1.3 59.7 + - + +
299A HIS* 3.1 6.4 + - - +
300A HIS* 2.9 27.4 + - - +
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Residues in contact with THR 297 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
216A GLN* 3.1 23.7 + - - +
292A LEU* 4.4 21.3 - - + -
293A TRP 3.3 14.1 - - - +
294A LEU* 2.7 33.0 + - + -
296A ASP* 1.3 77.0 - - + +
298A ALA* 1.3 54.7 + - - +
300A HIS* 3.0 12.2 - - - +
301A HIS* 2.8 41.2 + - - -
379A PRO* 4.9 6.1 - - + +
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Residues in contact with ALA 298 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
213A ALA* 3.8 8.8 - - - +
216A GLN* 3.8 27.8 - - + -
217A ILE* 4.0 22.2 - - + +
221A LEU* 4.2 5.4 - - + -
278A PHE 4.2 4.0 - - - +
279A LEU* 4.4 2.4 - - - +
294A LEU 3.1 12.6 + - - +
295A SER 3.9 5.4 - - - +
296A ASP 3.2 0.2 - - - -
297A THR* 1.3 81.7 + - - +
299A HIS* 1.3 58.0 + - - +
301A HIS* 3.3 2.0 + - - +
302A LEU* 3.0 27.9 + - - +
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Residues in contact with HIS 299 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
279A LEU* 3.8 39.5 - - + +
280A THR 3.0 26.6 + - - +
281A PHE* 4.2 21.7 - + + -
295A SER 3.5 7.1 + - - +
296A ASP 3.1 9.4 + - - +
298A ALA* 1.3 76.8 - - - +
300A HIS* 1.3 64.6 + - - +
302A LEU* 3.2 8.5 + - + +
303A ALA* 2.9 30.7 + - + +
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Residues in contact with HIS 300 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
296A ASP 2.9 12.6 + - - +
297A THR* 3.0 17.7 - - - +
299A HIS* 1.3 78.9 - - - +
301A HIS* 1.3 81.9 + + - +
303A ALA* 3.2 5.0 + - - +
304A ILE* 2.9 60.6 + - + +
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Residues in contact with HIS 301 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
209A SER* 3.3 40.1 + - - +
212A TRP* 3.7 26.9 - + + -
213A ALA* 3.9 12.6 - - + -
216A GLN* 3.1 19.1 + - - -
297A THR* 2.8 32.2 + - - +
300A HIS* 1.3 92.7 + + - +
302A LEU* 1.3 56.3 + - - +
304A ILE* 4.0 6.3 - - + -
305A ALA* 2.9 24.9 + - - +
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Residues in contact with LEU 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* 4.6 20.9 - - + -
213A ALA* 4.0 10.5 - - + +
217A ILE* 5.5 4.7 - - + -
267A PHE* 6.3 3.1 - - + -
275A TYR* 6.0 0.7 - - + -
279A LEU* 3.6 36.1 - - + -
298A ALA 3.0 16.5 + - - +
299A HIS* 3.4 11.4 - - + +
301A HIS* 1.3 75.5 - - - +
303A ALA* 1.3 65.7 + - - +
305A ALA* 3.1 6.6 + - + +
306A VAL* 3.0 36.0 + - + +
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Residues in contact with ALA 303 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
299A HIS* 2.9 23.4 + - + +
300A HIS* 3.7 5.4 - - - +
302A LEU* 1.3 76.6 - - - +
304A ILE* 1.3 67.0 + - + +
306A VAL* 3.2 10.0 + - - +
307A LEU* 2.9 31.7 + - + +
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Residues in contact with ILE 304 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
205A LEU 5.4 0.2 - - - +
209A SER* 3.6 15.3 - - - +
300A HIS* 2.9 58.6 + - + +
301A HIS* 3.5 10.8 - - + +
303A ALA* 1.3 78.4 - - + +
305A ALA* 1.3 63.0 + - - +
307A LEU* 3.2 15.0 + - + +
308A PHE* 2.9 58.0 + - + -
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Residues in contact with ALA 305 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
206A GLY* 3.5 18.4 - - - +
209A SER* 3.3 14.3 + - - +
210A LEU* 3.6 26.2 - - + -
301A HIS 2.9 15.5 + - - +
302A LEU* 3.3 11.4 - - + +
304A ILE* 1.3 75.1 - - - +
306A VAL* 1.3 63.8 + - + +
308A PHE* 3.4 0.7 + - - +
309A ILE* 2.9 31.5 + - + +
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Residues in contact with VAL 306 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
302A LEU* 3.0 28.6 + - + +
303A ALA* 3.5 9.4 - - - +
305A ALA* 1.3 75.5 - - + +
307A LEU* 1.3 67.0 + - + +
309A ILE* 3.3 6.3 + - - +
310A ILE* 3.0 46.8 + - + +
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Residues in contact with LEU 307 (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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303A ALA* 2.9 17.5 + - + +
304A ILE* 3.5 20.2 - - + +
306A VAL* 1.3 77.8 - - + +
308A PHE* 1.3 62.0 + - + +
310A ILE* 3.2 17.5 + - + +
311A ALA* 2.9 28.2 + - - +
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Residues in contact with PHE 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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201A LEU* 3.6 35.5 - - + +
202A ALA* 3.6 8.1 + - - -
205A LEU* 3.5 35.2 - - + -
206A GLY* 3.7 12.1 - - - -
304A ILE* 2.9 58.1 + - + +
307A LEU* 1.3 72.5 - - + +
309A ILE* 1.3 66.6 + - - +
311A ALA* 3.1 9.2 + - + +
312A GLY 2.9 20.3 + - - -
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Residues in contact with ILE 309 (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* 3.1 33.8 - - + +
206A GLY* 3.7 13.5 - - - +
207A LEU* 4.0 15.7 - - + +
210A LEU* 5.6 5.8 - - + -
305A ALA* 2.9 30.1 + - + +
306A VAL* 3.7 5.4 - - - +
308A PHE* 1.3 73.0 - - - +
310A ILE* 1.3 59.4 + - + +
312A GLY* 3.2 8.1 + - - -
313A HIS* 2.7 47.5 + - + -
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Residues in contact with ILE 310 (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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306A VAL* 3.0 37.7 + - + +
307A LEU* 3.4 17.7 - - + +
309A ILE* 1.3 77.9 - - + +
311A ALA* 1.3 62.9 + - - +
313A HIS* 3.2 23.2 + - - +
314A MET* 5.3 0.3 - - - +
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Residues in contact with ALA 311 (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* 4.8 0.9 - - - +
201A LEU* 4.9 18.1 - - + +
307A LEU 2.9 13.1 + - - +
308A PHE* 3.1 15.9 + - + +
310A ILE* 1.3 72.6 - - - +
312A GLY* 1.3 57.7 + - - +
313A HIS 3.0 11.5 + - - -
314A MET* 3.1 24.4 + - - +
315A TYR* 5.3 0.9 - - - -
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Residues in contact with GLY 312 (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* 3.0 42.2 + - - +
201A LEU* 4.3 4.2 - - - +
202A ALA* 3.5 27.9 - - - +
308A PHE 2.9 10.5 + - - -
309A ILE 3.2 1.4 + - - -
311A ALA* 1.3 74.3 - - - +
313A HIS* 1.3 61.8 + - - +
314A MET 3.3 2.0 - - - -
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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