Contacts of the helix formed by residues 233 - 247 (chain A) in PDB entry 5FSJ
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 ASN 233 (chain A).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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159A ASN 5.6 3.4 + - - -
160A GLU* 5.9 4.6 - - - +
163A ALA* 3.8 16.0 - - + +
214A PRO* 3.7 10.1 - - - +
220A ARG* 3.3 16.7 - - - +
221A TYR* 2.8 52.3 + - - +
228A GLY 3.7 17.0 + - - -
229A GLY 2.8 13.3 + - - +
232A ILE* 1.3 69.1 - - - +
234A SER* 1.3 64.1 + - - +
235A GLY 3.0 3.3 + - - -
236A ILE* 3.1 20.9 + - + +
237A ILE 4.0 0.3 + - - -
281A PHE* 3.6 16.8 - - + -
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Residues in contact with SER 234 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
163A ALA* 3.6 21.7 - - - +
166A GLU* 3.8 11.0 - - - +
167A ALA* 3.9 9.4 - - - +
170A ASP* 4.4 1.2 + - - -
203A ARG* 4.3 6.9 + - - -
230A VAL 3.4 16.9 + - - -
231A HIS* 3.3 23.4 + - - -
232A ILE 3.1 0.2 - - - -
233A ASN* 1.3 77.4 - - - +
235A GLY* 1.3 57.7 + - - +
237A ILE* 3.1 5.6 + - - +
238A ASN* 2.8 38.9 + - - +
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Residues in contact with GLY 235 (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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203A ARG* 6.5 0.2 - - - -
204A SER 5.6 0.2 - - - -
208A PRO* 3.4 19.2 - - - +
213A ASP* 4.6 3.1 - - - +
214A PRO 3.2 16.1 - - - +
232A ILE 3.0 9.9 + - - -
233A ASN 3.0 2.6 - - - -
234A SER* 1.3 80.2 + - - +
236A ILE* 1.3 56.4 + - - +
238A ASN* 4.2 7.6 - - - -
239A LYS* 2.9 32.1 + - - +
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Residues in contact with ILE 236 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
214A PRO* 3.8 23.1 - - + +
215A ASP* 4.6 4.9 - - - +
216A HIS 3.7 26.5 - - - +
217A TYR* 4.0 5.8 - - + +
220A ARG* 3.9 25.6 - - + -
233A ASN* 3.1 16.2 + - - +
235A GLY* 1.3 77.5 - - - +
237A ILE* 1.3 62.2 + - + +
240A ALA 3.2 15.4 + - - -
281A PHE* 4.0 22.9 - - + -
313A VAL* 3.7 40.9 - - + +
315A VAL* 4.1 9.6 - - + -
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Residues in contact with ILE 237 (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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163A ALA 5.0 0.9 - - - +
164A ILE* 4.6 5.8 - - + -
167A ALA* 3.6 26.7 - - + -
168A ILE* 6.4 0.7 - - + -
171A ILE* 4.5 2.2 - - + -
233A ASN 4.6 0.4 - - - +
234A SER 3.1 2.9 + - - +
236A ILE* 1.3 79.4 - - + +
238A ASN* 1.3 64.2 + - - +
240A ALA* 3.1 4.1 + - - +
241A ALA* 2.9 22.2 + - - +
267A PHE* 4.4 14.8 - - + -
281A PHE* 3.8 47.8 - - + -
284A LEU* 3.6 36.3 - - + -
310A PHE* 4.2 15.9 - - + -
313A VAL* 5.7 0.2 - - + -
315A VAL* 4.9 2.2 - - + -
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Residues in contact with ASN 238 (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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167A ALA* 3.4 29.2 - - - +
170A ASP* 3.0 29.5 + - - +
171A ILE* 4.1 0.7 - - - +
188A ILE* 5.4 0.2 - - - +
203A ARG* 4.9 6.7 - - - +
204A SER 5.2 2.0 + - - -
205A MET* 3.7 42.9 - - + +
208A PRO* 5.0 0.4 - - + -
234A SER* 2.8 31.3 + - - +
235A GLY* 3.9 8.2 - - - +
237A ILE* 1.3 71.8 - - - +
239A LYS* 1.3 57.5 + - - +
241A ALA* 3.3 3.4 + - - +
242A TYR* 2.9 29.5 + - - +
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Residues in contact with LYS 239 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
205A MET 3.6 8.2 + - - +
206A SER 2.7 29.1 + - - +
207A ASP* 4.7 3.0 + - - +
208A PRO* 3.9 16.4 - - + -
215A ASP* 4.3 5.4 - - + +
235A GLY 2.9 19.4 + - - +
236A ILE 3.8 4.7 - - - +
238A ASN* 1.3 78.5 - - - +
240A ALA* 1.3 57.0 + - - +
242A TYR* 3.3 11.1 + - + +
243A LEU* 2.9 49.6 + - + +
250A HIS* 3.7 47.5 + - + +
313A VAL* 3.8 10.3 - - + -
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Residues in contact with ALA 240 (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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236A ILE 3.2 11.5 + - - +
237A ILE* 3.1 11.9 + - + +
239A LYS* 1.3 78.3 - - - +
241A ALA* 1.3 57.9 + - - +
243A LEU* 3.2 3.0 + - - +
244A ILE* 2.9 34.1 + - - +
267A PHE* 5.8 0.2 - - + -
309A ALA* 3.6 18.3 - - + +
310A PHE* 4.4 22.7 - - + -
313A VAL* 3.9 21.9 - - + +
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Residues in contact with ALA 241 (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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171A ILE* 3.6 33.0 - - + -
186A TRP* 4.9 0.2 - - - -
205A MET* 4.4 2.5 - - + -
237A ILE 2.9 15.9 + - - +
238A ASN 3.6 4.5 - - - +
240A ALA* 1.3 73.1 - - - +
242A TYR* 1.3 66.9 + - - +
244A ILE* 3.2 7.3 + - - +
245A SER* 3.1 18.0 + - - -
263A LEU* 3.6 33.0 - - + +
267A PHE* 4.4 5.1 - - + -
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Residues in contact with TYR 242 (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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186A TRP* 3.6 44.3 - + + -
205A MET 3.6 10.8 - - - +
206A SER* 3.5 41.5 - - - -
238A ASN 2.9 17.6 + - - +
239A LYS* 3.5 11.9 - - - +
241A ALA* 1.3 74.9 - - - +
243A LEU* 1.3 69.6 + - + +
245A SER 3.3 1.0 + - - -
246A GLN* 2.8 54.9 + - + +
247A GLY 4.2 14.2 + - - -
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Residues in contact with LEU 243 (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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239A LYS* 2.9 46.7 + - + +
240A ALA 3.6 4.0 - - - +
242A TYR* 1.3 79.8 - - + +
244A ILE* 1.3 64.0 + - - +
247A GLY* 2.8 45.9 + - - +
248A GLY* 4.0 21.8 - - - +
250A HIS* 3.9 15.9 - - + -
255A VAL* 3.5 15.4 - - + +
309A ALA* 4.1 14.1 - - + +
312A ALA* 3.9 28.3 - - + -
313A VAL* 4.5 1.1 - - + -
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Residues in contact with ILE 244 (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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240A ALA 2.9 22.0 + - - +
241A ALA* 3.6 6.3 - - - +
243A LEU* 1.3 77.3 - - - +
245A SER* 1.3 59.7 + - - +
255A VAL* 4.5 5.2 - - - -
256A VAL 4.1 1.4 - - - +
257A GLY* 3.4 1.9 - - - -
258A ILE* 2.8 50.3 + - + +
263A LEU* 3.9 16.4 - - + -
266A ILE* 4.9 2.0 - - + -
267A PHE* 3.9 26.0 - - + -
305A SER* 4.2 9.2 - - - +
306A VAL* 4.2 25.4 - - + +
309A ALA* 3.4 18.8 - - + -
310A PHE* 4.3 12.8 - - + -
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Residues in contact with SER 245 (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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186A TRP* 3.6 20.8 - - - -
241A ALA 3.1 11.5 + - - -
242A TYR 3.8 0.4 - - - -
244A ILE* 1.3 79.6 - - - +
246A GLN* 1.3 81.3 + - - +
247A GLY 3.6 0.2 - - - -
257A GLY* 3.6 2.4 - - - -
258A ILE 3.4 5.2 + - - -
259A GLY* 2.8 35.5 + - - +
260A ARG* 3.1 26.0 + - - +
263A LEU* 4.0 7.9 - - - -
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Residues in contact with GLN 246 (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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186A TRP* 3.6 27.7 - - + +
242A TYR* 2.8 53.7 + - + +
245A SER* 1.3 95.3 + - - +
247A GLY* 1.3 63.3 + - - +
257A GLY* 3.9 4.3 - - - -
259A GLY* 4.8 1.2 - - - -
260A ARG* 4.0 17.6 + - - +
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Residues in contact with GLY 247 (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 TYR* 4.2 8.0 + - - -
243A LEU* 2.8 33.0 + - - +
246A GLN* 1.3 88.2 - - - +
248A GLY* 1.3 58.2 + - - -
255A VAL 3.2 14.4 - - - -
257A GLY* 3.5 11.2 - - - -
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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