Contacts of the strand formed by residues 224 - 237 (chain B) in PDB entry 5F0P
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 THR 224 (chain B).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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79B PHE* 3.7 23.5 - - + -
125B ASN* 3.8 24.9 + - - +
215B GLU 3.5 1.9 - - - +
216B ILE* 3.4 2.9 - - - +
217B THR* 2.8 33.9 + - - -
222B SER 5.4 0.9 - - - -
223B THR* 1.3 73.6 + - - +
225B THR* 1.3 69.4 + - - +
226B GLU* 4.2 1.6 - - - +
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Residues in contact with THR 225 (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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214B LYS* 4.4 12.1 - - + -
215B GLU 3.6 2.9 - - - +
216B ILE* 3.9 24.6 - - + +
223B THR* 4.0 11.4 - - - +
224B THR* 1.3 81.9 + - - +
226B GLU* 1.3 63.9 + - - +
227B THR* 4.0 16.6 + - - +
413B EDO 3.7 34.4 + - - +
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Residues in contact with GLU 226 (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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124B ALA* 3.8 18.6 - - + +
125B ASN* 4.7 12.6 + - - +
213B LYS 3.7 1.7 - - - +
214B LYS* 3.5 2.3 - - - -
215B GLU* 2.8 52.0 + - + +
224B THR* 4.2 2.0 - - - +
225B THR* 1.3 73.5 - - - +
227B THR* 1.3 66.7 + - - +
406B EDO 3.7 30.1 - - - -
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Residues in contact with THR 227 (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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212B ILE* 3.9 24.7 - - + -
213B LYS 3.6 3.4 - - - -
214B LYS* 3.8 24.6 + - - +
225B THR* 4.0 9.8 + - - +
226B GLU* 1.3 81.8 - - - +
228B GLU* 1.3 68.7 + - - +
229B THR* 4.8 6.1 - - - +
406B EDO 4.5 0.7 - - - -
413B EDO 4.7 2.6 + - - -
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Residues in contact with GLU 228 (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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30B LYS* 5.7 6.4 - - - -
212B ILE* 3.7 0.7 - - - +
213B LYS* 2.9 41.4 + - + +
227B THR* 1.3 79.9 - - - +
229B THR* 1.3 66.2 + - - +
230B ILE* 3.4 22.8 + - - +
406B EDO 2.7 42.7 + - - -
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Residues in contact with THR 229 (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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210B GLN* 4.1 18.6 + - - +
211B LEU 3.9 6.1 - - - +
212B ILE* 4.1 15.8 - - + +
227B THR* 4.8 5.6 - - - +
228B GLU* 1.3 74.5 - - - +
230B ILE* 1.3 60.6 + - - +
231B ALA* 3.6 20.8 - - - +
232B LYS* 4.2 23.4 - - + +
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Residues in contact with ILE 230 (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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30B LYS* 6.3 0.9 - - - +
211B LEU* 2.9 22.8 + - + +
213B LYS* 3.6 44.0 - - + +
228B GLU* 3.4 21.2 + - - +
229B THR* 1.3 73.3 - - - +
231B ALA* 1.3 58.8 + - - +
255B TYR* 3.6 43.8 - - + +
257B PRO* 4.8 8.1 - - + -
272B TYR* 3.9 15.3 - - + +
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Residues in contact with ALA 231 (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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209B LEU 5.4 0.7 - - - +
210B GLN* 3.1 10.8 - - - +
211B LEU* 3.1 39.7 + - + +
229B THR* 3.5 5.7 - - - +
230B ILE* 1.3 78.9 - - - +
232B LYS* 1.3 63.9 + - - +
233B TYR 4.1 1.3 - - - +
250B LEU* 5.3 5.6 - - + -
255B TYR* 3.3 42.0 - - + +
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Residues in contact with LYS 232 (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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102A GLY* 4.1 16.1 - - - +
208B GLU* 3.8 23.6 + - - +
209B LEU 3.9 2.9 - - - -
210B GLN* 4.0 17.9 - - + +
229B THR* 4.2 20.0 - - + +
231B ALA* 1.3 78.3 - - - +
233B TYR* 1.3 60.5 + - - +
234B GLU 4.0 1.1 + - - -
255B TYR* 5.0 2.7 + - - -
285B ARG* 5.1 8.3 - - - +
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Residues in contact with TYR 233 (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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99A GLN* 2.7 30.8 + - - +
100A TYR* 4.0 5.8 - - - -
101A ALA 3.7 5.6 - - - -
102A GLY* 4.1 2.9 - - - -
107A ARG* 3.0 42.1 + - - -
208B GLU* 3.8 3.5 - - - +
209B LEU* 2.7 45.8 + - + +
231B ALA* 5.5 1.3 - - + -
232B LYS* 1.3 72.3 - - - +
234B GLU* 1.3 65.6 + - - +
235B ILE* 3.4 21.8 + - + +
248B ILE* 5.5 0.7 - - + -
249B ARG 3.3 33.2 + - - -
250B LEU* 3.7 30.1 - - + -
251B PHE* 5.6 0.8 - + - -
255B TYR* 3.7 18.2 - - - +
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Residues in contact with GLU 234 (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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54A ARG* 4.5 2.0 + - - -
102A GLY 3.0 17.5 + - - +
103A ASN* 3.4 11.8 - - - +
104A ILE* 2.8 38.8 + - + +
107A ARG* 2.4 33.7 + - - -
505A EDO 3.0 36.3 + - - -
206B HIS* 3.6 25.6 - - + +
207B MSE 3.6 8.1 - - - +
208B GLU* 3.8 6.3 + - + +
232B LYS 4.0 1.4 + - - -
233B TYR* 1.3 72.5 - - - +
235B ILE* 1.3 55.6 + - - +
236B MSE 3.6 14.6 - - - +
237B ASP* 3.8 2.8 - - - +
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Residues in contact with ILE 235 (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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104A ILE* 3.3 21.6 - - - +
107A ARG* 4.2 1.1 - - - +
139A GLY* 3.7 3.5 - - - -
195B ILE* 3.8 28.7 - - + -
207B MSE 3.0 30.2 + - + +
208B GLU* 4.3 2.0 - - - -
209B LEU* 4.3 11.7 - - + -
233B TYR* 3.4 28.7 + - + +
234B GLU* 1.3 76.6 - - - +
236B MSE 1.3 59.7 + - - +
246B ILE* 3.3 20.8 - - + +
247B PRO 4.6 7.9 - - - +
248B ILE* 3.9 27.8 - - + -
276B LEU* 4.0 16.4 - - + -
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Residues in contact with MSE 236 (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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104A ILE* 4.4 0.9 - - - -
139A GLY 3.2 12.3 - - - +
141A GLN* 3.9 14.8 - - + -
197B PHE* 3.8 19.5 - - + -
204B ILE* 3.5 25.1 - - + -
206B HIS* 3.3 8.4 - - - +
207B MSE 3.0 51.7 + - + +
234B GLU* 3.6 6.6 - - - +
235B ILE* 1.3 79.1 - - - +
237B ASP* 1.3 62.3 + - - +
238B GLY 3.4 18.4 - - - +
240B PRO* 3.7 26.7 - - + -
246B ILE* 3.7 23.8 - - + -
278B LEU* 5.2 0.2 - - + -
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Residues in contact with ASP 237 (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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104A ILE* 3.7 21.1 - - + +
105A ILE* 3.9 3.1 - - - +
139A GLY 3.0 8.1 + - - +
140A VAL* 3.5 16.6 - - - +
141A GLN 2.7 29.5 + - - -
142A HIS* 3.0 5.8 + - - +
145A ARG* 2.9 42.2 + - - -
505A EDO 3.4 22.5 + - - -
205B GLN* 4.1 8.1 + - - +
206B HIS* 4.4 0.2 - - - -
234B GLU* 3.8 7.9 - - - +
236B MSE 1.3 73.7 - - - +
238B GLY* 1.3 57.5 + - - +
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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