Contacts of the strand formed by residues 238 - 250 (chain J) in PDB entry 1DU3
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 GLY 238 (chain J).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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190J PHE 3.6 0.2 - - - +
191J ARG* 3.3 4.5 - - - +
192J PHE* 2.7 44.7 + - - +
237J TYR* 1.3 76.6 - - - +
239J LEU* 1.3 67.6 + - - +
240J TYR* 3.4 23.8 - - - -
228L ASN* 3.5 5.8 - - - -
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Residues in contact with LEU 239 (chain J).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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98G GLU* 4.0 9.4 - - + -
99G MET* 3.8 16.8 - - + -
189J TYR* 3.0 31.4 - - + +
190J PHE 3.3 4.7 - - - -
191J ARG* 3.7 19.5 - - - -
237J TYR* 4.0 21.5 - - + -
238J GLY* 1.3 76.2 - - - +
240J TYR* 1.3 66.1 + - - +
205L GLN* 4.0 25.1 - - + +
226L ALA* 3.8 12.3 - - + -
227L ARG* 3.2 35.9 - - - +
228L ASN* 3.4 13.5 + - + +
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Residues in contact with TYR 240 (chain J).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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188J THR 3.5 2.6 - - - +
189J TYR* 4.0 1.0 - - - -
190J PHE* 2.7 38.0 + - + +
192J PHE* 3.5 15.8 - + - -
206J MET* 3.7 30.1 - - + -
227J ARG* 4.5 23.3 - - + +
228J ASN 4.0 15.0 - - - -
229J SER* 3.3 8.8 - - - -
230J CYS* 3.2 27.6 + - - +
237J TYR 5.1 0.5 + - - -
238J GLY* 3.4 25.7 - - - -
239J LEU* 1.3 78.0 - - - +
241J SER* 1.3 66.0 + - - +
242J ILE* 3.6 0.5 + - - +
226L ALA 3.9 1.1 - - - -
227L ARG* 4.8 9.0 - - - +
228L ASN* 3.4 19.7 + - - -
231L TRP* 5.7 0.3 - - - -
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Residues in contact with SER 241 (chain J).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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187J GLN* 4.6 11.9 - - - -
188J THR 3.6 6.5 - - - -
189J TYR* 3.2 23.0 - - - +
227J ARG* 3.5 6.4 + - - -
240J TYR* 1.3 73.5 - - - +
242J ILE* 1.3 60.7 + - - +
224L LYS 4.4 1.3 + - - -
225L SER* 3.4 28.7 - - - -
226L ALA 2.9 26.9 + - - -
227L ARG* 3.4 23.2 + - - -
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Residues in contact with ILE 242 (chain J).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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187J GLN* 3.0 5.4 - - - -
188J THR* 2.9 38.0 + - - +
190J PHE* 3.8 27.6 - - + -
206J MET* 3.8 20.9 - - + +
207J VAL* 4.7 1.3 - - - +
208J GLN* 3.3 22.1 - - + +
225J SER* 3.2 36.6 - - - +
227J ARG* 3.3 44.9 - - + +
240J TYR* 4.4 2.7 - - + +
241J SER* 1.3 75.6 - - - +
243J TYR* 1.3 61.3 + - - +
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Residues in contact with TYR 243 (chain J).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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183J TYR* 2.8 16.7 + - - -
185J TYR* 3.4 26.5 - + + +
186J SER 3.2 12.8 - - - -
187J GLN* 3.3 28.7 - - + +
225J SER* 4.2 5.2 + - - -
227J ARG* 3.9 8.1 + - - +
241J SER 4.2 0.6 + - - -
242J ILE* 1.3 73.7 - - - +
244J GLN* 1.3 88.5 + - - +
187K GLN* 4.0 2.3 - - - +
243K TYR* 3.5 45.8 - + - +
183L TYR* 2.8 26.0 + - - -
227L ARG* 5.8 1.4 - - - +
243L TYR* 3.5 21.8 - + + +
244L GLN* 4.5 0.2 - - - -
245L GLY 3.3 33.2 - - - -
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Residues in contact with GLN 244 (chain J).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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185J TYR* 3.2 4.2 - - - +
186J SER 3.1 28.2 + - - -
208J GLN* 3.0 46.0 + - - +
210J ILE* 3.5 17.4 - - + +
223J MET* 3.5 21.0 + - - -
224J LYS 2.9 28.8 + - - -
225J SER* 3.0 8.7 + - - -
243J TYR* 1.3 88.6 - - - +
245J GLY* 1.3 60.5 + - - +
187K GLN* 3.1 28.0 + - - +
243K TYR* 4.2 3.6 - - - -
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Residues in contact with GLY 245 (chain J).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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183J TYR* 3.4 21.3 - - - -
184J ILE 2.9 15.3 - - - -
185J TYR* 3.9 0.7 - - - -
223J MET* 3.6 7.6 - - - -
244J GLN* 1.3 78.1 - - - +
246J GLY* 1.3 59.6 + - - -
185K TYR* 3.7 0.9 - - - -
243K TYR* 3.3 15.3 - - - -
274K PHE* 3.2 21.0 - - - -
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Residues in contact with GLY 246 (chain J).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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182J TYR 3.2 1.0 - - - +
183J TYR* 3.5 6.7 - - - -
184J ILE* 2.7 31.3 + - - +
223J MET* 3.7 9.5 - - - -
245J GLY* 1.3 74.8 - - - -
247J ILE* 1.3 63.0 + - - -
248J PHE* 4.0 8.9 - - - -
125K HIS* 4.3 4.5 - - - -
185K TYR* 3.6 17.5 - - - -
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Residues in contact with ILE 247 (chain J).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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181J PHE* 3.5 15.7 - - + -
182J TYR 3.1 8.1 - - - +
183J TYR* 4.1 16.4 - - + -
246J GLY* 1.3 74.1 - - - -
248J PHE* 1.3 71.3 + - - +
280J VAL* 3.4 29.8 - - + -
123K ALA* 4.9 0.2 - - + -
124K ALA 4.1 17.0 - - - +
125K HIS* 3.2 25.6 + - - +
163K PHE* 3.7 16.1 - - + -
185K TYR* 3.0 39.0 + - + +
277K ALA 4.3 5.4 - - - +
278K PHE* 3.7 21.1 - - + -
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Residues in contact with PHE 248 (chain J).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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181J PHE* 4.4 2.0 - - - -
182J TYR 2.9 27.7 + - - +
184J ILE* 4.3 11.0 - - + -
212J LYS* 6.3 0.4 - - - +
222J LEU* 3.1 56.1 - - + -
223J MET* 3.2 39.0 - - + -
246J GLY 4.0 5.4 - - - -
247J ILE* 1.3 84.0 - - - +
249J GLU* 1.3 64.2 + - - +
250J LEU* 3.5 15.1 + - + +
125K HIS* 3.7 16.8 - + - -
127K THR* 5.5 1.6 - - + -
160K GLY 5.0 2.5 - - - -
161K HIS* 3.8 38.8 - - + -
163K PHE* 4.8 2.9 - - - -
270K HIS 5.7 0.4 - - - -
274K PHE* 5.8 0.2 - + - -
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Residues in contact with GLU 249 (chain J).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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179J LYS* 3.6 30.2 + - - -
180J GLY 3.5 8.7 - - - +
181J PHE* 3.6 34.8 - - + -
212J LYS* 4.2 10.7 + - - -
248J PHE* 1.3 72.5 - - - +
250J LEU* 1.3 69.5 + - - +
251J LYS* 5.8 0.3 - - - +
121K ARG* 4.6 4.0 + - - -
158K ARG* 3.7 31.7 + - - -
163K PHE* 4.8 13.2 - - + +
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Residues in contact with LEU 250 (chain J).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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176J ILE* 3.8 38.1 - - + -
178J GLU 4.7 0.2 - - - +
179J LYS* 3.3 9.4 - - - +
180J GLY 3.1 29.6 + - - -
182J TYR* 3.9 15.9 - - + -
184J ILE* 3.8 23.3 - - + -
212J LYS* 3.7 28.5 - - + -
222J LEU* 4.7 2.7 - - + -
248J PHE* 3.7 17.9 - - + +
249J GLU* 1.3 84.2 - - - +
251J LYS* 1.3 61.0 + - - +
254J ASP* 3.4 7.6 - - + +
256J ILE* 4.0 16.8 - - + -
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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