Contacts of the strand formed by residues 238 - 250 (chain K) 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 K).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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99H MET* 4.8 0.3 - - - +
228J ASN* 3.3 10.5 - - - -
191K ARG* 3.3 5.0 - - - -
192K PHE* 2.8 42.3 + - - +
237K TYR* 1.3 76.2 - - - +
239K LEU* 1.3 67.3 + - - +
240K TYR* 3.7 17.7 - - - -
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Residues in contact with LEU 239 (chain K).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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98H GLU* 4.1 9.4 - - + +
99H MET* 3.6 12.6 - - + -
205J GLN* 4.2 18.8 - - + +
226J ALA* 3.5 10.5 - - + +
227J ARG* 3.1 38.2 - - - +
228J ASN* 2.7 19.2 + - + +
189K TYR* 2.9 31.0 - - + +
190K PHE 3.6 3.4 - - - -
191K ARG* 3.4 21.3 - - + -
237K TYR* 3.5 29.8 - - + -
238K GLY* 1.3 75.0 - - - -
240K TYR* 1.3 62.7 + - - +
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Residues in contact with TYR 240 (chain K).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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226J ALA 3.7 0.9 - - - -
227J ARG* 4.9 6.5 - - - +
228J ASN* 3.8 18.9 + - - -
189K TYR* 4.1 1.2 - - - -
190K PHE* 2.9 36.6 + - - +
192K PHE* 3.6 27.8 - + - -
206K MET* 3.4 26.5 - - + -
227K ARG* 4.4 22.7 - - + -
228K ASN 3.4 18.8 - - - -
229K SER* 3.2 7.4 - - - -
230K CYS* 2.9 31.4 + - - +
237K TYR 5.4 0.3 + - - -
238K GLY* 3.7 11.9 - - - -
239K LEU* 1.3 77.5 - - - +
241K SER* 1.3 65.2 + - - +
242K ILE* 3.5 4.8 + - + +
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Residues in contact with SER 241 (chain K).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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224J LYS 3.8 5.2 + - - -
225J SER* 3.3 21.5 - - - -
226J ALA 3.1 36.1 + - - -
227J ARG* 3.2 21.6 + - - +
187K GLN* 4.3 6.0 + - - -
188K THR 3.9 5.2 - - - -
189K TYR* 3.5 25.5 - - - +
227K ARG* 4.0 6.6 + - - -
240K TYR* 1.3 72.8 - - - +
242K ILE* 1.3 58.9 + - - +
243K TYR 4.2 0.9 + - - -
272K ALA 4.6 1.6 + - - -
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Residues in contact with ILE 242 (chain K).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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187K GLN* 3.1 5.7 - - - +
188K THR* 2.9 40.5 + - - +
190K PHE* 4.1 16.4 - - + -
206K MET* 3.7 19.5 - - + +
208K GLN* 3.2 20.1 - - + +
225K SER* 3.6 37.0 - - - +
227K ARG* 3.3 40.6 - - + +
240K TYR 3.7 10.3 - - - +
241K SER* 1.3 75.1 - - - +
243K TYR* 1.3 60.9 + - - +
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Residues in contact with TYR 243 (chain K).
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* 2.7 21.9 + - - -
227J ARG* 6.0 0.8 - - - +
243J TYR* 3.5 22.4 - + - +
244J GLN* 4.2 1.6 - - - -
245J GLY 3.3 34.5 - - - -
183K TYR* 3.0 16.6 + - - -
185K TYR* 3.2 29.8 - + + +
186K SER 3.5 8.7 - - - -
187K GLN* 3.6 25.8 + - + +
225K SER* 4.2 7.8 + - - -
227K ARG* 4.1 8.9 + - - +
241K SER 4.2 1.6 + - - -
242K ILE* 1.3 74.8 - - - +
244K GLN* 1.3 88.3 + - - +
243L TYR* 3.5 47.1 - + - +
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Residues in contact with GLN 244 (chain K).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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185K TYR* 3.1 22.3 - - - +
186K SER 3.1 9.8 + - - -
208K GLN* 3.2 41.2 + - - +
210K ILE* 3.4 17.2 - - + +
223K MET* 3.5 28.0 + - + +
224K LYS 2.9 33.6 + - - +
225K SER* 3.1 10.6 + - - -
243K TYR* 1.3 86.4 - - - +
245K GLY* 1.3 60.2 + - - +
187L GLN* 3.4 20.7 + - - +
243L TYR* 4.2 2.2 - - - -
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Residues in contact with GLY 245 (chain K).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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183K TYR* 3.2 23.6 - - - -
184K ILE 3.0 12.8 - - - -
185K TYR* 4.0 1.3 - - - -
223K MET* 3.3 7.5 - - - +
244K GLN* 1.3 75.3 - - - +
246K GLY* 1.3 56.9 + - - -
185L TYR* 4.2 0.3 - - - -
243L TYR* 3.5 14.5 - - - -
274L PHE* 2.8 25.1 - - - -
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Residues in contact with GLY 246 (chain K).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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182K TYR 3.4 1.6 - - - +
183K TYR* 3.2 13.8 - - - -
184K ILE* 2.8 28.6 + - - +
223K MET* 3.6 8.4 - - - +
245K GLY* 1.3 75.5 - - - -
247K ILE* 1.3 63.9 + - - -
248K PHE* 3.7 12.5 - - - -
125L HIS* 4.4 0.7 - - - -
185L TYR* 3.9 12.6 - - - -
274L PHE* 4.3 2.0 - - - -
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Residues in contact with ILE 247 (chain K).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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181K PHE* 3.8 17.0 - - + -
182K TYR 3.1 28.3 - - - +
183K TYR* 4.2 4.7 - - + +
246K GLY* 1.3 70.4 - - - -
248K PHE* 1.3 72.6 + - - +
280K VAL* 3.9 6.3 - - + -
123L ALA* 4.3 6.7 - - + -
124L ALA 4.1 6.5 - - - +
125L HIS* 3.3 21.2 + - - +
163L PHE* 3.9 14.1 - - + -
185L TYR* 3.0 26.9 + - + +
277L ALA 4.1 9.0 - - - +
278L PHE* 3.3 42.6 - - + -
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Residues in contact with PHE 248 (chain K).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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180K GLY 3.7 0.3 - - - +
181K PHE* 3.5 4.8 - - - -
182K TYR* 2.9 31.5 + - - +
184K ILE* 4.3 9.2 - - + -
212K LYS* 6.2 0.7 - - - +
222K LEU* 3.4 65.5 - - + -
223K MET* 3.4 36.6 - - + -
246K GLY* 3.7 13.0 - - - -
247K ILE* 1.3 91.9 - - - +
249K GLU* 1.3 66.0 + - - +
250K LEU* 3.8 3.7 + - + +
125L HIS* 3.7 15.7 - - - -
127L THR* 5.8 0.7 - - + -
160L GLY 5.3 0.9 - - - -
161L HIS* 4.0 34.8 - - + -
163L PHE* 4.8 4.9 - - - -
270L HIS 6.1 0.4 - - - -
274L PHE* 5.7 0.4 - + - -
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Residues in contact with GLU 249 (chain K).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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179K LYS* 5.4 7.8 - - + +
180K GLY* 3.5 17.0 + - - +
181K PHE* 4.1 27.3 - - + -
212K LYS* 4.0 13.2 + - - -
248K PHE* 1.3 74.5 - - - +
250K LEU* 1.3 73.7 + - - +
251K LYS* 5.7 0.7 - - - +
158L ARG* 3.9 26.5 + - - -
163L PHE* 5.2 8.7 - - + +
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Residues in contact with LEU 250 (chain K).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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176K ILE* 3.5 38.1 - - + -
178K GLU 4.4 0.2 - - - +
179K LYS* 3.2 23.8 - - - +
180K GLY 3.1 10.6 + - - -
182K TYR* 3.8 26.5 - - + -
184K ILE* 4.1 12.3 - - + -
212K LYS* 4.3 14.8 - - + +
222K LEU* 4.6 10.8 - - + -
248K PHE* 4.2 9.9 - - + +
249K GLU* 1.3 86.6 - - - +
251K LYS* 1.3 62.7 + - - +
254K ASP* 4.1 14.6 - - + +
256K ILE* 4.1 23.3 - - + -
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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