Contacts of the strand formed by residues 238 - 250 (chain L) 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 L).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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228K ASN* 3.8 2.9 - - - -
191L ARG* 3.2 7.3 - - - -
192L PHE* 3.0 40.6 + - - -
237L TYR* 1.3 80.3 - - - +
239L LEU* 1.3 67.3 + - - +
240L TYR* 3.5 23.1 - - - -
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Residues in contact with LEU 239 (chain L).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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98I GLU* 3.8 26.2 - - + -
99I MET* 3.5 30.1 - - + -
205K GLN* 4.2 19.5 - - + +
226K ALA* 3.5 16.6 - - + +
227K ARG* 3.3 29.4 - - - +
228K ASN* 3.0 27.4 + - + +
189L TYR* 3.9 17.0 - - - +
190L PHE 3.5 3.1 - - - -
191L ARG* 4.1 3.4 - - + -
237L TYR* 3.6 10.3 - - + -
238L GLY* 1.3 85.8 - - - +
240L TYR* 1.3 65.3 + - - +
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Residues in contact with TYR 240 (chain L).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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226K ALA 3.7 1.1 - - - -
227K ARG* 4.8 7.0 - - + +
228K ASN* 3.6 18.5 + - - -
188L THR 3.4 3.5 - - - +
189L TYR* 4.1 1.6 - - - -
190L PHE* 2.8 34.9 + - + +
192L PHE* 3.7 13.9 - + - -
206L MET* 3.6 30.5 - - + -
227L ARG* 4.3 24.0 - - + -
228L ASN 4.0 14.8 - - - -
229L SER* 3.6 6.8 - - - -
230L CYS* 3.1 29.9 + - - +
237L TYR 5.0 1.2 + - - -
238L GLY* 3.5 26.5 - - - -
239L LEU* 1.3 79.7 - - - +
241L SER* 1.3 66.0 + - - +
242L ILE* 3.5 2.3 + - + +
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Residues in contact with SER 241 (chain L).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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224K LYS 4.1 2.4 + - - -
225K SER* 3.3 29.7 - - - -
226K ALA 3.0 27.9 + - - -
227K ARG* 3.7 20.4 + - - +
187L GLN* 4.4 11.2 - - - -
188L THR 3.4 7.0 - - - -
189L TYR* 3.1 23.4 - - - +
227L ARG* 4.3 3.6 + - - -
240L TYR* 1.3 75.6 - - - +
242L ILE* 1.3 62.3 + - - +
243L TYR 4.2 0.4 - - - -
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Residues in contact with ILE 242 (chain L).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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187L GLN* 3.0 4.9 - - - +
188L THR* 2.8 43.0 + - - +
190L PHE* 3.7 29.2 - - + -
206L MET* 3.8 18.6 - - + +
207L VAL* 4.7 0.9 - - - +
208L GLN* 3.3 19.3 - - + +
225L SER* 2.9 38.6 - - - +
227L ARG* 3.6 37.9 - - + +
240L TYR* 4.0 2.9 - - + +
241L SER* 1.3 79.0 - - - +
243L TYR* 1.3 63.5 + - - +
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Residues in contact with TYR 243 (chain L).
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* 4.2 1.2 - - - +
243J TYR* 3.5 28.1 - + - +
183K TYR* 2.5 24.3 + - - -
225K SER* 5.8 0.7 - - - +
227K ARG* 5.6 2.6 - - - +
243K TYR* 3.5 39.9 - + - +
245K GLY 3.5 34.3 - - - -
183L TYR* 2.5 17.5 + - - -
185L TYR* 3.1 28.7 - + + +
186L SER 3.4 9.9 - - - -
187L GLN* 3.7 24.9 - - + +
225L SER* 4.6 2.4 + - - -
227L ARG* 4.6 7.3 + - - +
241L SER 4.2 1.0 + - - -
242L ILE* 1.3 78.7 - - - +
244L GLN* 1.3 89.6 + - - +
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Residues in contact with GLN 244 (chain L).
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* 2.9 26.7 + - - +
243J TYR* 4.3 2.0 - - - -
185L TYR* 3.0 24.6 - - - +
186L SER 3.2 10.4 + - - -
208L GLN* 2.9 47.3 + - - +
210L ILE* 3.4 15.5 - - + +
223L MET* 3.4 20.0 - - + -
224L LYS 2.7 36.1 + - - +
225L SER* 3.1 6.6 + - - -
243L TYR* 1.3 88.2 - - - +
245L GLY* 1.3 62.3 + - - +
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Residues in contact with GLY 245 (chain L).
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* 4.1 0.7 - - - -
243J TYR* 3.3 15.6 - - - -
274J PHE* 3.0 22.9 - - - -
183L TYR* 3.7 20.6 - - - -
184L ILE 2.9 13.2 - - - -
185L TYR* 3.9 0.4 - - - -
223L MET* 3.3 8.1 - - - -
244L GLN* 1.3 79.6 - - - +
246L GLY* 1.3 58.2 + - - -
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Residues in contact with GLY 246 (chain L).
Click here for Legend to table.
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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125J HIS* 3.9 6.1 - - - -
185J TYR* 3.8 16.2 - - - -
182L TYR 3.2 1.7 - - - +
183L TYR* 3.6 8.0 - - - -
184L ILE 2.9 27.9 + - - +
223L MET* 3.4 9.9 - - - -
245L GLY* 1.3 75.2 - - - -
247L ILE* 1.3 66.1 + - - -
248L PHE* 3.5 9.2 - - - -
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Residues in contact with ILE 247 (chain L).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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123J ALA* 3.9 9.6 - - + -
124J ALA 3.8 14.6 - - - +
125J HIS* 3.3 20.7 + - + +
163J PHE* 3.9 12.2 - - + -
185J TYR* 3.1 25.5 + - + +
277J ALA 4.2 0.4 - - - +
278J PHE* 3.5 40.4 - - + -
181L PHE* 3.6 28.9 - - + -
182L TYR 3.1 16.4 - - - +
183L TYR* 4.1 7.2 - - + +
246L GLY* 1.3 72.1 - - - -
248L PHE* 1.3 76.1 + - - +
280L VAL* 4.2 5.6 - - + -
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Residues in contact with PHE 248 (chain L).
Click here for Legend to table.
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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125J HIS* 3.7 20.6 - - - -
127J THR* 6.0 0.2 - - + -
160J GLY 5.2 2.5 - - - -
161J HIS* 4.3 29.2 - - + -
163J PHE* 4.7 3.8 - - - -
270J HIS 6.1 0.2 - - - -
274J PHE* 6.1 0.2 - + - -
181L PHE* 3.5 2.8 - - - -
182L TYR* 2.8 32.8 + - - +
184L ILE* 4.2 13.2 - - + -
212L LYS* 6.2 0.4 - - + -
222L LEU* 3.6 45.1 - - + -
223L MET* 3.1 52.0 - - + -
246L GLY* 3.5 11.9 - - - -
247L ILE* 1.3 90.2 - - - +
249L GLU* 1.3 67.6 + - - +
250L LEU* 3.5 4.2 + - + +
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Residues in contact with GLU 249 (chain L).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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121J ARG* 4.8 3.7 + - - +
158J ARG* 3.6 37.6 + - - -
159J SER 5.3 1.7 - - - +
163J PHE* 4.5 13.0 - - + +
179L LYS* 5.9 3.1 + - - +
180L GLY* 3.5 8.1 - - - +
181L PHE* 3.5 35.2 - - + +
212L LYS* 4.3 9.5 + - - -
248L PHE* 1.3 73.4 - - - +
250L LEU* 1.3 71.5 + - - +
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Residues in contact with LEU 250 (chain L).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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176L ILE* 3.7 30.7 - - + -
179L LYS* 3.1 5.8 - - - +
180L GLY 2.8 30.9 + - - -
182L TYR* 3.9 19.7 - - + -
184L ILE* 3.9 14.4 - - + -
212L LYS* 3.9 23.3 - - + -
222L LEU* 4.7 5.6 - - + -
248L PHE* 3.9 9.0 - - + +
249L GLU* 1.3 84.8 - - - +
251L LYS* 1.3 63.4 + - - +
254L ASP* 3.6 17.0 - - + +
256L ILE* 3.8 27.8 - - + -
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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