Contacts of the strand formed by residues 220 - 228 (chain F) 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 ILE 220 (chain F).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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57A LEU* 4.5 6.3 - - + -
61A LEU* 4.4 18.4 - - + -
132D ARG* 4.0 23.1 - - - +
270D HIS* 5.9 2.9 - - - +
211F TYR* 3.5 3.1 - - - -
212F LYS* 2.9 49.0 + - + +
214F THR* 4.1 22.2 - - + -
216F TYR* 3.9 26.0 - - + -
218F ASP 3.9 6.1 - - - +
219F PRO* 1.3 79.6 - - - +
221F LEU* 1.3 72.2 + - - +
222F LEU* 3.5 5.8 - - + +
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Residues in contact with LEU 221 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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132D ARG* 5.3 3.0 - - - +
133D SER* 4.4 12.1 - - - +
134D ASN 5.8 0.9 - - - +
270D HIS* 4.5 4.9 + - - -
271D GLU* 3.9 43.6 + - + +
147F LEU* 5.5 4.3 - - + -
209F TYR* 3.2 47.3 - - + -
210F ILE 4.1 0.9 - - - +
211F TYR* 3.2 33.1 - - + +
219F PRO 4.2 0.2 + - - -
220F ILE* 1.3 79.9 - - - +
222F LEU* 1.3 65.2 - - - +
223F MET 3.5 15.5 - - - +
224F LYS* 4.1 14.8 - - + -
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Residues in contact with LEU 222 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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160D GLY 5.8 2.0 - - - +
161D HIS* 6.3 1.6 - - + -
270D HIS* 4.7 4.0 - - - +
271D GLU* 3.8 19.1 - - - +
274D PHE* 5.6 0.5 - - - -
184F ILE* 4.3 7.4 - - + -
210F ILE* 2.7 25.1 + - + +
211F TYR 4.6 0.7 - - - +
212F LYS* 3.6 43.1 - - + -
220F ILE* 3.5 13.0 - - + +
221F LEU* 1.3 82.4 - - - +
223F MET* 1.3 67.8 + - + +
248F PHE* 3.4 55.2 - - + -
250F LEU* 4.7 1.1 - - + -
256F ILE* 4.3 13.7 - - + -
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Residues in contact with MET 223 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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271D GLU* 3.9 7.2 - - - -
274D PHE* 3.8 19.7 - - + -
184F ILE* 3.4 33.0 - - + +
210F ILE* 3.1 32.7 + - + -
221F LEU* 3.5 9.5 - - - +
222F LEU* 1.3 92.3 - - + +
224F LYS* 1.3 65.6 + - - +
244F GLN* 3.5 20.9 - - + +
245F GLY* 3.3 13.7 - - - +
246F GLY* 3.3 23.3 - - - +
248F PHE* 3.2 33.4 - - + -
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Residues in contact with LYS 224 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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98A GLU* 3.0 40.7 + - - +
133D SER* 3.8 30.1 + - - -
187D GLN* 3.1 11.4 + - - -
189D TYR* 3.7 12.5 - - + -
191D ARG* 5.4 1.0 - - - +
241D SER* 4.4 1.9 + - - -
267D ASP* 4.7 5.1 + - - -
269D ASP* 5.0 1.8 + - - -
271D GLU 3.6 14.1 + - - +
272D ALA* 4.0 25.7 - - - +
207F VAL* 4.7 3.1 - - + -
208F GLN 3.1 11.4 - - - +
209F TYR* 3.8 23.6 - - + -
221F LEU* 4.1 7.4 - - + -
223F MET* 1.3 76.1 - - - +
225F SER* 1.3 58.4 + - - +
244F GLN* 2.7 14.3 + - - +
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Residues in contact with SER 225 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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187D GLN* 4.2 5.6 - - - -
189D TYR* 6.1 0.2 - - - -
241D SER* 3.4 14.5 - - - -
206F MET 4.1 0.5 - - - +
207F VAL* 3.3 3.1 - - - -
208F GLN 2.9 28.8 + - - -
224F LYS* 1.3 76.4 - - - +
226F ALA* 1.3 59.4 + - - +
227F ARG* 2.6 32.6 + - - -
242F ILE* 3.2 20.7 - - - +
243F TYR 4.7 1.1 + - - -
244F GLN* 3.0 19.9 + - - -
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Residues in contact with ALA 226 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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98A GLU* 4.1 2.5 - - + -
189D TYR* 3.5 27.1 - - + +
239D LEU* 3.5 14.5 - - + +
241D SER* 2.9 20.2 + - - -
206F MET 3.2 9.2 - - - +
207F VAL* 3.8 20.9 - - + -
224F LYS* 6.1 0.4 - - + -
225F SER* 1.3 75.0 + - - +
227F ARG* 1.3 83.1 + - - +
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Residues in contact with ARG 227 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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227D ARG* 4.3 16.5 - - - +
239D LEU* 3.4 17.3 - - - +
240D TYR* 4.8 7.6 - - - +
241D SER* 3.4 25.6 + - - +
243D TYR* 5.7 1.4 - - - +
227E ARG* 4.8 12.3 - - - +
205F GLN* 3.5 5.2 - - - -
206F MET* 2.8 33.8 + - + +
225F SER* 2.6 29.1 + - - -
226F ALA* 1.3 100.1 + - - +
228F ASN* 1.3 60.5 + - - +
229F SER 4.3 0.4 - - - -
240F TYR* 4.2 25.4 - - + -
241F SER 4.4 5.5 + - - -
242F ILE* 3.6 38.5 - - + +
243F TYR 4.6 8.1 + - - +
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Residues in contact with ASN 228 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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230D CYS* 5.2 0.9 - - - +
237D TYR* 4.0 15.5 - - + +
238D GLY* 3.5 2.2 - - - -
239D LEU* 3.3 36.9 + - + +
240D TYR* 3.4 28.8 + - - -
203F ASP* 6.5 0.4 - - + -
204F LYS 3.2 9.6 - - - +
206F MET* 3.8 2.5 - - - -
227F ARG* 1.3 77.7 - - - +
229F SER* 1.3 76.2 + - - +
230F CYS* 3.5 1.7 + - - -
231F TRP* 2.8 32.9 + - + +
240F TYR* 3.9 9.2 - - - -
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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