Contacts of the strand formed by residues 205 - 213 (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 GLN 205 (chain F).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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95A ASP 3.2 18.5 + - - +
96A SER* 3.2 24.8 - - - -
98A GLU* 2.9 34.8 + - - +
99A MET* 3.1 28.9 + - - +
101A ARG* 3.8 3.8 - - - +
237D TYR* 3.0 34.4 + - - +
239D LEU* 3.9 14.6 - - + -
203F ASP* 5.4 0.7 - - - +
204F LYS* 1.3 71.2 - - - +
206F MET* 1.3 64.2 + - - +
207F VAL* 3.7 7.6 - - + +
227F ARG 3.5 6.3 - - - -
261F THR* 2.8 16.3 + - - -
262F ASN* 3.2 7.3 + - - +
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Residues in contact with MET 206 (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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190F PHE* 3.5 45.3 - - + -
192F PHE* 4.0 9.2 - - + -
204F LYS* 4.0 14.4 - - + +
205F GLN* 1.3 75.1 - - - +
207F VAL* 1.3 56.4 + - - +
226F ALA* 3.2 2.3 - - - -
227F ARG* 2.8 37.5 + - + +
228F ASN* 3.8 5.2 - - - -
229F SER* 3.1 49.4 - - - +
240F TYR* 3.6 37.5 - - + -
242F ILE* 3.7 10.5 - - + +
261F THR* 3.6 3.4 - - - -
262F ASN* 4.5 3.8 - - - +
265F LEU* 5.6 1.1 - - + -
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Residues in contact with VAL 207 (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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97A PRO* 4.9 1.1 - - + -
98A GLU* 3.7 26.2 - - + -
190F PHE* 3.9 6.3 - - - -
205F GLN* 3.9 13.5 - - + +
206F MET* 1.3 78.2 - - - +
208F GLN* 1.3 64.8 + - - +
209F TYR* 3.4 39.3 - - + +
224F LYS* 4.7 3.6 - - + -
225F SER 3.3 16.2 - - - +
226F ALA* 3.8 12.1 - - + -
242F ILE* 5.1 0.7 - - - -
260F VAL* 3.5 8.3 - - - +
261F THR* 2.8 37.9 + - + +
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Residues in contact with GLN 208 (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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186F SER* 3.2 34.6 + - - +
188F THR* 3.3 22.8 + - + +
207F VAL* 1.3 75.1 - - - +
209F TYR* 1.3 62.8 + - - +
210F ILE* 3.1 22.2 - - - +
224F LYS* 3.1 6.9 - - - +
225F SER 2.9 28.3 + - - -
242F ILE* 3.3 29.2 - - + +
243F TYR* 4.6 0.2 - - - -
244F GLN* 2.9 30.4 + - - +
258F VAL* 3.7 17.3 - - + -
259F SER 3.7 3.6 - - - +
260F VAL* 4.4 2.0 - - + -
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Residues in contact with TYR 209 (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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97A PRO* 3.0 28.9 - - - +
98A GLU* 3.9 9.3 + - - -
147F LEU* 3.7 38.7 - - + +
148F GLY* 4.0 11.0 - - - -
207F VAL* 3.4 34.4 - - + +
208F GLN* 1.3 71.3 - - - +
210F ILE* 1.3 70.1 + - - +
211F TYR* 3.3 17.3 - + + -
221F LEU* 3.2 29.6 - - + -
223F MET 3.6 3.4 - - - -
224F LYS* 3.8 20.6 - - + -
258F VAL* 3.2 4.2 - - - +
259F SER* 2.8 42.1 + - - +
260F VAL* 4.5 0.9 - - - -
261F THR* 4.5 5.6 - - + -
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Residues in contact with ILE 210 (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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184F ILE* 4.0 22.9 - - + +
185F TYR 4.4 4.9 - - - +
186F SER* 3.9 20.2 - - - +
208F GLN* 3.1 29.2 - - - +
209F TYR* 1.3 81.2 - - - +
211F TYR* 1.3 58.1 + - - +
221F LEU* 4.1 0.4 - - - +
222F LEU* 2.7 40.1 + - + +
223F MET* 3.1 27.3 + - + +
244F GLN* 3.5 17.9 - - + +
256F ILE* 5.1 2.2 - - + -
257F PHE 3.4 11.4 - - - +
258F VAL* 4.2 5.4 - - + -
275F PHE* 4.6 6.5 - - + -
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Residues in contact with TYR 211 (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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146F ALA* 3.6 18.4 - - + -
147F LEU* 2.5 49.7 + - - +
209F TYR* 3.3 27.6 - - + -
210F ILE* 1.3 75.5 - - - +
212F LYS* 1.3 63.0 + - - +
219F PRO* 3.9 13.2 - - + -
220F ILE 3.4 14.4 - - - -
221F LEU* 3.2 43.3 - - + +
222F LEU* 4.2 1.7 - - - +
256F ILE* 3.3 9.4 - - - +
257F PHE* 3.0 62.0 + + + -
259F SER* 4.2 3.1 - - - -
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Residues in contact with LYS 212 (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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57A LEU* 6.2 1.4 - - - +
160D GLY 4.8 12.8 + - - -
211F TYR* 1.3 77.2 - - - +
213F TYR* 1.3 64.1 + - - +
214F THR* 4.3 24.5 + - + +
218F ASP 4.4 0.3 - - - +
219F PRO* 3.5 3.3 - - - +
220F ILE* 2.9 56.9 + - + +
222F LEU* 3.6 22.2 - - + -
248F PHE* 6.1 1.3 - - - -
249F GLU 4.3 12.7 + - - -
250F LEU* 3.8 20.0 - - + +
251F LYS* 6.3 0.6 - - - +
254F ASP* 4.6 4.0 + - - +
255F ARG 3.0 11.0 - - - +
256F ILE* 3.6 13.5 - - + +
257F PHE* 4.9 0.4 - - - -
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Residues in contact with TYR 213 (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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146F ALA* 5.5 1.0 + - - +
150F LYS* 5.7 0.2 - - - -
173F GLU* 4.1 10.5 - - - -
212F LYS* 1.3 73.8 - - - +
214F THR* 1.3 61.5 + - - +
216F TYR 4.5 4.3 - - - -
217F PRO 3.6 17.5 - - - -
218F ASP 4.0 11.0 - - - -
219F PRO* 3.6 34.6 - - + +
253F ASN 4.5 0.9 - - - +
254F ASP* 3.4 4.2 - - - +
255F ARG* 2.7 77.0 + - - +
257F PHE* 3.4 36.5 - + - -
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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