Contacts of the strand formed by residues 205 - 213 (chain D) in PDB entry 1D0G
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 D).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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237A TYR* 2.9 35.2 + - - +
239A LEU* 3.9 15.9 - - + -
203D ASP 5.4 0.4 - - - +
204D LYS* 1.3 71.6 - - - +
206D MET* 1.3 56.3 + - - +
207D VAL* 3.7 7.6 - - + +
227D ARG 3.6 5.6 - - - -
261D THR* 2.6 25.5 + - - -
262D ASN* 3.0 11.7 + - - +
95R ASP 3.5 10.5 + - - +
96R SER* 3.3 17.7 - - - -
98R GLU* 3.1 29.5 + - - +
99R MET* 3.0 33.5 + - - +
101R ARG* 3.6 11.1 - - - +
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Residues in contact with MET 206 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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190D PHE* 3.6 52.7 - - + -
192D PHE* 4.1 11.0 - - - -
204D LYS* 4.3 7.0 - - + +
205D GLN* 1.3 72.8 - - - +
207D VAL* 1.3 59.3 + - - +
226D ALA* 3.3 2.6 - - - -
227D ARG* 2.8 40.3 + - + +
228D ASN 3.7 4.9 - - - +
229D SER* 3.4 37.9 - - - +
240D TYR* 3.5 39.3 - - + -
242D ILE* 3.5 10.1 - - + +
261D THR* 3.7 2.5 - - - -
262D ASN* 4.5 7.4 - - + +
265D LEU* 5.3 2.0 - - + -
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Residues in contact with VAL 207 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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190D PHE* 3.9 6.2 - - - -
205D GLN* 4.0 13.0 - - + +
206D MET* 1.3 80.3 - - - +
208D GLN* 1.3 67.5 + - - +
209D TYR* 3.4 39.5 - - + +
224D LYS* 4.7 1.6 - - + -
225D SER 3.5 14.4 - - - +
226D ALA* 3.7 11.9 - - + -
259D SER 3.9 0.2 - - - +
260D VAL* 3.2 8.8 - - - +
261D THR* 3.1 40.7 + - + +
97R PRO* 4.9 1.1 - - + -
98R GLU* 3.7 27.8 - - + +
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Residues in contact with GLN 208 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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186D SER* 3.1 33.8 + - - +
188D THR* 3.2 30.1 + - + +
207D VAL* 1.3 74.0 - - - +
209D TYR* 1.3 63.0 + - - +
210D ILE* 3.4 16.2 - - - +
224D LYS* 3.3 4.0 - - - +
225D SER 3.0 35.0 + - - +
242D ILE* 3.3 19.5 - - + +
244D GLN* 3.0 40.2 + - - +
258D VAL* 3.7 17.7 - - + -
259D SER 3.6 2.5 - - - -
260D VAL* 4.2 1.8 - - + -
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Residues in contact with TYR 209 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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147D LEU* 3.5 50.9 - - + +
148D GLY 4.1 0.2 - - - -
207D VAL* 3.4 33.0 - - + +
208D GLN* 1.3 74.1 - - - +
210D ILE* 1.3 62.7 + - - +
211D TYR* 3.6 22.7 - + + -
221D LEU* 3.8 11.7 - - + -
223D MET 3.4 2.9 - - - -
224D LYS* 3.7 31.0 - - + -
257D PHE 3.8 0.3 - - - +
258D VAL* 3.3 7.4 - - - +
259D SER* 2.7 46.3 + - - +
260D VAL 4.6 0.2 - - - -
261D THR* 4.0 12.8 - - + -
97R PRO* 3.7 20.6 - - - +
98R GLU* 3.5 13.8 + - - -
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Residues in contact with ILE 210 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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184D ILE* 4.1 15.5 - - + -
185D TYR* 4.4 4.7 - - - +
186D SER* 4.1 20.9 - - - +
208D GLN* 3.4 29.6 - - - +
209D TYR* 1.3 75.8 - - - +
211D TYR* 1.3 59.5 + - - +
221D LEU* 3.9 0.7 - - - +
222D LEU* 2.9 40.2 + - + +
223D MET* 2.8 51.3 + - + +
244D GLN* 3.7 13.5 - - + +
256D ILE* 5.2 1.3 - - + -
257D PHE 3.3 8.5 - - - +
258D VAL* 4.5 5.4 - - + -
275D PHE* 4.6 6.1 - - + -
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Residues in contact with TYR 211 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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145D LYS 5.0 0.8 + - - -
146D ALA* 3.4 23.1 - - + -
147D LEU* 2.9 38.3 + - - +
209D TYR* 3.6 26.6 - + + -
210D ILE* 1.3 74.0 - - - +
212D LYS* 1.3 60.5 + - - +
219D PRO* 4.0 17.0 - - + -
220D ILE 3.5 5.8 - - - -
221D LEU* 3.4 44.1 - - + +
222D LEU* 4.4 3.8 - - - -
256D ILE* 3.1 8.5 - - - +
257D PHE* 2.8 73.8 + + + -
259D SER* 4.2 6.7 - - - -
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Residues in contact with LYS 212 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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158A ARG* 4.0 30.1 - - - +
161A HIS* 4.4 10.8 + - - -
211D TYR* 1.3 77.9 - - - +
213D TYR* 1.3 64.5 + - - +
214D THR* 3.9 13.7 + - - +
219D PRO* 3.5 3.4 - - - +
220D ILE* 2.9 64.2 + - + +
222D LEU* 4.0 23.6 - - + +
248D PHE* 6.3 0.6 - - - +
249D GLU 4.0 9.5 + - - -
250D LEU* 4.0 15.0 - - + +
254D ASP* 4.3 12.0 + - + +
255D ARG 3.0 9.4 - - - +
256D ILE* 4.0 12.3 - - + -
257D PHE* 5.1 0.2 - - - -
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Residues in contact with TYR 213 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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144D GLU 3.8 18.4 + - - -
150D LYS* 5.3 2.0 - - - -
173D GLU* 3.6 15.0 - - - -
212D LYS* 1.3 73.8 - - - +
214D THR* 1.3 61.8 + - - +
216D TYR 4.4 6.3 - - - -
217D PRO 3.7 16.0 + - - -
218D ASP 4.4 2.0 - - - -
219D PRO* 3.5 43.1 - - + +
253D ASN 4.6 0.3 - - - +
254D ASP* 3.4 7.3 - - - +
255D ARG* 2.7 76.8 + - + +
257D PHE* 3.5 33.4 - + - -
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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