Contacts of the strand formed by residues 220 - 228 (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 ILE 220 (chain D).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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161A HIS* 3.4 34.8 - - + +
211D TYR* 3.5 2.2 - - - -
212D LYS* 2.9 51.9 + - + +
214D THR* 4.0 26.7 - - + -
216D TYR* 4.7 7.2 - - + -
218D ASP 3.8 8.7 - - - +
219D PRO* 1.3 76.0 - - - +
221D LEU* 1.3 63.9 + - - +
222D LEU 3.6 0.3 + - - -
57R LEU* 4.6 10.1 - - + -
61R LEU* 4.1 32.3 - - + -
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Residues in contact with LEU 221 (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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161A HIS* 3.3 19.4 - - - -
270A HIS* 4.5 0.2 + - - -
271A GLU* 3.4 49.8 - - + +
147D LEU* 5.6 4.5 - - + -
209D TYR* 3.8 30.7 - - + -
210D ILE 3.9 5.4 - - - +
211D TYR* 3.4 27.6 - - + +
219D PRO 4.2 0.4 + - - -
220D ILE* 1.3 73.3 - - - +
222D LEU* 1.3 58.4 + - - +
223D MET 3.4 22.9 - - - +
224D LYS* 4.4 16.2 - - + +
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Residues in contact with LEU 222 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
161A HIS* 3.9 24.4 + - + +
270A HIS* 4.5 1.4 - - - +
271A GLU* 3.4 20.6 - - - +
274A PHE* 5.1 0.2 - - - -
184D ILE* 3.7 29.8 - - + -
210D ILE* 2.9 21.6 + - + +
211D TYR 4.6 0.2 - - - -
212D LYS* 4.0 44.4 - - + +
220D ILE 4.1 0.7 - - - +
221D LEU* 1.3 75.8 - - - +
223D MET* 1.3 69.7 + - + +
248D PHE* 3.6 44.6 - - + -
250D LEU* 4.7 2.5 - - + -
256D ILE* 4.3 7.0 - - + -
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Residues in contact with MET 223 (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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271A GLU* 3.3 6.3 - - - +
274A PHE* 3.7 17.0 - - + -
184D ILE* 3.5 31.4 - - + +
209D TYR* 3.4 0.5 - - - -
210D ILE* 2.8 60.4 + - + -
221D LEU* 3.4 8.9 - - - +
222D LEU* 1.3 88.0 - - + +
224D LYS* 1.3 62.5 + - - +
244D GLN* 3.3 15.3 + - - +
245D GLY* 3.2 34.1 - - - +
246D GLY* 3.3 3.1 - - - -
248D PHE* 3.6 27.1 - - + -
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Residues in contact with LYS 224 (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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130A ARG* 5.5 2.4 - - - +
187A GLN* 3.1 16.5 + - - -
189A TYR* 3.9 19.2 - - + -
191A ARG* 5.8 0.2 - - - +
241A SER* 4.5 1.7 + - - -
267A ASP* 5.2 1.8 + - - -
269A ASP* 4.5 15.7 + - - -
271A GLU* 3.0 12.5 + - + +
272A ALA* 3.9 21.9 - - + +
147D LEU* 6.0 1.8 - - + +
207D VAL* 4.7 2.7 - - + -
208D GLN 3.3 5.6 - - - +
209D TYR* 3.7 28.0 - - + -
221D LEU* 4.4 14.5 - - + +
223D MET* 1.3 74.2 - - - +
225D SER* 1.3 61.6 + - - +
226D ALA* 5.4 0.4 - - + +
244D GLN* 3.1 5.9 + - - -
98R GLU* 2.9 41.0 + - - +
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Residues in contact with SER 225 (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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187A GLN* 3.4 12.2 + - - -
241A SER* 3.2 23.4 + - - -
207D VAL* 3.5 2.3 - - - +
208D GLN 3.0 30.3 + - - -
224D LYS* 1.3 76.9 - - - +
226D ALA* 1.3 60.1 + - - +
227D ARG* 6.1 0.2 - - - +
242D ILE* 3.5 27.8 - - - +
243D TYR 4.3 3.8 + - - -
244D GLN* 3.4 22.0 + - - -
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Residues in contact with ALA 226 (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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189A TYR* 3.8 24.4 - - + +
239A LEU* 3.3 13.6 - - + +
241A SER* 2.8 36.1 + - - -
206D MET 3.3 8.5 - - - +
207D VAL* 3.7 21.8 - - + -
224D LYS* 5.4 0.9 - - + +
225D SER* 1.3 75.7 - - - +
227D ARG* 1.3 69.4 + - - +
242D ILE* 4.7 0.4 - - - -
98R GLU* 4.1 4.9 - - + -
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Residues in contact with ARG 227 (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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227A ARG* 2.9 28.4 - - - +
239A LEU* 2.9 19.6 + - - +
240A TYR* 2.9 39.2 + - - +
241A SER 4.8 8.7 - - - +
227B ARG* 2.9 27.0 - - - +
205D GLN* 3.6 2.9 - - - -
206D MET* 2.8 44.2 + - + +
225D SER* 6.1 0.2 - - - +
226D ALA* 1.3 81.7 - - - +
228D ASN* 1.3 95.8 + - - +
240D TYR* 4.0 14.0 - - + -
241D SER 5.9 0.7 - - - +
242D ILE* 4.3 22.0 - - + -
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Residues in contact with ASN 228 (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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230A CYS* 4.8 1.6 - - - +
237A TYR* 3.9 22.3 - - + +
238A GLY* 3.4 7.3 - - - -
239A LEU* 2.8 40.8 + - + +
240A TYR* 3.4 10.5 + - - -
204D LYS 3.2 9.2 - - - +
206D MET* 3.7 2.7 - - - -
227D ARG* 1.3 114.7 + - - +
229D SER* 1.3 81.1 + - - +
230D CYS 3.9 0.2 + - - -
231D TRP* 3.3 16.6 + - + +
240D TYR* 3.9 5.9 - - - -
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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