Contacts of the strand formed by residues 201 - 208 (chain D) in PDB entry 4DOH
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 TYR 201 (chain D).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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152D LEU* 4.0 17.5 - - + -
169D TYR* 5.3 1.3 - + - -
170D TRP 3.2 8.1 - - - +
171D ARG* 3.6 43.3 + - + -
193D GLU* 3.6 27.1 - - + -
194D THR 4.6 0.3 + - - -
195D MET* 3.2 52.8 - - + -
196D GLU* 2.8 36.9 + - - +
200D ALA* 1.3 88.0 - - - +
202D CYS* 1.3 63.9 + - - +
203D VAL* 5.1 1.8 - - - +
222D GLU 3.9 0.2 - - - +
223D CYS* 3.1 24.1 - - - +
224D VAL* 3.0 12.4 + - + +
225D GLU* 4.8 1.3 - - - -
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Residues in contact with CYS 202 (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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169D TYR* 2.9 25.1 - - - +
170D TRP* 2.8 53.5 + - + -
172D ARG* 3.9 19.7 - - - -
201D TYR* 1.3 72.9 - - - +
203D VAL* 1.3 63.5 + - - +
221D THR* 3.6 8.5 - - + -
222D GLU 3.4 0.2 - - - -
223D CYS* 2.0 42.2 - - - -
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Residues in contact with VAL 203 (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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143D MET* 3.4 23.4 - - + +
145D ILE* 3.7 33.0 - - + -
152D LEU* 3.7 24.0 - - + -
154D ILE* 4.5 5.8 - - + -
167D VAL* 5.9 0.9 - - + -
168D ALA 3.0 8.1 - - - +
169D TYR* 3.7 15.0 - - + -
170D TRP* 4.9 0.2 - - - -
192D LEU* 3.9 11.0 - - + -
201D TYR 5.1 1.6 - - - +
202D CYS* 1.3 80.7 - - - +
204D LYS* 1.3 60.6 + - - +
221D THR* 3.5 4.6 - - - -
222D GLU* 2.9 34.2 + - - +
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Residues in contact with LYS 204 (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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77B LEU* 6.1 3.8 - - - +
143D MET* 3.3 8.3 - - - +
167D VAL* 3.5 1.7 - - - +
168D ALA* 2.6 56.0 + - + +
170D TRP* 4.0 13.6 - - + -
178D GLU* 3.6 24.8 + - - -
203D VAL* 1.3 74.5 - - - +
205D ALA* 1.3 61.4 + - - +
218D PHE* 3.7 38.0 - - + -
219D SER* 3.7 19.1 - - - +
221D THR* 3.8 19.1 - - - +
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Residues in contact with ALA 205 (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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141D PRO* 3.2 14.9 - - + +
143D MET* 3.4 16.8 - - + -
154D ILE* 4.7 0.2 - - + -
156D LEU* 3.9 24.9 - - + -
165D PHE* 5.3 0.4 - - + -
166D LEU 3.2 12.1 - - - +
167D VAL* 4.3 6.5 - - + -
204D LYS* 1.3 79.1 - - - +
206D GLN* 1.3 60.6 + - - +
218D PHE* 3.4 5.7 - - - -
219D SER* 3.0 30.1 + - - +
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Residues in contact with GLN 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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121A LYS* 5.9 4.4 - - - +
124A ARG* 4.5 5.9 + - - -
141D PRO* 3.9 3.4 - - - -
165D PHE* 3.6 4.6 - - - +
166D LEU* 3.0 54.6 + - + +
205D ALA* 1.3 74.7 - - - +
207D THR* 1.3 63.7 + - - +
215D TYR* 3.5 25.0 - - + +
216D SER* 3.2 22.6 + - - +
217D ALA 3.5 13.9 - - - +
218D PHE* 3.3 38.8 - - + -
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Residues in contact with THR 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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138D LEU* 4.6 5.2 - - - +
139D THR 4.1 3.6 + - - +
141D PRO* 4.1 11.6 - - + +
159D LEU* 3.7 22.9 - - + -
163D PHE* 3.7 22.8 - - + -
164D GLU 3.4 5.2 - - - +
165D PHE* 3.5 29.6 - - + -
206D GLN* 1.3 74.4 - - - +
208D PHE* 1.3 59.8 + - - +
209D VAL* 4.3 0.4 - - - +
215D TYR* 3.0 10.7 - - - +
216D SER* 2.9 46.5 + - - +
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Residues in contact with PHE 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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125A LEU* 3.6 32.5 - - + -
129A HIS* 5.6 2.9 - + - -
25C LEU* 5.9 2.9 - - + -
162D GLN 4.0 0.5 - - - +
163D PHE 3.9 0.7 - - - -
164D GLU* 2.9 55.0 + - + +
166D LEU* 5.1 3.8 - - + -
182D MET* 4.6 7.0 - - + -
207D THR* 1.3 74.0 - - - +
209D VAL* 1.3 61.2 + - - +
210D LYS* 3.5 33.6 + - + -
213D GLY* 4.2 8.7 - - - -
214D ARG 3.6 22.4 - - - -
215D TYR* 3.3 46.9 - + + -
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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