Contacts of the strand formed by residues 158 - 168 (chain D) in PDB entry 6CU0
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 SER 158 (chain D).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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157D GLY* 1.3 75.8 - - - -
159D GLY* 1.3 60.0 + - - +
185D LEU* 3.7 16.2 - - - -
187D PRO* 4.1 24.0 - - - -
219D GLU 4.0 1.2 - - - +
220D ALA* 4.9 0.2 - - - -
221D ARG* 3.1 49.3 + - - +
222D ALA 5.5 0.5 - - - -
226D TRP* 4.2 2.9 - - - +
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Residues in contact with GLY 159 (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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158D SER* 1.3 79.1 + - - +
160D SER* 1.3 63.9 + - - -
184D ASP* 3.7 5.0 - - - +
185D LEU* 2.8 34.1 + - - +
219D GLU* 3.7 9.9 - - - -
221D ARG* 5.2 2.2 - - - -
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Residues in contact with SER 160 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
159D GLY* 1.3 74.9 - - - -
161D VAL* 1.3 71.3 + - - +
162D SER* 4.0 4.6 + - - -
182D THR* 3.3 23.0 - - - +
183D VAL 3.5 8.7 - - - -
184D ASP* 4.9 5.6 - - - -
185D LEU* 4.5 1.5 - - - +
218D THR* 3.4 2.9 + - - -
219D GLU* 3.0 42.8 + - - +
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Residues in contact with VAL 161 (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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102D LEU* 5.2 7.9 - - + -
147D LEU* 4.0 14.7 - - + +
149D LEU* 3.9 34.1 - - + -
160D SER* 1.3 83.7 + - - +
162D SER* 1.3 66.4 + - - +
182D THR* 3.4 1.9 - - - -
183D VAL* 2.9 32.7 + - - +
185D LEU* 5.6 7.0 - - + -
216D LEU* 3.5 29.4 - - + -
217D HIS 3.4 7.0 - - - +
218D THR* 4.2 13.2 - - + +
226D TRP* 6.2 3.8 - - + -
228D LEU* 5.3 0.2 - - + -
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Residues in contact with SER 162 (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* 4.9 0.4 - - - -
160D SER* 4.0 4.0 + - - -
161D VAL* 1.3 79.7 + - - +
163D LEU* 1.3 64.4 + - - +
181D LEU 3.2 13.0 - - - -
182D THR* 3.6 17.6 + - - +
215D HIS 3.5 1.6 - - - +
216D LEU* 3.3 7.1 - - - +
217D HIS* 2.7 53.2 + - - +
218D THR* 5.4 0.2 - - - -
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Residues in contact with LEU 163 (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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107D LEU* 6.0 3.6 - - + -
109D TRP* 5.7 2.7 - - + -
145D PHE* 3.7 41.1 - - + -
146D GLN 4.2 17.5 - - - +
147D LEU* 3.9 25.9 - - + +
162D SER* 1.3 74.6 - - - +
164D ALA* 1.3 64.3 + - - +
180D ALA* 3.6 3.3 - - - +
181D LEU* 3.1 33.4 + - + +
214D VAL* 4.1 16.6 - - + -
215D HIS 3.5 1.8 - - - -
216D LEU* 3.5 33.9 - - + -
228D LEU* 5.9 0.2 - - + -
233D THR* 4.4 12.8 - - + -
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Residues in contact with ALA 164 (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 PHE* 4.2 3.1 - - - -
162D SER* 6.3 0.4 - - - -
163D LEU* 1.3 76.0 - - - +
165D LEU* 1.3 60.8 + - - +
166D HIS* 3.7 23.4 + - + +
177D ALA* 4.2 12.6 - - + -
179D LEU 3.5 6.3 - - - -
180D ALA* 4.5 2.7 - - + +
214D VAL* 3.4 3.0 - - - +
215D HIS* 2.8 39.3 + - + +
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Residues in contact with LEU 165 (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 VAL* 4.1 13.7 - - + -
145D PHE* 3.8 9.2 - - + -
164D ALA* 1.3 70.1 - - - +
166D HIS* 1.3 64.1 + - - +
167D LEU* 4.6 6.1 - - + -
177D ALA* 3.6 4.3 - - - -
178D ALA* 2.9 34.9 + - + +
179D LEU* 2.8 32.2 + - + +
204D LEU* 3.7 29.8 - - + -
212D LEU* 4.1 21.8 - - + -
213D GLY 3.5 7.6 - - - +
214D VAL* 3.7 25.6 - - + +
235D LEU* 4.2 13.9 - - + -
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Residues in contact with HIS 166 (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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164D ALA* 3.7 22.2 + - + +
165D LEU* 1.3 74.8 + - - +
167D LEU* 1.3 64.8 + - - +
168D GLN* 3.9 0.5 + - - +
176D ALA* 4.4 11.5 + - + +
177D ALA* 3.9 30.5 - - + +
178D ALA 5.0 0.4 - - - +
211D ARG 3.9 0.9 - - - +
212D LEU* 3.7 2.4 - - - -
213D GLY* 2.8 35.0 + - - +
215D HIS* 4.2 16.8 - - + +
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Residues in contact with LEU 167 (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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165D LEU* 4.6 7.4 - - + -
166D HIS* 1.3 78.2 - - - +
168D GLN* 1.3 61.6 + - - +
169D PRO 3.6 13.3 - - - +
170D LEU* 3.7 9.2 + - - +
178D ALA* 4.0 27.6 - - + +
204D LEU* 5.0 2.9 - - + -
205D HIS 5.2 4.3 - - - +
206D LEU* 4.2 24.9 - - + -
210D GLN* 3.9 31.2 - - + +
211D ARG 3.9 1.6 - - - -
212D LEU* 4.3 16.2 - - + -
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Residues in contact with GLN 168 (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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132D GLU* 3.9 17.7 - - - +
166D HIS 3.9 0.8 + - - +
167D LEU* 1.3 74.5 - - - +
169D PRO* 1.3 69.9 - - + +
170D LEU* 3.5 17.2 + - - +
210D GLN* 3.3 3.2 - - - +
211D ARG* 2.9 44.1 + - + +
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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