Contacts of the strand formed by residues 188 - 197 (chain D) in PDB entry 3T0E
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 188 (chain D).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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149D GLY 3.1 20.3 + - - -
150D PHE* 2.9 35.5 + - + -
151D TYR* 4.8 8.2 - + - -
152D PRO* 4.1 7.4 - - + -
153D ASP* 3.3 49.6 + - + -
176D PRO* 4.4 12.3 - - + -
177D LEU* 3.4 9.0 - - - +
178D LYS* 3.1 56.2 - - + -
179D GLU* 3.2 2.6 - - - +
184D ASN 5.7 1.2 + - - -
186D SER* 4.8 15.2 + - - -
187D ARG* 1.3 76.4 - - - +
189D SER* 1.3 67.2 + - - +
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Residues in contact with SER 189 (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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152C TYR* 5.3 0.2 - - - -
174C TRP* 3.5 28.9 - - - -
147D ALA 3.5 6.1 - - - -
148D THR* 2.9 23.6 - - - +
150D PHE* 3.4 3.8 - - - -
176D PRO* 3.4 4.7 - - - +
177D LEU* 3.0 40.3 + - - +
179D GLU* 3.1 15.7 + - - +
188D TYR* 1.3 78.7 + - - +
190D LEU* 1.3 60.9 + - - +
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Residues in contact with LEU 190 (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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174C TRP* 5.7 0.2 - - - -
145D CYS 3.7 1.7 - - - +
146D LEU* 3.6 3.8 - - - +
147D ALA* 3.0 38.9 + - + +
150D PHE* 4.3 10.3 - - + -
155D VAL* 4.3 22.7 - - + +
157D LEU* 4.1 33.4 - - + +
172D THR* 4.0 11.9 - - + -
173D ASP* 3.9 31.6 - - + +
176D PRO* 4.0 26.9 - - + -
189D SER* 1.3 75.4 - - - +
191D SER* 1.3 65.0 + - - +
192D SER 4.3 0.2 + - - -
212D VAL* 6.2 1.1 - - + -
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Residues in contact with SER 191 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
154C THR* 3.8 5.6 - - - +
172C VAL* 3.5 24.6 - - - +
174C TRP* 4.6 6.0 - - - -
144D VAL* 5.3 4.5 - - - -
145D CYS 3.2 7.2 - - - -
146D LEU* 3.8 20.2 - - - -
172D THR* 4.8 0.9 - - - -
173D ASP* 2.2 63.1 + - - +
190D LEU* 1.3 78.6 - - - +
192D SER* 1.3 60.4 + - - +
193D ARG* 3.6 6.8 + - - -
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Residues in contact with SER 192 (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 VAL* 3.7 1.0 - - - +
145D CYS 2.9 32.3 + - - -
157D LEU* 3.5 25.2 - - - +
159D TRP* 3.4 27.3 + - - -
170D VAL* 4.2 1.4 - - - +
171D SER 3.9 3.8 - - - -
172D THR* 2.2 36.5 + - - +
191D SER* 1.3 74.5 - - - +
193D ARG* 1.3 62.1 + - - +
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Residues in contact with ARG 193 (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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133C LEU* 4.1 19.3 - - - -
154C THR* 4.8 0.6 + - - -
157C THR* 3.0 28.5 + - - +
159C LEU* 5.8 2.9 - - + -
170C SER* 2.9 48.9 + - - +
171C ALA* 4.7 1.1 - - - -
172C VAL* 3.9 17.8 - - + +
142D THR* 4.6 9.4 - - + -
143D LEU 4.0 5.6 - - - +
144D VAL* 3.7 22.2 - - + -
159D TRP* 4.4 2.0 - - - -
169D GLY 3.2 2.3 - - - +
170D VAL* 3.2 5.7 - - - +
171D SER* 2.9 60.5 + - - +
172D THR 4.9 0.4 - - - -
173D ASP* 3.9 7.7 + - - -
191D SER* 3.6 21.0 + - - -
192D SER* 1.3 76.2 - - - +
194D LEU* 1.3 59.6 + - - +
195D ARG 5.6 0.2 - - - +
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Residues in contact with LEU 194 (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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142D THR* 4.5 1.3 - - - -
143D LEU* 2.9 37.3 + - + +
159D TRP* 3.7 49.2 - - + +
161D VAL* 4.0 24.5 - - + -
166D VAL* 4.3 5.2 - - + -
168D SER 3.8 22.0 - - - +
169D GLY 3.6 1.8 - - - -
170D VAL* 3.9 9.4 - - + -
192D SER 4.3 0.6 + - - -
193D ARG* 1.3 75.7 - - - +
195D ARG* 1.3 69.8 + - - +
196D VAL* 4.2 12.1 - - + -
208D PHE* 4.2 15.7 - - + -
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Residues in contact with ARG 195 (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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135C THR* 3.0 43.1 + - - +
136C ASP* 3.2 24.2 + - - -
159C LEU* 3.3 31.0 - - + +
161C MET* 3.7 30.8 - - - +
166C PHE* 4.3 1.7 - - - -
168C SER* 4.2 6.6 + - - -
170C SER* 5.4 0.6 - - - -
134D GLU* 3.5 13.9 + - - +
138D THR* 4.3 2.8 + - - -
140D LYS* 3.6 23.1 - - + +
141D ALA 3.4 7.4 - - - +
142D THR* 2.5 32.0 + - + +
168D SER 5.0 0.2 - - - +
169D GLY* 3.3 20.9 + - - -
194D LEU* 1.3 74.0 - - - +
196D VAL* 1.3 73.9 + - - +
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Residues in contact with VAL 196 (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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161C MET* 4.2 9.4 - - - -
140D LYS* 3.6 5.9 - - - +
141D ALA* 2.7 57.3 + - + +
143D LEU* 4.6 5.4 - - + -
161D VAL* 5.4 2.7 - - + -
194D LEU* 4.2 16.4 - - + -
195D ARG* 1.3 79.0 - - - +
197D SER* 1.3 64.3 + - - +
200D PHE* 3.6 35.9 - - + -
201D TRP* 4.2 5.2 - - + -
208D PHE* 4.1 18.6 - - + -
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Residues in contact with SER 197 (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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161C MET* 4.4 9.7 - - - +
164C MET* 6.1 4.7 - - - -
139D GLN 4.6 3.6 - - - -
140D LYS* 4.7 1.6 - - - +
196D VAL* 1.3 76.5 - - - +
198D ALA* 1.3 68.7 + - - +
199D THR* 4.1 3.4 + - - -
200D PHE* 2.7 49.7 + - - +
201D TRP 3.4 2.9 + - - -
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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