Contacts of the strand formed by residues 186 - 195 (chain D) in PDB entry 4QRR
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 PHE 186 (chain D).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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134D ILE* 6.5 0.7 - - + -
136D ASN 6.0 2.9 - - - -
156D ASP* 3.3 22.9 - - - -
179D LEU* 4.1 1.1 - - + +
180D ASP* 3.9 0.3 - - - -
181D MET* 2.8 65.8 + - + +
184D MET* 4.3 10.3 - - + +
185D ASP* 1.3 76.6 - - - +
187D LYS* 1.3 68.7 + - - +
188D SER* 3.4 30.3 - - - -
153E LYS* 3.8 35.0 - - + -
208E ARG* 4.4 2.2 - - - -
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Residues in contact with LYS 187 (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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15D VAL* 5.8 4.1 - - + +
16D ARG* 5.6 6.1 - - - +
96D LEU* 3.8 23.3 - - + +
97D GLU* 6.0 0.2 + - - -
132D PRO* 4.3 21.3 - - + -
133D ASN 5.5 1.9 - - - +
134D ILE* 4.0 19.3 - - - +
178D VAL* 4.9 0.7 - - + -
179D LEU 3.4 14.6 - - - +
180D ASP* 3.5 28.4 + - - +
185D ASP* 4.3 16.4 + - - +
186D PHE* 1.3 87.9 - - - +
188D SER* 1.3 62.0 + - - +
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Residues in contact with SER 188 (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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134D ILE* 4.3 9.4 - - - -
155D THR* 4.1 1.2 + - - -
156D ASP* 4.2 15.9 - - - +
177D THR 4.0 0.3 - - - +
178D VAL* 5.0 3.7 - - - +
179D LEU* 3.3 38.4 + - - +
186D PHE* 3.4 23.4 - - - -
187D LYS* 1.3 75.0 - - - +
189D ASN* 1.3 64.2 + - - +
190D SER* 4.0 0.9 + - - -
208E ARG* 3.3 26.0 + - - -
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Residues in contact with ASN 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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131D HIS* 5.5 3.8 + - - -
132D PRO* 4.1 8.5 - - - +
134D ILE* 3.6 25.4 - - - +
155D THR* 2.8 19.1 + - - -
156D ASP 3.1 11.7 + - - +
157D PHE* 3.5 38.1 + - + +
158D ASP 4.2 1.6 + - - -
159D SER* 3.8 20.0 + - - +
176D LYS* 4.7 13.9 - - + +
177D THR 3.6 6.7 - - - +
178D VAL* 3.5 26.5 - - - +
188D SER* 1.3 74.0 - - - +
190D SER* 1.3 58.9 + - - +
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Residues in contact with SER 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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153D LEU* 4.1 14.1 - - - -
154D PHE 3.5 6.1 - - - -
155D THR* 3.5 16.2 - - - -
157D PHE* 3.7 3.8 - - - -
176D LYS* 3.4 4.0 - - - -
177D THR* 3.2 31.3 + - - -
179D LEU* 4.7 8.0 - - - +
188D SER 4.7 2.8 + - - -
189D ASN* 1.3 77.0 - - - +
191D ALA* 1.3 60.1 + - - +
155E THR* 5.9 1.6 - - - -
184E SER* 4.3 2.6 + - - -
206E ARG* 3.4 30.5 + - - +
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Residues in contact with ALA 191 (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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152D CYS 4.0 0.3 - - - +
153D LEU* 3.5 6.6 - - - +
154D PHE* 2.8 42.7 + - + +
157D PHE* 4.5 2.9 - - + -
163D VAL* 4.0 28.9 - - + -
174D THR 3.9 15.7 - - - +
176D LYS* 4.9 0.4 - - - -
190D SER* 1.3 74.7 - - - +
192D VAL* 1.3 63.1 + - - +
206D PHE* 4.2 11.6 - - + -
206E ARG* 4.1 3.8 - - - +
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Residues in contact with VAL 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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151D VAL* 3.6 24.5 - - + -
152D CYS 3.7 2.9 - - - -
153D LEU* 3.9 14.6 - - + -
172D TYR 4.0 0.7 - - - +
173D ILE* 3.5 1.9 - - - +
174D THR* 2.9 43.3 + - - +
191D ALA* 1.3 76.1 - - - +
193D ALA* 1.3 65.2 + - - +
194D TRP* 3.7 18.6 - - + -
206D PHE* 4.6 1.1 - - - -
157E VAL* 3.9 21.1 - - + -
159E LEU* 5.0 0.7 - - + -
204E SER* 3.9 13.0 - - - +
206E ARG* 3.5 25.8 - - + +
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Residues in contact with ALA 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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151D VAL* 3.8 1.3 - - - -
152D CYS* 2.9 39.7 + - - +
171D VAL* 5.0 6.3 - - + -
172D TYR 3.3 11.4 - - - +
173D ILE* 4.1 13.2 - - + -
192D VAL* 1.3 75.5 - - - +
194D TRP* 1.3 60.6 + - - +
205D ALA* 5.0 9.6 - - + +
206D PHE* 3.7 28.5 - - + -
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Residues in contact with TRP 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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149D LYS* 5.1 15.7 - - + +
150D SER 3.7 12.6 - - - +
151D VAL* 3.9 14.1 - - + -
171D VAL* 4.3 5.3 - - - +
172D TYR* 3.3 69.8 + + + -
174D THR* 3.7 31.6 - - + -
192D VAL* 3.7 22.7 - - + -
193D ALA* 1.3 72.6 - - - +
195D SER* 1.4 65.1 + - - +
196D ASN* 3.9 2.1 + - - -
159E LEU* 3.6 38.4 - - + -
161E THR* 4.3 11.5 - - + +
190E LEU* 4.7 4.7 - - + -
202E ALA* 4.0 26.0 - - + -
203E LEU 5.4 2.0 - - - -
204E SER* 4.4 2.0 - - - -
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Residues in contact with SER 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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149D LYS* 4.5 7.4 - - - +
150D SER* 3.0 38.4 + - - -
152D CYS* 5.9 2.9 - - - -
170D ASP 4.6 2.9 - - - -
171D VAL* 5.3 5.2 - - - -
194D TRP* 1.4 75.9 - - - +
196D ASN* 1.3 59.7 + - - +
197D LYS* 3.0 18.9 + - - -
198D SER* 5.3 4.7 - - - -
200D PHE* 4.5 0.5 - - - -
201D ALA* 4.1 35.6 + - - -
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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