Contacts of the strand formed by residues 188 - 197 (chain D) in PDB entry 4JRX
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 188 (chain D).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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158D ASP* 3.9 14.4 - - + -
181D LEU* 4.0 1.2 - - - +
182D ASP* 3.8 1.6 + - - -
183D MET* 3.0 44.9 + - - +
186D MET* 3.5 16.6 - - - +
187D ASP* 1.4 76.5 - - - +
189D LYS* 1.3 70.8 + - - +
190D SER* 3.5 14.6 - - - -
149E LYS* 3.6 35.4 - - + -
204E ARG* 3.5 24.5 - - - -
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Residues in contact with LYS 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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15D GLU* 2.8 42.7 + - - +
96D GLN* 5.6 1.2 - - - +
97D VAL* 5.3 14.1 - - + -
131D PRO* 3.9 24.5 - - + -
133D ILE* 4.1 12.5 - - - +
180D VAL* 5.1 6.7 - - + -
181D LEU 3.3 4.5 - - - +
182D ASP* 3.3 40.4 + - + +
187D ASP 4.5 0.4 + - - -
188D PHE* 1.3 83.0 - - - +
190D SER* 1.3 63.6 + - - +
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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
----------------------------------------------------------
131D PRO* 4.9 1.1 - - - +
133D ILE* 5.1 4.0 - - - -
157D THR* 4.7 0.7 + - - -
158D ASP* 3.3 26.0 - - - +
179D CYS 3.5 1.6 - - - +
180D VAL* 3.6 5.3 - - - +
181D LEU* 2.9 52.3 + - - +
188D PHE* 3.5 8.8 - - - -
189D LYS* 1.3 75.8 - - - +
191D ASN* 1.3 67.5 + - - +
192D SER* 5.3 0.2 + - - -
204E ARG* 2.9 18.9 + - - -
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Residues in contact with ASN 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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130D PHE* 3.8 14.0 - - - -
131D PRO* 3.8 17.8 - - - +
133D ILE* 4.3 6.7 - - - +
157D THR* 3.1 5.8 + - - -
158D ASP* 2.9 29.1 + - - +
159D PHE* 3.3 45.1 + - + +
160D ASP 3.9 0.8 + - - -
161D SER* 3.1 35.1 + - - +
178D LYS* 5.1 3.4 - - + -
179D CYS 3.4 5.5 - - - +
180D VAL* 3.9 6.4 - - - +
190D SER* 1.3 77.2 - - - +
192D SER* 1.3 60.1 + - - +
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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
----------------------------------------------------------
155D LEU* 3.9 17.0 - - - -
156D PHE 3.1 11.9 - - - -
157D THR* 3.9 9.4 - - - -
159D PHE* 3.7 5.6 - - - -
177D ASP 3.6 0.7 - - - +
178D LYS* 3.4 1.6 - - - -
179D CYS* 2.8 38.6 + - - +
181D LEU* 4.9 7.6 - - - +
190D SER 5.3 0.5 + - - -
191D ASN* 1.3 76.0 - - - +
193D ALA* 1.3 60.1 + - - +
180E CYS* 5.4 0.2 - - - +
202E ARG* 2.9 33.0 + - - +
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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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155D LEU* 3.7 2.8 - - - +
156D PHE* 2.8 32.3 + - + +
159D PHE* 4.3 4.5 - - + -
165D VAL* 3.9 31.2 - - + -
176D THR 3.8 14.4 - - - +
177D ASP 4.0 8.7 - - - +
192D SER* 1.3 73.9 - - - +
194D VAL* 1.3 65.1 + - - +
208D PHE* 3.9 12.1 - - + -
202E ARG* 4.1 1.3 - - - +
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Residues in contact with VAL 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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153D VAL* 3.6 29.6 - - + -
154D CYS 3.6 4.3 - - - +
155D LEU* 4.1 13.2 - - + -
174D TYR 3.7 1.1 - - - +
175D ILE* 3.2 3.8 - - - +
176D THR* 2.8 39.3 + - - +
193D ALA* 1.3 79.3 - - - +
195D ALA* 1.3 62.2 + - - +
196D TRP* 3.9 17.7 - - + -
208D PHE* 4.2 2.5 - - - -
153E VAL* 4.1 13.7 - - + -
155E LEU* 4.4 1.1 - - + -
200E SER* 3.9 10.1 - - - +
202E ARG* 3.6 32.8 - - + +
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Residues in contact with ALA 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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153D VAL* 3.6 0.7 - - - -
154D CYS* 2.7 39.0 + - + +
174D TYR 3.1 5.6 - - - -
175D ILE* 3.9 15.7 - - + -
194D VAL* 1.3 73.9 - - - +
196D TRP* 1.3 62.7 + - - +
202D PHE* 3.7 5.9 - - + -
207D ALA* 3.9 18.4 - - + -
208D PHE* 3.5 28.0 - - + -
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Residues in contact with TRP 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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151D LYS* 3.5 27.1 - - + +
152D SER 3.3 13.7 - - - +
153D VAL* 3.9 14.6 - - + -
173D VAL* 3.5 1.4 - - - +
174D TYR* 2.8 70.6 + + + -
176D THR* 3.3 33.9 - - + -
194D VAL* 3.9 11.7 - - + -
195D ALA* 1.3 75.6 - - - +
197D SER* 1.4 65.4 + - - +
202D PHE* 3.8 4.2 - - - -
155E LEU* 3.6 30.3 - - + -
157E THR* 3.9 18.9 - - + +
186E LEU* 3.8 12.1 - - + -
188E GLU* 5.7 0.4 + - - -
198E ALA* 3.8 24.9 - - + -
199E LEU 5.0 0.9 - - - -
200E SER* 4.1 7.4 - - - -
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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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150D ASP 4.4 0.2 - - - +
151D LYS* 3.4 6.9 - - - +
152D SER* 3.0 31.6 + - - +
172D ASP 2.8 23.8 + - - -
173D VAL* 3.6 5.8 - - - +
174D TYR* 5.1 2.2 - - - -
196D TRP* 1.4 82.4 - - - +
198D ASN* 1.3 65.3 + - - +
199D LYS* 3.0 21.0 + - - +
202D PHE* 3.6 29.8 - - - -
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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