Contacts of the strand formed by residues 181 - 188 (chain D) in PDB entry 1I3R
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 181 (chain D).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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27C ASP 5.5 0.2 - - - -
29C ASP* 4.8 1.1 - - - -
147D ASP* 3.0 24.6 + - - -
148D PHE* 3.0 42.4 + - + +
149D TYR* 4.0 20.6 - + - -
150D PRO 4.0 0.4 - - - -
151D GLY* 3.3 35.7 - - - -
173D LEU* 3.7 29.2 - - + -
174D VAL 3.3 17.0 - - - -
175D ARG* 3.3 55.0 - - + -
176D ASN* 3.8 4.1 + - - +
179D TRP 5.5 0.4 - - - -
180D THR* 1.3 76.3 - - - +
182D GLN* 1.3 62.1 + - - +
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Residues in contact with GLN 182 (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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92C LEU* 3.7 16.7 - - - +
93C SER* 2.8 30.0 + - - +
94C ARG 3.2 10.3 + - - +
95C SER* 4.7 4.9 + - - -
145D VAL 3.3 12.3 - - - +
146D SER* 4.1 12.5 - - - -
148D PHE* 3.9 3.2 - - - -
173D LEU* 3.9 0.9 - - - -
174D VAL* 2.9 42.0 + - + +
176D ASN* 2.6 30.8 + - - +
181D PHE* 1.3 77.7 - - - +
183D THR* 1.3 65.3 + - - +
184D LEU* 5.5 7.8 - - - +
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Residues in contact with THR 183 (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 CYS 4.0 0.7 - - - +
145D VAL* 2.9 50.0 + - + +
148D PHE* 4.2 12.3 - - + -
153D ILE* 4.6 10.3 - - + -
155D VAL* 5.1 0.7 - - + -
170D SER* 3.6 13.3 + - - -
171D THR* 3.9 2.9 - - - -
172D GLY 3.1 22.8 + - - -
173D LEU* 4.3 4.8 + - - -
174D VAL* 5.2 0.4 - - - -
182D GLN* 1.3 80.8 - - - +
184D LEU* 1.3 70.1 + - - +
185D VAL* 4.3 11.5 - - + +
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Residues in contact with LEU 184 (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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128D TYR* 4.3 8.5 - - - +
142D VAL* 4.1 19.5 - - + -
143D CYS 3.8 1.8 - - - -
144D SER* 3.7 29.2 - - - +
170D SER* 3.1 18.2 + - - -
171D THR* 3.1 39.0 + - + +
182D GLN* 5.5 7.4 - - - +
183D THR* 1.3 83.9 + - - +
185D VAL* 1.3 62.8 + - - +
186D MET* 3.8 17.2 + - + +
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Residues in contact with VAL 185 (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 CYS* 3.1 31.1 + - - +
145D VAL* 5.6 0.2 - - + -
155D VAL* 3.7 50.7 - - + +
156D ARG* 6.1 0.2 - - - -
157D TRP* 3.3 18.9 + - + +
168D ILE* 3.8 25.4 - - + -
169D VAL 3.6 3.4 - - - +
170D SER* 4.0 13.7 - - - +
183D THR* 4.3 11.4 - - + +
184D LEU* 1.3 73.5 - - - +
186D MET* 1.3 60.1 + - - +
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Residues in contact with MET 186 (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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301A NAG 6.5 0.2 - - - -
20B VAL* 4.9 16.4 - - - -
130D THR* 5.0 3.4 - - + +
140D LEU* 3.3 41.3 - - + -
141D LEU 3.5 3.1 - - - +
142D VAL* 3.6 32.1 - - + -
157D TRP* 4.0 1.6 - - - -
167D GLY 3.6 0.6 - - - +
168D ILE* 3.2 7.4 - - - +
169D VAL* 2.6 49.2 + - + +
171D THR* 5.1 2.7 - - + -
184D LEU* 3.8 26.0 + - + +
185D VAL* 1.3 75.6 - - - +
187D LEU* 1.3 60.9 + - - +
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Residues in contact with LEU 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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140D LEU* 3.4 6.7 - - - +
141D LEU* 2.9 37.2 + - + +
157D TRP* 3.5 41.5 - - + +
158D PHE 5.7 0.2 - - - +
164D GLU* 4.1 19.3 - - + +
166D THR 3.8 17.3 - - - +
167D GLY 3.5 1.1 - - - +
168D ILE* 3.3 20.9 - - + -
186D MET* 1.3 71.9 - - - +
188D GLU* 1.3 67.2 + - - +
189D THR* 3.5 27.5 + - + +
197D TYR* 4.1 20.9 - - + -
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Residues in contact with GLU 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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301A NAG 5.7 3.6 - - - +
139D ASN 3.5 9.4 - - - +
140D LEU* 3.9 16.2 - - + -
166D THR 5.1 0.9 - - - +
167D GLY* 2.8 39.1 + - - +
169D VAL* 4.1 16.9 - - + +
187D LEU* 1.3 72.8 - - - +
189D THR* 1.3 70.6 + - - +
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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