Contacts of the strand formed by residues 190 - 197 (chain D) in PDB entry 1L9X
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 190 (chain D).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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116D LEU* 4.2 12.3 - - + -
120D ILE* 3.6 32.8 - - + -
180D PHE* 3.6 27.4 - - + -
186D LEU* 2.9 34.0 + - + +
187D LYS 3.6 3.5 - - - +
189D PHE* 1.3 95.9 - + + +
191D ASN* 1.3 58.9 + - - +
192D VAL 3.8 0.5 + - - -
207D MET* 3.7 48.5 - - + -
208D GLU* 3.6 17.3 - - - -
210D TYR* 3.1 18.1 + - - -
214D VAL* 3.9 25.8 - - + -
215D TYR* 5.2 0.9 - - - -
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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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143D GLY* 3.6 31.7 + - - -
146D HIS 5.6 0.8 + - - -
147D SER* 5.0 2.0 - - - +
190D PHE* 1.3 71.1 - - - +
192D VAL* 1.3 73.4 + - - +
193D LEU* 3.3 14.6 + - - +
207D MET* 4.3 0.9 - - - -
208D GLU* 2.7 46.5 + - + +
210D TYR* 3.4 43.1 + - + +
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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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141D THR* 2.6 29.5 + - + -
143D GLY* 4.2 0.3 - - - -
180D PHE* 3.5 39.0 - - + -
190D PHE 3.8 1.2 + - - -
191D ASN* 1.3 80.6 + - - +
193D LEU* 1.3 55.5 + - - +
194D THR 3.6 21.5 - - - +
195D THR* 3.8 12.1 - - + -
204D ILE* 3.7 34.3 - - + -
206D THR 3.8 5.8 - - - +
207D MET* 4.1 3.1 - - + -
210D TYR* 5.0 0.6 + - - -
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Residues in contact with LEU 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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140D PHE* 3.5 5.5 - - - -
141D THR* 3.0 25.0 + - - -
143D GLY 3.5 27.1 - - - +
144D GLN* 4.1 4.3 - - - +
147D SER* 3.6 20.9 - - - -
149D MET* 3.8 11.2 - - + -
150D PHE* 3.8 31.9 - - + -
191D ASN* 3.6 26.9 - - - +
192D VAL* 1.3 73.7 - - - +
194D THR* 1.3 64.9 + - - +
206D THR* 2.8 24.3 + - + +
207D MET* 4.3 1.3 - - - -
208D GLU* 3.8 22.2 - - + +
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Residues in contact with THR 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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138D LEU* 3.8 21.8 - - + +
139D ASN 3.3 9.4 - - - -
140D PHE* 3.5 31.6 - - + -
141D THR* 4.2 1.1 - - - -
150D PHE* 4.3 4.3 - - + -
192D VAL* 3.6 7.3 - - - +
193D LEU* 1.3 82.9 - - - +
195D THR* 1.3 65.2 + - - +
205D SER* 2.6 39.8 + - - -
206D THR* 2.7 37.9 + - - +
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Residues in contact with THR 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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139D ASN* 2.9 44.9 + - - +
141D THR* 4.0 11.4 - - + +
177D VAL* 4.1 13.0 - - + -
192D VAL* 3.8 17.3 - - + -
194D THR* 1.3 78.7 - - - +
196D ASN* 1.3 67.7 + - - +
202D GLU* 2.9 29.2 + - - +
203D PHE 3.1 15.5 - - - +
204D ILE* 4.2 1.6 - - + -
205D SER* 3.3 6.4 + - - -
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Residues in contact with ASN 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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136D MET* 3.9 24.0 - - + +
137D PRO* 2.8 34.9 + - - +
138D LEU* 3.8 5.9 - - - +
139D ASN* 3.6 14.2 - - - +
167D THR* 5.1 1.0 + - - -
169D ASN* 5.3 2.8 + - - +
195D THR* 1.3 76.9 + - - +
197D THR* 1.3 59.7 + - - +
202D GLU* 3.2 6.6 - - - +
203D PHE* 2.7 59.1 + - + -
205D SER* 2.8 28.4 + - - -
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Residues in contact with THR 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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136D MET* 3.3 19.4 - - - +
139D ASN* 4.2 12.3 - - - +
196D ASN* 1.3 77.4 - - - +
198D ASP* 1.3 58.7 + - - +
199D GLY* 2.9 25.3 + - - +
200D LYS 3.8 1.4 + - - -
201D ILE 3.3 14.7 + - - -
202D GLU* 4.2 10.3 - - - +
203D PHE* 4.2 1.8 - - - -
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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