Contacts of the strand formed by residues 209 - 219 (chain B) in PDB entry 1LE9
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 VAL 209 (chain B).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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55B PHE* 4.5 0.7 - - - -
100B ASN* 4.0 32.6 + - + +
107B HIS* 3.1 20.8 + - - -
206B ASP* 3.6 25.4 + - + +
207B LEU 3.6 0.6 - - - -
208B SER* 1.3 81.1 - - - +
210B VAL* 1.3 75.9 + - - +
236B ALA* 4.4 3.8 - - + -
237B ILE 3.0 18.4 - - - +
238B TYR* 3.6 30.7 - - + -
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Residues in contact with VAL 210 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
55B PHE* 3.9 20.2 - - + -
97B LEU* 3.7 27.8 - - + -
98B VAL 3.9 7.2 - - - +
100B ASN 5.3 0.9 - - - +
107B HIS* 3.4 26.9 - - + +
109B HIS* 3.6 18.4 - - + +
139B ILE* 4.2 8.3 - - + -
209B VAL* 1.3 83.6 - - - +
211B ARG* 1.3 73.0 + - - +
236B ALA* 3.4 1.2 - - - -
237B ILE* 2.9 38.9 + - + +
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Residues in contact with ARG 211 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
97B LEU* 3.5 2.9 - - - -
98B VAL* 2.7 45.6 + - + +
99B THR 4.0 3.8 + - - -
100B ASN* 3.2 46.1 - - + +
101B GLY 5.2 0.6 + - - -
104B ILE* 3.2 30.7 - - - +
210B VAL* 1.3 86.6 - - - +
212B LEU* 1.3 67.9 + - - +
233B VAL* 3.0 21.8 - - + +
234B SER* 3.0 23.9 + - - +
235B ASP* 3.0 21.5 + - - +
236B ALA* 4.1 3.1 - - - +
237B ILE* 4.9 2.5 - - - +
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Residues in contact with LEU 212 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
48B PRO* 4.2 7.4 - - + -
67B LEU* 4.2 12.8 - - + -
80B PRO* 4.4 6.5 - - + -
95B VAL* 4.1 9.4 - - + -
96B GLN 3.9 2.0 - - - -
97B LEU* 3.5 25.4 - - + -
111B LEU* 3.8 13.9 - - + -
137B LEU* 5.0 5.6 - - + -
211B ARG* 1.3 76.4 - - - +
213B MET* 1.3 59.5 + - - +
214B PHE* 3.8 31.6 - - + -
233B VAL* 3.1 6.9 - - - +
234B SER* 2.8 48.5 + - - +
237B ILE* 4.1 23.7 - - + +
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Residues in contact with MET 213 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
94B ILE 3.5 0.9 - - - +
95B VAL* 3.5 18.2 - - - +
96B GLN* 3.0 25.1 + - + +
98B VAL* 3.2 24.0 - - + -
104B ILE* 4.5 2.5 - - + -
164B ASN* 3.2 28.3 - - - +
167B LEU* 4.4 7.4 - - + -
168B LEU* 3.8 22.9 - - + -
212B LEU* 1.3 72.7 - - - +
214B PHE* 1.3 60.6 + - - +
215B THR* 3.4 14.8 + - - +
231B PRO* 3.4 25.8 - - + -
232B VAL 4.1 0.7 - - - -
233B VAL* 3.3 31.2 - - + -
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Residues in contact with PHE 214 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
42B LEU* 3.2 15.8 - - + +
44B ILE* 4.0 24.9 - - + -
47B GLN* 6.2 1.1 - - - -
48B PRO* 6.0 0.4 - - + -
80B PRO* 4.4 14.6 - - + -
81B GLN 5.7 1.1 - - - -
82B VAL* 4.0 23.6 - - + -
93B VAL* 4.7 2.9 - - + -
94B ILE 4.0 1.8 - - - -
95B VAL* 3.6 29.2 - - + -
134B PHE* 3.5 32.1 - + - -
137B LEU* 5.9 2.0 - - + -
212B LEU* 3.8 32.8 - - + -
213B MET* 1.3 69.8 - - - +
215B THR* 1.3 59.7 + - - +
231B PRO* 3.2 2.4 - - - +
232B VAL* 2.9 53.0 + - + -
234B SER* 4.6 4.9 - - - -
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Residues in contact with THR 215 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
42B LEU* 4.0 1.1 - - - -
92B LYS 3.9 0.3 - - - +
93B VAL* 3.1 6.6 - - - +
94B ILE* 2.8 55.6 + - + +
96B GLN* 5.1 1.0 + - - -
164B ASN* 4.9 11.7 + - - +
213B MET* 3.5 12.1 + - - +
214B PHE* 1.3 75.2 - - - +
216B ALA* 1.3 62.9 + - - +
217B PHE* 3.5 28.1 - - + -
228B ARG* 5.3 2.9 - - + -
229B LEU 3.9 16.4 - - - +
231B PRO* 3.6 19.3 - - + +
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Residues in contact with ALA 216 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
42B LEU* 3.7 23.2 - - + +
84B ILE* 4.9 6.1 - - + -
91B ALA* 5.8 0.2 - - + -
92B LYS 3.6 3.4 - - - -
93B VAL* 4.2 13.0 - - + +
215B THR* 1.3 76.4 - - - +
217B PHE* 1.3 65.5 + - - +
218B LEU* 4.2 3.6 - - + -
227B ARG 3.2 1.7 - - - +
228B ARG* 3.9 0.3 - - - -
229B LEU* 2.9 59.4 + - + +
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Residues in contact with PHE 217 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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91B ALA* 3.5 2.3 - - - -
92B LYS* 2.6 63.3 + - + +
94B ILE* 3.9 18.6 - - + -
162B GLY 4.0 18.8 - - - -
163B TYR* 4.4 6.7 - + - -
164B ASN 4.8 6.7 - - - -
177B GLN* 6.1 1.1 - - - -
215B THR* 3.5 31.4 - - + -
216B ALA* 1.3 73.7 - - - +
218B LEU* 1.3 63.4 + - - +
225B PHE* 3.4 36.4 - - + +
226B THR* 4.2 2.7 - - - -
227B ARG 3.3 14.4 - - - -
228B ARG* 3.2 34.5 - - + -
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Residues in contact with LEU 218 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
39B GLY 4.0 18.4 - - - +
40B PRO* 4.4 1.1 - - + -
84B ILE* 5.0 4.3 - - + -
88B VAL* 3.3 40.2 - - + -
91B ALA* 3.8 14.8 - - + -
216B ALA* 4.4 2.2 - - + -
217B PHE* 1.3 82.4 - - - +
219B PRO* 1.3 79.7 - - + +
225B PHE* 3.8 2.0 - - - -
226B THR 3.6 4.7 + - - -
227B ARG* 3.4 35.0 + - + +
229B LEU* 3.2 39.3 - - + -
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Residues in contact with PRO 219 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
88B VAL* 3.7 14.6 - - + +
90B PRO* 3.3 33.4 - - + +
218B LEU* 1.3 99.1 - - + +
220B ASP* 1.3 62.6 + - - +
223B GLY* 4.0 14.6 - - - +
224B SER 2.9 12.6 - - - +
225B PHE* 3.4 16.2 - - + -
227B ARG* 3.9 7.8 - - - +
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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