Contacts of the strand formed by residues 156 - 163 (chain D) in PDB entry 4LOE
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 ARG 156 (chain D).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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154D GLY 3.6 13.9 + - - +
155D THR* 1.3 78.1 - - - +
157D VAL* 1.3 65.1 + - - +
158D ARG* 3.8 19.6 - - - +
204D GLU* 3.0 44.3 + - - +
217D VAL* 3.7 20.8 - - + +
218D VAL 3.4 11.0 - - - +
219D PRO* 4.3 8.8 - - + +
220D TYR 4.1 0.2 - - - +
257D LEU* 3.7 4.0 - - - +
258D GLU* 2.7 54.0 + - + +
259D ASP 4.7 7.4 + - - -
260D SER* 4.7 8.6 + - - +
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Residues in contact with VAL 157 (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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109D PHE* 5.4 0.4 - - + -
145D LEU* 3.7 25.8 - - + -
156D ARG* 1.3 78.0 - - - +
158D ARG* 1.3 61.3 + - - +
216D VAL 3.8 1.0 - - - +
217D VAL* 3.2 4.2 - - - -
218D VAL* 2.8 35.8 + - + +
220D TYR* 3.9 25.4 - - + -
232D ILE* 3.8 25.8 - - + -
234D TYR* 4.2 5.2 + - - +
255D ILE* 3.7 26.9 - - + -
256D THR 3.4 5.6 - - - +
257D LEU* 4.1 9.6 - - + -
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Residues in contact with ARG 158 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
156D ARG* 3.8 19.0 - - - +
157D VAL* 1.3 73.9 - - - +
159D ALA* 1.3 63.5 + - - +
160D MET* 5.1 9.0 - - + -
204D GLU* 5.0 1.2 + - - -
206D LEU* 3.5 27.5 - - - +
215D SER* 2.9 38.9 + - - -
216D VAL 3.4 6.1 - - - +
217D VAL* 4.2 17.8 - - + +
234D TYR* 4.7 1.6 - - - -
254D ILE 3.5 1.1 - - - +
255D ILE* 3.2 7.1 - - - +
256D THR* 2.9 48.0 + - - +
258D GLU* 3.0 38.7 + - - +
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Residues in contact with ALA 159 (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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158D ARG* 1.3 74.2 - - - +
160D MET* 1.3 60.8 + - - +
195D ILE* 4.5 6.6 - - + +
215D SER* 3.2 7.4 - - - -
216D VAL* 2.8 39.9 + - + +
234D TYR* 3.5 37.0 + - + +
253D THR* 4.3 7.6 - - + -
254D ILE 3.3 4.3 - - - -
255D ILE* 3.6 11.7 - - + -
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Residues in contact with MET 160 (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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98D PRO* 3.6 34.8 - - + -
158D ARG* 5.1 9.0 - - + -
159D ALA* 1.3 75.8 - - - +
161D ALA* 1.3 70.6 + - - +
162D ILE* 4.5 3.8 - - + -
195D ILE* 4.1 7.7 - - - +
206D LEU* 6.4 0.7 - - + -
208D ASP* 6.1 2.0 - - + -
211D THR* 5.8 0.4 - - - +
213D ARG* 4.0 23.3 - - + +
214D HIS 3.5 17.7 - - - +
215D SER* 4.1 19.3 - - - +
252D LEU 3.6 0.5 - - - +
253D THR* 3.3 1.7 - - - -
254D ILE* 2.7 49.4 + - + +
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Residues in contact with ALA 161 (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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160D MET* 1.3 78.5 - - - +
162D ILE* 1.3 69.4 + - - +
173D VAL* 3.7 34.6 + - + +
194D LEU* 4.3 6.1 - - + -
195D ILE* 4.0 19.0 - - + +
213D ARG* 4.4 5.7 + - - +
214D HIS 4.7 2.5 + - - +
251D ILE* 4.2 15.3 - - + -
252D LEU 3.2 9.6 - - - +
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Residues in contact with ILE 162 (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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97D VAL* 4.9 1.8 - - + -
98D PRO* 4.3 24.2 - - + +
100D GLN* 3.5 27.8 - - + +
160D MET* 4.5 4.7 - - - -
161D ALA* 1.3 80.4 - - - +
163D TYR* 1.3 68.2 + - - +
169D MET* 4.8 12.6 - - + +
173D VAL* 3.7 10.3 - - - -
213D ARG* 3.9 20.2 - - - +
251D ILE* 3.2 4.6 - - - +
252D LEU* 2.7 47.6 + - + -
254D ILE* 3.8 32.3 - - + -
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Residues in contact with TYR 163 (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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162D ILE* 1.3 79.2 - - - +
164D LYS* 1.3 65.1 + - - +
165D GLN 3.6 1.3 + - - +
168D HIS* 3.3 45.0 + - + +
169D MET* 3.9 22.0 + - - +
171D GLU* 3.4 31.3 + - + -
172D VAL 4.1 1.1 + - - -
173D VAL* 3.5 27.1 - - + +
174D ARG 4.8 2.4 + - - -
245D GLY 3.6 2.9 + - - -
246D MET* 3.4 23.8 + - + +
249D ARG* 3.0 53.1 + - + -
250D PRO 3.7 7.9 - - - -
251D ILE* 3.6 22.7 - - + -
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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