Contacts of the helix formed by residues 154 - 162 (chain D) in PDB entry 5FL6
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 ASN 154 (chain D).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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152D GLU 3.6 2.4 + - - -
153D GLU* 1.3 69.2 - - - +
155D SER* 1.3 58.0 + - - +
156D ALA* 3.0 22.9 + - - +
157D TYR* 3.1 21.6 + - + -
158D GLU* 3.0 11.8 + - - +
183D ALA 4.9 4.0 + - - -
217D VAL* 3.5 22.8 - - - +
218D MET 3.1 27.9 + - - +
219D LEU* 4.4 1.8 - - + -
223D GLN* 2.7 38.8 + - - +
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Residues in contact with SER 155 (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 GLU* 3.4 12.7 + - - -
154D ASN* 1.3 71.3 + - - +
156D ALA* 1.3 67.2 + - - +
158D GLU* 3.4 15.7 + - - +
159D GLN* 3.6 15.8 + - - +
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Residues in contact with ALA 156 (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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154D ASN* 3.0 10.4 + - - +
155D SER* 1.3 82.3 + - - +
157D TYR* 1.3 62.0 + - - +
159D GLN* 3.4 22.9 - - - +
160D LEU* 4.2 1.0 + - - +
179D LEU* 3.8 11.8 - - + +
180D ASP 5.2 1.6 - - - +
183D ALA* 3.5 42.0 - - + +
184D LEU* 3.8 9.7 - - + +
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Residues in contact with TYR 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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95D LEU* 4.3 20.6 - - + -
118D ILE* 3.4 16.4 - - + +
147D LEU* 3.4 33.6 - - + +
154D ASN* 3.1 33.7 + - + +
156D ALA* 1.3 74.6 - - + +
158D GLU* 1.3 61.4 + - - +
160D LEU* 2.9 14.0 + - + +
161D LEU* 2.8 46.8 + - + +
184D LEU* 2.6 55.2 + - + -
217D VAL* 3.7 15.7 - - + -
219D LEU* 3.9 17.9 - - + -
223D GLN* 4.4 0.2 - - - +
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Residues in contact with GLU 158 (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 GLU* 3.7 26.1 - - - +
154D ASN 3.0 16.3 + - - +
155D SER* 3.6 11.7 - - - +
156D ALA 3.3 0.8 - - - -
157D TYR* 1.3 75.9 - - - +
159D GLN* 1.3 55.9 + - - +
161D LEU* 4.3 5.7 - - - +
162D SER* 2.9 54.7 + - - -
222D LYS* 5.5 3.6 + - - -
223D GLN* 3.0 28.5 + - - +
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Residues in contact with GLN 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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155D SER 3.6 14.1 + - - +
156D ALA* 3.4 13.0 + - - +
158D GLU* 1.3 78.0 - - - +
160D LEU* 1.3 61.4 + - + +
162D SER* 3.5 5.2 + - - -
163D ARG* 3.3 22.7 - - - +
176D VAL* 5.4 2.3 - - - +
177D PRO* 4.6 16.0 + - - +
178D GLY 4.3 6.7 + - - -
179D LEU* 3.6 38.1 - - + +
180D ASP 5.3 0.2 + - - -
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Residues in contact with LEU 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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63D LEU* 4.2 21.2 - - + +
72D LEU* 4.3 21.3 - - + -
93D LEU* 4.6 9.0 - - + -
95D LEU* 5.9 7.4 - - + -
156D ALA 4.9 0.9 - - - +
157D TYR* 2.9 14.4 + - + +
159D GLN* 1.3 77.8 - - - +
161D LEU* 1.3 70.0 + - + +
162D SER 3.2 0.4 - - - -
163D ARG* 3.0 20.7 + - - +
164D LEU* 3.6 13.5 + - + +
176D VAL* 4.2 25.4 - - + -
179D LEU* 4.4 17.0 - - + -
184D LEU* 4.1 31.4 - - + -
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Residues in contact with LEU 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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95D LEU* 5.2 5.8 - - + -
157D TYR* 2.8 36.8 + - + +
158D GLU* 4.2 8.7 - - - +
160D LEU* 1.3 78.5 - - + +
162D SER* 1.3 60.8 + - - +
163D ARG 3.2 1.2 + - - -
164D LEU* 3.2 32.6 + - + +
165D GLU 4.8 0.9 + - - -
219D LEU* 4.0 6.7 - - + -
223D GLN* 3.5 43.7 - - + +
226D THR* 3.6 21.3 - - + +
227D LEU* 3.9 37.5 - - + +
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Residues in contact with SER 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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158D GLU* 2.9 38.3 + - - -
159D GLN* 3.5 10.7 + - - -
161D LEU* 1.3 76.3 - - - +
163D ARG* 1.3 68.8 + - - +
164D LEU 3.5 0.6 + - - -
165D GLU* 4.7 7.6 + - - +
166D GLU* 4.5 2.9 - - - +
226D THR* 5.7 0.4 - - - -
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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