Contacts of the helix formed by residues 176 - 190 (chain B) in PDB entry 1FT9
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 SER 176 (chain B).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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170B ALA* 3.9 2.2 - - - -
175B SER* 1.3 82.5 + - - +
177B ARG* 1.3 70.6 + - - +
178B GLN* 2.9 12.9 + - - +
179B THR* 2.9 27.4 + - - -
180B THR* 3.0 14.0 + - - +
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Residues in contact with ARG 177 (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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166B VAL* 3.7 17.6 - - + +
167B GLU* 3.4 44.0 + - + +
170B ALA* 3.8 16.6 - - + +
171B ASN* 5.7 0.8 + - - -
175B SER 4.1 0.2 + - - -
176B SER* 1.3 74.4 + - - +
178B GLN* 1.3 61.9 + - - +
180B THR* 3.5 1.6 + - - -
181B SER* 2.9 37.0 + - - -
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Residues in contact with GLN 178 (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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176B SER* 3.0 9.0 + - - +
177B ARG* 1.3 82.3 - - - +
179B THR* 1.3 71.5 + - - +
181B SER* 3.1 15.0 + - - -
182B THR* 3.0 30.5 + - - +
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Residues in contact with THR 179 (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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59A GLU* 6.1 3.4 - - - +
132B PHE* 5.1 2.7 - - + -
135B ILE* 3.4 22.0 - - + -
175B SER* 3.3 16.1 + - - +
176B SER* 2.9 21.5 + - - -
178B GLN* 1.3 78.4 - - - +
180B THR* 1.3 62.4 + - - -
182B THR* 2.9 23.3 + - - +
183B ALA* 3.2 9.2 + - - +
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Residues in contact with THR 180 (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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135B ILE* 3.8 7.4 - - + -
139B ILE* 3.4 22.4 - - + +
166B VAL* 3.6 10.9 + - - +
169B ILE* 5.3 3.0 - - - +
170B ALA* 3.4 38.9 - - + +
173B ILE* 4.7 4.7 - - + -
175B SER* 3.5 21.1 - - - +
176B SER 3.0 14.3 + - - +
177B ARG 3.5 5.9 + - - -
179B THR* 1.3 71.8 - - - +
181B SER* 1.3 56.8 + - - +
183B ALA 3.1 0.5 + - - -
184B LEU* 2.6 39.6 + - - +
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Residues in contact with SER 181 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
166B VAL* 3.8 19.8 - - - +
177B ARG* 2.9 27.8 + - - -
178B GLN* 3.1 11.3 + - - -
180B THR* 1.3 82.5 + - - +
182B THR* 1.3 54.4 + - - +
184B LEU* 3.6 3.9 - - - +
185B ASN* 2.6 48.9 + - - -
195B ARG* 5.7 1.2 + - - -
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Residues in contact with THR 182 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
132B PHE* 3.7 15.6 - - - -
178B GLN* 3.0 32.2 + - - +
179B THR* 2.9 21.0 + - - +
181B SER* 1.3 75.0 - - - +
183B ALA* 1.3 64.9 + - - +
185B ASN* 4.1 8.1 - - - +
186B SER* 3.2 21.1 + - - -
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Residues in contact with ALA 183 (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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132B PHE* 3.4 17.5 - - + -
135B ILE* 3.5 32.5 - - + -
136B LYS* 3.7 10.0 - - + +
139B ILE* 4.0 10.3 - - + -
179B THR 3.2 7.5 + - - +
180B THR 3.1 7.0 + - - +
182B THR* 1.3 77.8 + - - +
184B LEU* 1.3 59.9 - - - +
186B SER* 3.1 5.2 - - - -
187B LEU* 3.0 30.0 + - - +
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Residues in contact with LEU 184 (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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139B ILE* 3.8 29.1 - - + +
143B PHE* 3.8 17.0 - - + -
166B VAL* 4.4 17.0 - - + -
169B ILE* 4.4 13.9 - - + -
180B THR* 2.6 22.9 + - - +
181B SER* 3.6 4.9 - - - +
183B ALA* 1.3 68.7 - - - +
185B ASN* 1.3 59.7 + - - +
186B SER 2.9 4.3 - - - -
187B LEU* 2.6 29.1 + - + +
188B ILE* 2.9 20.8 + - + +
193B ILE* 4.2 17.3 - - + -
195B ARG* 6.0 0.7 - - - +
201B TYR* 3.8 29.8 - - + +
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Residues in contact with ASN 185 (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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181B SER* 2.6 36.9 + - - +
182B THR* 4.2 8.7 - - - +
184B LEU* 1.3 81.1 - - - +
186B SER* 1.3 57.3 + - - +
188B ILE* 3.2 15.7 + - - +
189B LYS* 3.0 43.7 + - - +
195B ARG* 3.2 35.1 + - - +
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Residues in contact with SER 186 (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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132B PHE* 3.7 10.1 - - - -
136B LYS* 2.7 32.9 + - - -
182B THR 3.2 15.8 + - - -
183B ALA 3.1 12.1 - - - -
185B ASN* 1.3 74.8 - - - +
187B LEU* 1.3 63.1 + - - +
188B ILE 3.0 5.4 + - - -
189B LYS* 3.2 17.6 + - - +
190B GLU* 3.2 27.2 + - - +
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Residues in contact with LEU 187 (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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136B LYS* 3.6 47.3 - - + +
139B ILE* 3.8 26.5 - - + -
140B ALA* 4.4 9.0 - - + +
183B ALA 3.0 18.0 + - - +
184B LEU* 2.6 14.9 + - - +
186B SER* 1.3 72.0 - - - +
188B ILE* 1.3 55.4 + - - +
190B GLU* 3.9 10.9 + - - +
191B GLY 3.7 2.8 + - - -
192B TYR* 3.2 38.8 + - + +
193B ILE* 3.8 23.2 + - + -
209B LEU* 5.8 1.6 - - + -
212B ALA* 5.5 7.6 - - + -
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Residues in contact with ILE 188 (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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184B LEU* 2.9 17.7 + - + +
185B ASN* 3.4 29.4 - - - +
186B SER 3.0 0.2 - - - -
187B LEU* 1.3 75.5 - - - +
189B LYS* 1.3 60.8 + - + +
190B GLU 3.0 1.6 - - - -
191B GLY* 2.7 26.7 + - - -
193B ILE* 3.5 30.8 - - + +
194B SER* 4.8 1.1 - - - -
195B ARG* 3.8 39.0 - - + +
201B TYR* 4.3 11.4 - - + -
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Residues in contact with LYS 189 (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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185B ASN* 3.0 30.6 + - - +
186B SER* 3.2 10.9 + - - +
188B ILE* 1.3 78.6 - - + +
190B GLU* 1.3 62.3 + - + +
191B GLY 3.3 3.1 + - - -
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Residues in contact with GLU 190 (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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136B LYS* 3.3 27.6 + - - +
186B SER* 3.2 22.3 + - - +
187B LEU* 4.0 10.3 - - - +
188B ILE 3.0 1.0 - - - -
189B LYS* 1.3 79.8 - - + +
191B GLY* 1.3 58.8 + - - +
192B TYR* 2.9 38.4 - - + -
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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