Contacts of the helix formed by residues 179 - 187 (chain B) in PDB entry 1F0J
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 179 (chain B).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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169B GLU* 4.0 10.1 + - - +
172B ASP* 5.5 0.6 + - - -
177B GLY 3.4 4.4 + - - +
178B LEU* 1.3 76.7 - - - +
180B ILE* 1.3 62.1 + - - +
181B PHE* 3.0 24.9 + - - +
182B ASN* 3.0 45.2 + - - +
183B VAL* 3.3 13.7 + - - +
401B GLU* 4.4 15.6 + - - -
402B LEU* 3.4 25.6 - - + +
405B GLN* 4.9 2.4 - - - +
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Residues in contact with ILE 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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178B LEU* 3.4 21.2 + - + +
179B ASN* 1.3 71.0 + - - +
181B PHE* 1.3 68.3 + - + +
183B VAL* 3.2 15.9 + - + +
184B ALA 2.9 24.1 + - - -
191B PRO* 4.1 5.4 - - + -
195B ILE* 4.2 19.1 - - + -
237B LEU* 3.6 28.0 - - + +
240B ALA* 3.8 28.7 - - + -
241B ASP* 4.3 13.9 - - + +
244B GLN* 5.2 1.6 - - + +
402B LEU* 5.2 0.8 - - + +
406B TRP* 3.7 29.2 - - + -
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Residues in contact with PHE 181 (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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179B ASN* 3.0 9.3 + - - +
180B ILE* 1.3 81.1 - - + +
182B ASN* 1.3 63.2 + - - +
184B ALA* 3.3 4.8 + - - +
185B GLY* 3.1 18.7 + - - -
237B LEU* 3.4 30.1 - - + -
402B LEU* 3.4 33.7 - - + -
405B GLN* 3.6 43.3 - - + +
406B TRP* 3.7 42.0 - + - -
409B ARG* 3.6 22.9 - - - -
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Residues in contact with ASN 182 (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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169B GLU* 3.3 39.1 + - + +
179B ASN* 3.0 32.2 + - - +
181B PHE* 1.3 78.8 - - - +
183B VAL* 1.3 64.3 + - - +
185B GLY* 3.2 3.4 + - - -
186B TYR* 3.0 38.8 + - + -
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Residues in contact with VAL 183 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
166B LEU* 4.1 12.3 - - + +
169B GLU* 4.1 18.2 - - + -
170B LEU* 4.5 12.1 - - + -
178B LEU* 4.3 13.7 - - + -
179B ASN 3.6 13.9 - - - +
180B ILE* 3.2 25.0 + - + +
182B ASN* 1.3 78.2 - - - +
184B ALA* 1.3 55.3 + - - +
186B TYR* 3.3 2.0 + - - -
187B SER* 2.7 35.0 + - - +
191B PRO* 4.4 7.6 - - + +
194B CYS* 4.0 25.8 - - + -
195B ILE* 4.6 7.4 - - + -
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Residues in contact with ALA 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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180B ILE 2.9 13.1 + - - +
181B PHE* 3.6 9.2 - - - +
182B ASN 3.2 0.2 - - - -
183B VAL* 1.3 76.9 - - - +
185B GLY* 1.3 63.9 + - - +
187B SER* 3.2 11.3 + - - -
189B ASN* 2.9 37.8 + - - +
191B PRO* 3.8 26.5 - - + -
237B LEU* 3.8 13.5 - - + -
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Residues in contact with GLY 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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162B ASN* 4.9 4.3 + - - -
181B PHE 3.1 14.9 + - - -
182B ASN* 3.2 5.5 + - - -
184B ALA* 1.3 77.6 - - - +
186B TYR* 1.3 64.8 + - - +
187B SER 3.8 0.3 + - - -
188B HIS* 4.4 3.8 + - - -
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Residues in contact with TYR 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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158B VAL* 3.5 27.0 - - - +
159B ASN* 5.3 0.5 + - - -
162B ASN* 3.5 32.4 + - + +
165B HIS* 3.5 45.5 + + + -
166B LEU* 4.0 30.1 - - + +
169B GLU* 3.7 32.1 + - + -
182B ASN* 3.0 32.5 + - + +
184B ALA 3.2 0.2 - - - -
185B GLY* 1.3 81.5 - - - +
187B SER* 1.3 58.1 + - - +
188B HIS* 3.6 3.8 + - - -
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Residues in contact with SER 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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156B PHE* 4.7 9.5 - - - +
158B VAL* 4.6 9.0 - - - -
166B LEU* 4.8 5.2 - - - -
183B VAL 2.7 21.9 + - - -
184B ALA* 3.2 6.0 + - - -
186B TYR* 1.3 79.6 - - - +
188B HIS* 1.3 72.4 + - - +
189B ASN 3.2 0.2 - - - -
190B ARG* 3.2 33.4 + - - +
191B PRO* 3.8 1.0 - - - +
194B CYS* 4.2 24.5 - - - +
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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