Contacts of the helix formed by residues 178 - 190 (chain u) in PDB entry 6AH0
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 GLY 178 (chain u).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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173u PHE 4.3 0.3 - - - +
174u VAL* 2.8 41.2 + - - -
175u ALA 4.4 0.6 - - - -
176u ARG 3.3 3.2 + - - -
177u ASN* 1.3 77.9 - - - +
179u ARG* 1.3 59.1 + - - -
181u PHE 4.5 0.3 + - - -
182u LEU* 4.4 8.0 + - - -
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Residues in contact with ARG 179 (chain u).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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177u ASN 3.2 0.2 + - - -
178u GLY* 1.3 72.4 - - - -
180u GLN* 1.3 58.1 + - - +
181u PHE 3.4 1.8 - - - -
182u LEU* 4.6 0.7 - - - +
183u THR* 2.6 38.8 + - - +
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Residues in contact with GLN 180 (chain u).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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177u ASN* 2.7 22.4 + - - +
179u ARG* 1.3 72.9 - - - +
181u PHE* 1.3 56.6 + - - +
184u GLN* 4.0 9.7 + - - -
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Residues in contact with PHE 181 (chain u).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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177u ASN* 4.0 8.8 + - - +
178u GLY 4.5 1.2 + - - -
180u GLN* 1.3 76.1 - - - +
182u LEU* 1.3 60.0 + - - +
184u GLN* 3.5 1.3 + - - -
185u LEU* 2.9 23.9 + - - -
111w GLU* 5.9 8.2 - - - +
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Residues in contact with LEU 182 (chain u).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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173u PHE 6.3 1.2 - - - -
174u VAL* 6.0 1.3 - - - +
178u GLY 4.4 6.9 + - - -
179u ARG* 3.7 3.7 + - - +
181u PHE* 1.3 74.5 - - - +
183u THR* 1.3 56.1 + - - +
184u GLN 3.0 4.9 - - - -
185u LEU* 3.6 1.7 - - - +
186u MET* 2.9 28.4 + - - -
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Residues in contact with THR 183 (chain u).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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179u ARG* 2.6 29.9 + - - +
182u LEU* 1.3 72.9 - - - +
184u GLN* 1.3 57.5 + - - +
186u MET* 4.3 2.1 - - - +
187u GLN* 4.1 9.9 + - - -
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Residues in contact with GLN 184 (chain u).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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179u ARG 3.9 2.0 + - - -
180u GLN 4.0 8.5 + - - -
181u PHE 3.5 6.7 + - - -
182u LEU 3.0 0.4 - - - -
183u THR* 1.3 78.8 - - - +
185u LEU* 1.3 58.8 + - - +
186u MET 3.3 0.2 - - - -
187u GLN* 3.2 3.0 + - - +
188u LYS* 2.9 26.3 + - - -
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Residues in contact with LEU 185 (chain u).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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181u PHE 2.9 16.5 + - - -
182u LEU* 3.1 3.8 + - - +
184u GLN* 1.3 78.4 - - - +
186u MET* 1.3 60.7 + - - +
188u LYS* 3.1 1.3 + - - +
189u GLU* 2.9 27.0 + - - +
191u ARG 5.4 0.2 + - - -
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Residues in contact with MET 186 (chain u).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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182u LEU 2.9 15.2 + - - -
183u THR* 4.8 1.8 - - - +
184u GLN 3.3 0.2 - - - -
185u LEU* 1.3 76.3 - - - +
187u GLN* 1.3 55.8 + - - +
190u GLN* 3.2 27.8 + - - +
191u ARG 4.0 8.2 + - - +
194u GLN* 5.7 9.0 - - - +
195u PHE* 5.8 1.6 - - - +
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Residues in contact with GLN 187 (chain u).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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183u THR 4.1 7.5 + - - -
184u GLN 3.2 8.1 + - - -
185u LEU 3.2 0.2 - - - -
186u MET* 1.3 74.3 - - - +
188u LYS* 1.3 63.6 + - - +
190u GLN* 4.2 4.1 + - - +
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Residues in contact with LYS 188 (chain u).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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184u GLN 2.9 14.7 + - - -
185u LEU* 3.7 2.0 - - - +
187u GLN* 1.3 78.4 - - - +
189u GLU* 1.3 63.5 + - - +
190u GLN* 4.7 0.3 - - - -
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Residues in contact with GLU 189 (chain u).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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185u LEU* 2.9 13.9 + - - +
188u LYS* 1.3 73.4 - - - +
190u GLN* 1.3 62.0 + - - +
191u ARG 3.3 4.3 + - - +
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Residues in contact with GLN 190 (chain u).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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186u MET 3.2 18.5 + - - -
187u GLN* 4.6 3.8 - - - +
188u LYS 3.3 2.9 - - - -
189u GLU* 1.3 77.4 - - - +
191u ARG* 1.3 63.6 + - - +
192u ASN* 3.3 2.8 + - - -
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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