Contacts of the helix formed by residues 158 - 172 (chain F) in PDB entry 6ACQ
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 158 (chain F).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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132F ASP* 3.0 27.6 + - - +
153F ARG* 3.7 0.9 - - - -
156F ALA 3.3 3.1 + - - -
157F THR* 1.3 80.3 - - - +
159F GLN* 1.3 66.0 + - - +
160F GLU* 3.8 20.1 + - - +
161F THR* 2.8 31.9 + - - -
162F PHE* 3.0 19.2 + - - +
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Residues in contact with GLN 159 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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153F ARG* 3.1 29.0 + - - +
158F SER* 1.3 73.1 - - - +
160F GLU* 1.3 56.5 + - + +
162F PHE* 3.2 16.4 + - - +
163F ASP* 2.7 71.3 + - - +
178F GLU* 5.5 1.0 + - - -
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Residues in contact with GLU 160 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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158F SER* 4.1 16.5 - - - +
159F GLN* 1.3 78.1 - - + +
161F THR* 1.3 58.9 + - - +
163F ASP* 3.4 9.0 + - - +
164F ALA* 3.0 29.8 + - - +
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Residues in contact with THR 161 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
111F ILE* 3.7 39.4 - - + +
132F ASP 2.7 24.3 + - - +
133F LYS* 3.5 23.9 + - - +
135F ILE* 4.1 16.6 - - + -
157F THR* 4.5 1.8 - - + -
158F SER* 2.8 18.1 + - - -
160F GLU* 1.3 75.3 - - - +
162F PHE* 1.3 65.9 + - - +
164F ALA* 3.4 2.3 + - - +
165F VAL* 3.0 23.6 + - - +
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Residues in contact with PHE 162 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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135F ILE* 3.9 11.4 - - + +
151F VAL* 3.7 32.8 - - + -
153F ARG* 4.0 30.1 - - + +
158F SER 3.0 13.9 + - - +
159F GLN* 3.6 16.4 - - - +
161F THR* 1.3 77.8 - - - +
163F ASP* 1.3 73.4 + - - +
165F VAL* 3.1 2.6 + - - +
166F LYS* 2.9 63.3 + - + +
176F PRO* 6.2 0.9 - - + -
177F VAL 4.9 0.7 - - - -
178F GLU* 3.6 42.6 - - + -
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Residues in contact with ASP 163 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
159F GLN* 2.7 53.9 + - - +
160F GLU* 3.6 8.4 - - - +
162F PHE* 1.3 80.6 - - - +
164F ALA* 1.3 57.9 + - - +
166F LYS* 3.5 7.7 + - - +
167F GLU* 3.1 34.5 + - + +
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Residues in contact with ALA 164 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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0F HIS* 6.5 0.9 - - + -
1F MET* 4.6 14.0 - - + +
111F ILE* 3.9 17.9 - - + -
160F GLU 3.0 17.0 + - - +
161F THR 3.8 4.3 - - - +
163F ASP* 1.3 76.9 - - - +
165F VAL* 1.3 64.2 + - - +
167F GLU* 3.5 13.5 - - - +
168F THR* 3.1 28.2 + - - -
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Residues in contact with VAL 165 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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1F MET* 5.6 1.6 - - - -
83F LEU* 4.8 6.5 - - + -
111F ILE* 4.2 16.2 - - + -
135F ILE* 3.9 27.1 - - + -
137F MET* 3.7 39.1 - - + +
151F VAL* 3.9 19.1 - - + -
161F THR 3.0 16.8 + - - +
162F PHE 3.6 4.0 - - - +
164F ALA* 1.3 73.9 - - - +
166F LYS* 1.3 62.0 + - - +
168F THR* 4.0 4.4 - - - -
169F SER* 2.8 36.8 + - - +
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Residues in contact with LYS 166 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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151F VAL* 5.4 1.3 - - - -
162F PHE* 2.9 47.2 + - + +
163F ASP* 3.7 8.7 - - - +
165F VAL* 1.3 75.8 - - - +
167F GLU* 1.3 59.9 + - - +
169F SER* 3.2 6.9 + - - -
170F ILE* 3.0 43.7 + - + +
176F PRO* 3.8 26.9 - - + -
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Residues in contact with GLU 167 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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-2F GLY 3.4 22.9 - - - +
-1F SER* 4.9 0.4 - - - -
0F HIS* 3.2 38.6 + - - +
163F ASP* 3.1 16.5 + - + +
164F ALA* 3.5 14.5 - - - +
166F LYS* 1.3 79.5 - - - +
168F THR* 1.3 58.8 + - - +
170F ILE* 3.4 9.6 + - - +
171F ALA* 2.9 28.2 + - - +
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Residues in contact with THR 168 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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-1F SER* 3.1 24.6 + - - +
0F HIS 4.9 0.3 + - - -
1F MET* 3.8 17.9 + - + +
4F VAL* 5.5 0.2 - - + -
20F PHE* 3.7 31.0 - - + -
25F PHE* 4.1 9.2 - - + -
83F LEU* 4.5 11.4 - - + -
137F MET* 5.3 2.0 - - + -
164F ALA 3.1 16.4 + - - -
165F VAL* 4.0 5.2 - - - -
167F GLU* 1.3 79.1 + - - +
169F SER* 1.3 66.9 + - - +
171F ALA* 3.2 7.3 + - - +
172F ILE* 3.1 21.8 + - - +
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Residues in contact with SER 169 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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137F MET* 3.8 15.7 - - - +
149F VAL* 3.8 20.6 - - - +
151F VAL* 4.6 0.2 - - - +
165F VAL* 2.8 26.7 + - - +
166F LYS 3.3 5.6 - - - -
167F GLU 3.2 0.2 - - - -
168F THR* 1.3 78.4 - - - +
170F ILE* 1.3 64.0 + - - +
172F ILE* 3.2 19.7 - - - +
174F LYS* 3.0 23.1 + - - +
176F PRO* 3.8 22.9 - - - +
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Residues in contact with ILE 170 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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166F LYS* 3.0 43.0 + - + +
167F GLU* 3.7 7.6 - - - +
169F SER* 1.3 75.2 - - - +
171F ALA* 1.3 58.4 + - - +
173F GLY* 2.9 22.3 + - - -
174F LYS 3.5 8.9 - - - +
176F PRO* 3.9 17.3 - - + -
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Residues in contact with ALA 171 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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-4F PRO* 3.6 38.4 - - + +
-2F GLY* 4.7 2.9 - - - -
-1F SER* 3.7 21.8 - - - +
23F LYS* 3.9 9.9 - - - +
25F PHE* 4.9 0.2 - - + -
167F GLU 2.9 18.3 + - - +
168F THR 3.4 6.3 - - - +
169F SER 3.2 0.2 - - - -
170F ILE* 1.3 78.2 - - - +
172F ILE* 1.3 58.0 + - + +
173F GLY 3.2 2.9 + - - -
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Residues in contact with ILE 172 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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19F ALA* 4.5 10.3 - - + +
20F PHE* 3.7 43.7 - - + -
23F LYS* 3.8 31.0 + - + +
25F PHE* 3.4 33.7 - - + -
137F MET* 5.5 1.1 - - + -
139F PHE* 4.4 9.2 - - + -
168F THR 3.1 11.1 + - - +
169F SER* 3.2 17.9 - - - +
171F ALA* 1.3 75.6 - - - +
173F GLY* 1.3 58.1 + - - +
174F LYS* 3.4 31.1 + - + +
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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