Contacts of the strand formed by residues 166 - 173 (chain F) in PDB entry 6S1M
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 166 (chain F).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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161F SER 4.2 0.9 - - - +
162F CYS* 3.9 0.8 - - - -
163F ALA* 3.0 29.7 + - - +
164F LYS 3.6 0.6 - - - -
165F ASP* 1.3 89.9 + - - +
167F VAL* 1.3 61.6 + - - +
182F LEU 3.2 13.9 - - - -
183F SER* 4.2 3.4 - - - -
197F ILE* 3.4 13.7 - - - -
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Residues in contact with VAL 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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137F VAL* 4.3 21.3 - - + -
160F ILE* 3.9 24.9 - - + -
161F SER 3.4 11.0 - - - +
162F CYS* 4.3 14.8 - - + +
166F GLY* 1.3 74.8 - - - -
168F LYS* 1.3 65.8 + - - +
169F PHE* 4.1 19.5 - - + -
180F ILE 4.1 0.3 - - - +
181F LYS* 3.7 1.9 - - - +
182F LEU* 2.9 53.1 + - + +
197F ILE* 4.2 11.2 - - + -
227F LEU* 6.1 0.4 - - + -
229F MET* 4.6 0.2 - - + -
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Residues in contact with LYS 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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159F VAL 3.1 3.7 - - - +
160F ILE* 3.3 2.8 - - - +
161F SER* 2.6 60.8 + - - +
167F VAL* 1.3 77.3 - - - +
169F PHE* 1.3 73.6 + - - +
170F SER* 4.5 11.2 - - - -
179F ASN* 4.2 17.1 - - + +
180F ILE 3.5 10.5 - - - +
181F LYS* 3.9 34.2 - - + +
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Residues in contact with PHE 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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139F MET* 4.0 21.1 - - + -
144F PHE* 4.5 10.3 - + - -
147F ILE* 3.8 37.5 - - + -
148F CYS* 6.4 0.9 - - - -
151F LEU* 3.5 21.6 - - + +
158F VAL* 3.8 7.0 - - + -
159F VAL 3.3 4.9 - - - -
160F ILE* 3.7 39.9 - - + -
167F VAL* 4.1 29.2 - - + -
168F LYS* 1.3 75.1 - - - +
170F SER* 1.3 61.3 + - - +
179F ASN* 3.1 4.7 - - - +
180F ILE* 2.8 41.3 + - + +
182F LEU* 4.2 6.5 - - + -
212F LEU* 6.4 0.2 - - + -
227F LEU* 4.0 11.4 - - + -
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Residues in contact with SER 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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151F LEU* 4.6 2.7 - - - -
158F VAL* 3.3 9.3 - - - +
159F VAL* 2.8 54.5 + - - +
161F SER* 5.8 0.3 + - - -
168F LYS* 4.5 11.5 - - - -
169F PHE* 1.3 75.0 - - - +
171F ALA* 1.3 61.6 + - - +
178F GLY 3.4 6.5 - - - -
179F ASN* 3.2 25.4 - - - -
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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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151F LEU* 4.4 17.2 - - + +
154F ILE* 3.7 9.2 - - + -
155F GLY* 4.2 16.6 - - - +
157F ALA 3.1 24.7 - - - +
158F VAL* 4.7 0.2 - - - -
159F VAL* 5.9 0.9 - - - -
170F SER* 1.3 73.8 - - - +
172F SER* 1.3 64.7 + - - +
177F ASN* 2.9 19.1 - - - +
178F GLY 3.0 16.1 + - - +
209F LEU* 4.6 0.7 - - + -
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Residues in contact with SER 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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154F ILE* 3.7 6.9 - - - +
155F GLY* 3.7 11.4 - - - -
156F ASP* 4.9 4.2 + - - +
157F ALA 4.9 0.4 + - - -
171F ALA* 1.3 78.5 - - - +
173F GLY* 1.3 58.6 + - - +
176F GLY 3.5 2.9 - - - -
177F ASN* 3.2 27.1 - - - -
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Residues in contact with GLY 173 (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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117E LYS* 3.8 10.6 + - - -
154F ILE 3.5 11.9 + - - -
155F GLY* 4.8 1.1 - - - -
172F SER* 1.3 75.5 - - - +
174F GLU* 1.3 67.6 + - - +
175F LEU 3.3 2.5 - - - -
176F GLY* 2.8 18.8 + - - +
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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