Contacts of the strand formed by residues 166 - 173 (chain G) 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 G).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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161G SER 4.2 0.5 - - - +
162G CYS* 5.0 0.4 - - - -
163G ALA* 3.0 30.6 + - - +
164G LYS 3.6 0.2 - - - -
165G ASP* 1.3 90.6 - - - +
167G VAL* 1.3 60.6 + - - -
182G LEU 3.3 13.5 - - - -
183G SER* 4.2 3.1 - - - -
197G ILE* 3.3 13.5 - - - -
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Residues in contact with VAL 167 (chain G).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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137G VAL* 4.3 23.8 - - + -
160G ILE* 3.9 24.0 - - + -
161G SER 3.4 11.4 - - - +
162G CYS* 4.3 14.6 - - + +
166G GLY* 1.3 75.7 - - - -
168G LYS* 1.3 65.0 + - - +
169G PHE* 4.0 19.6 - - + -
180G ILE 4.1 0.2 - - - +
181G LYS* 3.7 1.7 - - - +
182G LEU* 2.9 53.0 + - + +
197G ILE* 4.2 10.1 - - + -
227G LEU* 6.1 0.2 - - + -
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Residues in contact with LYS 168 (chain G).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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159G VAL 3.1 3.3 - - - +
160G ILE* 3.3 2.5 - - - +
161G SER* 2.6 61.0 + - - +
167G VAL* 1.3 77.3 - - - +
169G PHE* 1.3 72.1 + - - +
170G SER* 4.5 12.6 - - - -
179G ASN* 4.3 16.3 - - + +
180G ILE 3.5 11.9 - - - +
181G LYS* 3.9 33.5 - - + +
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Residues in contact with PHE 169 (chain G).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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139G MET* 4.0 22.2 - - + -
144G PHE* 4.5 10.1 - + - -
147G ILE* 3.7 36.6 - - + -
148G CYS* 6.4 0.4 - - - -
151G LEU* 3.5 22.4 - - + +
158G VAL* 3.7 7.2 - - + -
159G VAL 3.3 5.2 - - - -
160G ILE* 3.7 39.9 - - + -
167G VAL* 4.0 20.6 - - + -
168G LYS* 1.3 74.5 - - - +
170G SER* 1.3 62.0 + - - +
179G ASN* 3.0 5.7 - - - +
180G ILE* 2.8 41.2 + - + +
182G LEU* 4.2 14.1 - - + -
212G LEU* 6.4 0.4 - - + -
227G LEU* 4.1 11.0 - - + -
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Residues in contact with SER 170 (chain G).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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151G LEU* 4.5 3.1 - - - -
157G ALA 3.9 0.3 - - - +
158G VAL* 3.4 8.8 - - - +
159G VAL* 2.9 50.1 + - - +
168G LYS* 4.5 12.2 - - - -
169G PHE* 1.3 77.8 - - - +
171G ALA* 1.3 62.0 + - - +
178G GLY 3.4 6.3 - - - -
179G ASN* 3.2 23.6 - - - +
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Residues in contact with ALA 171 (chain G).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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151G LEU* 4.3 17.0 - - + +
154G ILE* 3.7 10.1 - - + -
155G GLY* 4.1 18.8 - - - +
157G ALA 3.3 21.8 - - - +
158G VAL* 4.8 0.4 - - - -
159G VAL* 5.9 0.2 - - - -
170G SER* 1.3 74.8 - - - +
172G SER* 1.3 63.8 + - - +
177G ASN* 2.8 19.9 - - - +
178G GLY 3.0 16.0 + - - +
209G LEU* 4.6 0.9 - - + -
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Residues in contact with SER 172 (chain G).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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154G ILE* 3.8 6.5 - - - -
155G GLY* 3.6 12.0 - - - -
156G ASP* 4.8 4.2 + - - +
157G ALA 4.9 0.8 + - - -
171G ALA* 1.3 78.8 - - - +
173G GLY* 1.3 60.2 + - - +
176G GLY 3.4 1.3 - - - -
177G ASN* 3.2 27.4 - - - -
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Residues in contact with GLY 173 (chain G).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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117F LYS* 4.0 9.0 + - - -
154G ILE 3.5 12.9 + - - -
155G GLY* 4.8 1.3 - - - -
172G SER* 1.3 76.1 - - - +
174G GLU* 1.3 67.4 + - - +
175G LEU 3.3 2.9 - - - -
176G GLY* 2.7 19.3 + - - +
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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