Contacts of the strand formed by residues 159 - 167 (chain G) in PDB entry 6A3V
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 159 (chain G).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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158G SER* 1.3 78.1 - - - +
160G SER* 1.3 61.5 + - - -
184G ASP* 3.7 5.5 - - - +
185G LEU* 2.7 42.3 + - - +
219G GLU 3.2 11.0 - - - -
220G ALA* 3.9 3.1 - - - -
221G ARG* 4.9 0.4 - - - -
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Residues in contact with SER 160 (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 GLY* 1.3 77.1 + - - -
161G VAL* 1.3 63.2 + - - +
162G SER* 4.2 2.6 + - - -
182G THR* 4.5 16.6 - - - -
183G VAL 3.6 7.2 - - - -
184G ASP* 4.2 11.2 + - - -
185G LEU* 4.7 0.4 - - - +
217G HIS 4.2 0.2 - - - +
218G THR* 3.6 1.4 - - - -
219G GLU* 2.7 41.6 + - - +
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Residues in contact with VAL 161 (chain G).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
102G LEU* 3.7 13.0 - - + -
147G LEU* 4.0 21.1 - - + +
149G LEU* 3.6 30.5 - - + -
160G SER* 1.3 74.8 - - - +
162G SER* 1.3 63.5 + - - +
181G LEU 4.1 0.2 - - - +
182G THR* 3.6 2.1 - - - +
183G VAL* 2.9 36.5 + - - +
185G LEU* 3.7 25.4 - - + -
216G LEU* 4.3 26.0 - - + -
217G HIS 3.7 5.8 - - - +
218G THR* 4.0 7.0 - - - +
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Residues in contact with SER 162 (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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160G SER* 5.0 3.1 + - - -
161G VAL* 1.3 76.9 + - - +
163G LEU* 1.3 67.6 + - - +
181G LEU 3.2 8.3 - - - -
182G THR* 3.7 19.7 + - - +
216G LEU* 3.4 7.1 - - - +
217G HIS* 2.6 55.0 + - - +
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Residues in contact with LEU 163 (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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107G LEU* 3.8 26.5 - - + -
109G TRP* 6.1 1.3 - - + -
145G PHE* 3.7 35.7 - - + -
146G GLN 4.1 7.6 - - - +
147G LEU* 3.7 40.6 - - + +
162G SER* 1.3 83.7 - - - +
164G ALA* 1.3 62.9 + - - +
180G ALA* 3.1 7.1 - - - +
181G LEU* 3.0 37.6 + - + +
214G VAL* 4.4 4.0 - - + -
215G HIS 3.3 5.2 - - - +
216G LEU* 3.9 18.4 - - + -
233G THR* 4.9 4.3 - - + -
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Residues in contact with ALA 164 (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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145G PHE* 3.8 4.0 - - - -
163G LEU* 1.3 79.1 - - - +
165G LEU* 1.3 61.4 + - - +
166G HIS* 3.6 27.8 + - + +
177G ALA* 4.4 4.7 - - + -
179G LEU 3.4 11.7 - - - +
180G ALA* 4.1 2.5 - - + +
214G VAL* 3.1 6.1 - - - +
215G HIS* 2.7 40.4 + - + +
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Residues in contact with LEU 165 (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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143G VAL* 3.9 12.6 - - + -
145G PHE* 3.6 10.2 - - + -
164G ALA* 1.3 71.8 - - - +
166G HIS* 1.3 60.8 + - - +
167G LEU* 4.1 20.0 - - + -
178G ALA* 3.2 27.7 + - + +
179G LEU* 3.1 27.3 + - + -
204G LEU* 3.9 26.5 - - + -
212G LEU* 4.1 16.6 - - + -
213G GLY 3.2 10.5 - - - +
214G VAL* 4.3 10.1 - - + -
235G LEU* 3.8 31.2 - - + -
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Residues in contact with HIS 166 (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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164G ALA* 3.6 16.8 - - + +
165G LEU* 1.3 75.4 - - - +
167G LEU* 1.3 66.3 + - - +
168G GLN* 3.8 16.1 + - - +
176G ALA* 3.2 26.3 + - - +
177G ALA* 3.5 19.5 - - + +
178G ALA 5.0 0.7 - - - +
212G LEU* 3.6 4.3 - - - -
213G GLY 2.9 32.3 + - - +
215G HIS* 3.1 48.5 + + + +
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Residues in contact with LEU 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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165G LEU* 4.1 12.1 - - + -
166G HIS* 1.3 77.0 - - - +
168G GLN* 1.3 66.9 + - - +
169G PRO 3.5 8.0 - - - +
176G ALA 5.2 1.6 + - - -
178G ALA* 4.6 19.6 - - + +
204G LEU* 5.6 3.8 - - + -
205G HIS 4.8 5.2 - - - +
206G LEU* 4.3 13.7 - - + -
210G GLN* 3.7 30.3 - - + +
211G ARG 3.5 5.6 - - - +
212G LEU* 3.7 32.8 - - + -
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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