Contacts of the strand formed by residues 171 - 179 (chain J) in PDB entry 6G2T
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 171 (chain J).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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166J VAL* 4.8 3.9 - - - +
169J GLY 5.0 1.0 + - - -
170J GLY* 1.3 76.3 + - - -
172J ILE* 1.3 61.3 + - - +
173J THR* 5.6 0.4 - - - -
226J ILE 3.2 11.0 - - - -
227J THR* 3.4 25.2 - - - +
228J ASP 4.1 1.4 + - - -
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Residues in contact with ILE 172 (chain J).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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164J GLY* 3.6 17.3 - - - -
165J GLU 4.0 4.3 - - - +
166J VAL* 3.3 36.9 - - + +
171J SER* 1.3 73.0 - - - +
173J THR* 1.3 69.6 + - - +
174J PHE* 3.4 36.3 + - + -
224J LEU 3.9 1.0 - - - +
225J HIS* 3.9 0.3 - - - -
226J ILE* 2.9 60.3 + - + +
254J LEU* 4.0 10.8 - - + -
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Residues in contact with THR 173 (chain J).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
171J SER* 5.6 0.7 - - - -
172J ILE* 1.3 81.3 + - - +
174J PHE* 1.3 77.8 + - - +
175J SER* 4.4 2.4 + - - -
223J GLU* 4.5 13.0 - - + +
224J LEU 3.5 5.8 - - - +
225J HIS* 3.0 39.9 + - + +
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Residues in contact with PHE 174 (chain J).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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161J PRO* 5.1 4.5 - - + -
162J GLN* 2.9 30.3 - - + -
163J ASP 4.0 0.4 - - - -
164J GLY* 3.6 18.4 - - - -
172J ILE* 3.4 35.7 - - + -
173J THR* 1.3 82.3 - - - +
175J SER* 1.3 59.6 + - - +
191J TRP* 4.2 7.2 - - + -
223J GLU* 3.5 2.6 - - - +
224J LEU* 2.7 56.8 + - + +
226J ILE* 4.7 5.6 - - + -
237J TYR* 5.0 0.2 - + - -
252J PHE* 3.5 34.8 - + + -
253J ASN 4.8 0.2 - - - -
254J LEU* 3.7 28.7 - - + -
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Residues in contact with SER 175 (chain J).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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159J MET* 4.5 10.6 - - - +
160J ARG 4.2 3.8 - - - +
161J PRO* 3.7 19.5 - - - +
162J GLN 5.7 0.6 - - - +
173J THR* 5.2 2.2 - - - -
174J PHE* 1.3 76.9 - - - +
176J ALA* 1.3 61.0 + - - +
177J ARG* 4.3 2.5 - - - +
191J TRP* 4.6 4.0 - - - -
221J LEU* 3.8 15.4 - - - +
222J PHE 3.1 12.6 - - - -
223J GLU* 3.8 17.5 - - - -
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Residues in contact with ALA 176 (chain J).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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157J PHE* 4.3 14.8 - - + -
159J MET 3.7 10.5 - - - +
161J PRO* 4.2 17.7 - - + -
175J SER* 1.3 75.1 - - - +
177J ARG* 1.3 63.7 + - - +
191J TRP* 4.5 3.5 - - + -
220J TYR 3.7 1.2 - - - +
222J PHE* 2.8 46.2 + - + +
239J CYS* 4.2 17.0 - - - -
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Residues in contact with ARG 177 (chain J).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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157J PHE* 3.4 4.7 - - - -
158J VAL* 2.6 45.9 + - + +
159J MET* 3.5 44.6 + - - +
175J SER* 5.2 1.6 - - - +
176J ALA* 1.3 73.5 - - - +
178J VAL* 1.3 57.7 + - - +
214J ASP* 5.3 6.3 + - - -
217J SER* 5.1 7.1 - - - -
219J VAL* 3.4 38.5 + - + +
220J TYR 3.2 5.6 - - - +
221J LEU* 3.5 40.7 - - + +
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Residues in contact with VAL 178 (chain J).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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156J LEU* 3.3 38.8 - - + +
157J PHE* 3.8 10.3 - - + -
176J ALA 4.9 0.2 - - - +
177J ARG* 1.3 77.9 - - - +
179J ALA* 1.3 74.5 + - - +
187J PRO* 4.1 20.9 - - + -
219J VAL* 4.3 2.9 - - - -
220J TYR* 2.8 43.1 + - + +
222J PHE* 3.8 19.7 - - + -
241J VAL* 3.8 23.1 - - + -
243J THR* 4.7 2.2 - - + -
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Residues in contact with ALA 179 (chain J).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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156J LEU* 4.7 1.7 + - - +
158J VAL* 3.7 23.4 - - + +
178J VAL* 1.3 86.7 - - - +
180J GLY* 1.3 65.5 + - - +
187J PRO* 5.2 2.4 - - - +
218J LYS 3.8 5.6 - - - +
219J VAL* 4.5 5.4 - - + +
220J TYR* 4.8 1.0 - - - -
243J THR* 5.9 0.7 - - - +
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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