Contacts of the strand formed by residues 153 - 159 (chain G) in PDB entry 3X0X
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 TYR 153 (chain G).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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145G ALA* 3.8 23.6 - - + -
146G THR 2.9 20.0 - - - +
147G PRO* 3.5 20.0 - - + -
148G THR 4.3 0.7 - - - +
151G GLY 4.1 9.2 - - - -
152G GLY* 1.3 86.5 - - - -
154G VAL* 1.3 62.5 + - - +
155G LEU* 4.6 3.4 - - + -
177G VAL* 4.0 10.1 - - + -
183G GLN* 3.3 16.7 + - - -
188G ILE* 3.5 32.9 - - + +
223G VAL 3.2 1.0 - - - +
224G LYS* 3.5 2.7 - - - +
225G VAL* 2.6 49.7 + - + +
230G VAL* 3.7 28.9 - - + -
234G PRO* 3.4 22.9 - - + +
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Residues in contact with VAL 154 (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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144G ARG* 3.4 2.8 - - - +
146G THR* 2.8 47.9 + - + +
148G THR* 3.7 21.3 - - + -
153G TYR* 1.3 77.1 - - - +
155G LEU* 1.3 61.2 + - - +
156G ASN* 3.9 20.3 + - - +
222G ASN* 4.3 14.1 - - + +
223G VAL 3.2 12.3 - - - +
224G LYS* 4.5 13.2 - - + -
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Residues in contact with LEU 155 (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* 4.3 11.0 - - + -
144G ARG 3.1 4.3 - - - +
145G ALA* 3.6 31.2 - - + +
153G TYR* 4.6 3.6 - - + -
154G VAL* 1.3 73.2 - - - +
156G ASN* 1.3 60.7 + - - +
173G VAL* 3.4 38.8 - - + +
174G PHE 5.4 0.4 - - - -
175G GLY* 4.6 4.7 - - - +
188G ILE* 5.8 2.7 - - + -
190G ALA* 5.8 0.7 - - + -
220G PHE* 3.6 25.8 - - + +
222G ASN 3.0 8.3 + - - -
223G VAL* 2.8 39.6 + - + +
225G VAL* 3.7 29.4 - - + -
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Residues in contact with ASN 156 (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* 3.4 2.3 - - - -
144G ARG* 2.7 73.9 + - + +
146G THR* 5.6 2.8 + - - -
154G VAL* 3.9 14.3 + - - +
155G LEU* 1.3 76.9 + - - +
157G GLY* 1.3 58.6 + - - +
220G PHE* 3.3 5.0 - - - +
221G HIS* 3.7 12.6 + - - -
222G ASN* 3.0 39.1 + - - +
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Residues in contact with GLY 157 (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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142G LYS 3.6 11.7 - - - -
143G VAL* 4.2 4.7 - - - -
144G ARG* 3.9 10.2 - - - +
156G ASN* 1.3 75.0 - - - +
158G THR* 1.3 57.0 + - - -
159G LYS 4.1 0.4 - - - -
219G ASP* 3.2 7.9 - - - +
220G PHE* 2.6 45.2 + - - +
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Residues in contact with THR 158 (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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142G LYS* 3.0 29.2 + - - +
143G VAL* 4.3 0.7 - - - -
157G GLY* 1.3 71.1 - - - -
159G LYS* 1.3 67.3 + - - +
160G HIS* 3.5 16.9 + - + +
202G ASN* 4.8 3.1 - - - +
217G SER* 4.1 21.3 - - - +
218G THR 3.4 13.0 - - - +
219G ASP* 2.7 23.1 + - + +
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Residues in contact with LYS 159 (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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129G ASN* 6.0 0.4 - - - +
130G ALA* 3.9 16.4 - - + +
131G SER 3.2 31.9 - - - +
132G SER 2.9 24.5 + - - -
133G GLU* 3.9 25.2 - - + +
141G TRP* 6.1 0.4 - - + -
142G LYS* 4.5 2.9 - - - -
143G VAL* 3.8 22.9 - - + +
158G THR* 1.3 73.0 - - - +
160G HIS* 1.3 63.1 - - - +
161G PHE* 3.0 30.4 + - - +
162G CYS* 3.7 21.1 - - - -
174G PHE 6.0 0.2 - - - +
217G SER* 3.4 1.7 - - - -
218G THR 2.9 34.8 + - - +
220G PHE* 4.6 0.2 - - + -
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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