Contacts of the strand formed by residues 228 - 237 (chain G) in PDB entry 5M5X
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 LYS 228 (chain G).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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134G GLU* 3.1 41.1 + - + +
135G GLY 3.7 4.7 - - - -
136G TYR* 5.3 0.4 - - - +
226G ASP* 3.4 19.4 + - - +
227G GLY* 1.3 71.7 - - - +
229G LEU* 1.3 61.7 - - - +
230G ARG* 4.0 24.4 + - + +
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Residues in contact with LEU 229 (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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134G GLU* 4.9 0.7 - - - -
135G GLY* 2.9 36.2 + - - +
137G ILE* 4.2 14.1 - - + -
145G ILE* 4.2 19.7 - - + -
147G LEU* 5.2 8.0 - - + +
166G TRP* 5.3 7.0 - - + -
225G ILE* 4.1 34.8 - - + -
226G ASP 4.3 6.3 - - - +
227G GLY 3.1 8.2 + - - +
228G LYS* 1.3 76.9 - - - +
230G ARG* 1.3 62.4 + - - +
231G PHE* 3.5 36.5 + - + -
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Residues in contact with ARG 230 (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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132G VAL* 3.6 26.2 - - + -
133G LEU 3.2 20.4 - - - +
134G GLU* 4.2 19.2 + - + +
228G LYS* 4.0 29.7 + - + +
229G LEU* 1.3 75.8 - - - +
231G PHE* 1.3 72.1 + - - +
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Residues in contact with PHE 231 (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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132G VAL* 3.3 7.9 - - - +
133G LEU* 2.9 31.4 + - - +
145G ILE* 5.6 1.6 - - + -
147G LEU* 5.2 5.8 - - + -
157G ILE* 3.6 28.7 - - + -
161G ASN 5.7 1.6 - - - -
163G PRO* 6.2 0.9 - - + -
166G TRP* 3.7 34.1 - + - -
229G LEU* 3.5 39.6 + - + +
230G ARG* 1.3 80.4 - - - +
232G THR* 1.3 65.3 + - - +
247G GLY* 5.2 2.9 - - - -
248G THR 3.2 25.6 - - - +
249G LEU* 4.6 13.0 - - + -
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Residues in contact with THR 232 (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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130G GLY* 3.3 25.8 - - - +
131G ASP 3.3 14.4 - - - +
132G VAL* 3.5 16.9 - - + +
231G PHE* 1.3 80.3 - - - +
233G VAL* 1.3 67.8 + - - +
247G GLY* 3.2 6.0 - - - -
248G THR* 2.8 45.7 + - + +
251G SER* 6.0 4.0 - - - -
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Residues in contact with VAL 233 (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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127G PRO* 4.4 3.4 - - + +
128G GLN 3.3 31.2 - - - +
129G VAL* 4.2 3.5 - - - +
130G GLY 3.3 17.9 + - - +
131G ASP* 2.8 21.2 + - + +
133G LEU* 3.7 30.3 - - + -
232G THR* 1.3 77.1 - - - +
234G ARG* 1.3 62.4 + - - +
235G ASN 4.1 8.3 - - - +
236G VAL* 4.2 13.0 - - + -
245G VAL* 3.6 27.4 - - + -
246G ASP 3.4 4.7 - - - +
248G THR* 4.1 4.7 - - - +
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Residues in contact with ARG 234 (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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1152B PHE* 4.8 2.9 - - - -
129G VAL* 3.3 20.1 - - - +
158G LYS* 5.3 8.0 - - - +
160G ASN* 4.9 12.0 - - - +
161G ASN* 3.5 26.3 + - - +
232G THR 3.4 0.2 + - - -
233G VAL* 1.3 73.7 - - - +
235G ASN* 1.3 69.0 + - + +
237G HIS* 6.4 0.2 - - - -
246G ASP* 2.5 59.9 + - + +
247G GLY 3.6 3.1 - - - -
248G THR* 3.5 24.5 - - + -
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Residues in contact with ASN 235 (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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1152B PHE* 3.2 35.7 - - + -
1153B ILE 4.3 1.9 - - - +
1154B ASP* 4.7 2.3 - - - +
1155B ASP* 3.5 22.8 + - - +
129G VAL* 4.3 6.4 - - - +
233G VAL* 4.1 1.7 - - - +
234G ARG* 1.3 93.2 - - + +
236G VAL* 1.3 83.3 + - - +
237G HIS* 4.0 14.9 + - - +
244G SER 3.8 1.0 - - - +
245G VAL* 3.6 1.2 - - - -
246G ASP* 2.7 40.5 + - + +
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Residues in contact with VAL 236 (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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1154B ASP* 3.5 20.6 - - - +
1155B ASP* 2.9 17.8 - - - +
73G TYR* 4.7 16.2 - - + +
127G PRO* 3.3 37.7 - - + +
128G GLN* 5.3 1.6 - - - -
129G VAL* 5.2 3.7 - - + +
233G VAL* 4.2 14.6 - - + -
235G ASN* 1.3 84.1 + - - +
237G HIS* 1.3 65.4 + - - +
238G THR* 4.5 2.0 + - - +
243G VAL* 3.9 24.5 - - + -
244G SER 3.8 4.0 - - - +
245G VAL* 4.6 6.1 - - + -
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Residues in contact with HIS 237 (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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1155B ASP* 3.9 14.3 + - - +
156G SER* 5.1 4.2 + - - -
158G LYS* 5.5 12.6 - - - -
234G ARG* 6.4 0.2 - - - -
235G ASN* 4.2 22.2 + - - -
236G VAL* 1.3 73.0 - - - +
238G THR* 1.3 61.4 + - - +
239G THR* 5.3 0.9 - - - +
240G GLY* 4.9 7.6 + - - +
242G VAL 4.6 1.9 - - - +
243G VAL* 3.7 29.3 - - - +
244G SER* 2.9 45.4 + - - +
246G ASP* 4.5 19.8 + - + +
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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