Contacts of the strand formed by residues 194 - 204 (chain G) in PDB entry 5MGX
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 LEU 194 (chain G).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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129G THR* 3.8 26.0 - - + -
130G SER 3.6 6.3 - - - +
131G LEU* 3.8 29.2 - - + -
137G VAL* 4.8 0.7 - - + -
153G ILE* 4.8 5.4 - - + -
172G THR* 3.4 3.6 - - - -
173G ALA 2.8 40.6 + - - -
178G CYS* 3.7 22.7 - - + -
179G TYR* 3.7 32.3 - - + -
188G ILE* 4.3 12.1 - - + -
192G ALA 3.9 8.3 - - - +
193G ALA* 1.3 75.5 - - - +
195G CYS* 1.3 62.2 + - - +
196G LEU* 3.4 15.1 - - + +
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Residues in contact with CYS 195 (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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128G GLN 3.4 4.7 - - - +
129G THR* 3.6 0.7 - - - -
130G SER* 2.9 45.9 + - - +
131G LEU 4.4 14.6 - - - -
132G GLU* 4.9 9.4 - - - -
170G MET* 3.4 18.6 - - + +
171G VAL 3.5 5.4 - - - -
172G THR* 3.8 21.5 - - - -
194G LEU* 1.3 72.8 - - - +
196G LEU* 1.3 60.4 + - - +
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Residues in contact with LEU 196 (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 LEU* 3.7 17.9 - - + -
128G GLN 3.6 4.9 - - - -
129G THR* 4.9 8.5 - - + +
153G ILE* 3.8 27.6 - - + -
155G ALA* 4.0 13.0 - - + -
156G LEU* 4.3 16.8 - - + +
159G SER* 5.7 0.4 - - - +
169G ALA 3.8 0.2 - - - +
170G MET* 3.4 2.7 - - - +
171G VAL* 2.8 57.6 + - + +
173G ALA* 4.2 11.0 - - + -
178G CYS* 4.8 0.4 - - - -
194G LEU* 3.4 31.9 - - + +
195G CYS* 1.3 75.1 - - - +
197G GLU* 1.3 60.3 + - - +
198G VAL* 3.5 7.2 + - + +
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Residues in contact with GLU 197 (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 30.3 - - + +
126G HIS 3.5 5.2 - - - +
127G LEU* 3.6 0.7 - - - -
128G GLN* 2.9 63.3 + - + +
168G THR* 4.8 7.8 - - + +
169G ALA 3.6 3.8 - - - +
170G MET* 3.9 18.0 - - + +
196G LEU* 1.3 69.2 - - - +
198G VAL* 1.3 59.3 + - - +
199G THR* 5.6 0.4 - - - -
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Residues in contact with VAL 198 (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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125G VAL* 3.7 36.1 - - + -
126G HIS 3.4 3.6 - - - +
127G LEU* 3.9 13.5 - - + -
156G LEU* 4.8 8.3 - - + -
159G SER* 5.3 1.8 - - - +
160G VAL* 4.5 8.5 - - + -
163G MET* 3.4 26.6 - - - +
168G THR* 3.3 2.6 - - - +
169G ALA 2.8 41.3 + - - +
171G VAL* 4.5 13.9 - - + -
196G LEU* 4.1 10.8 - - + +
197G GLU* 1.3 74.3 - - - +
199G THR* 1.4 64.7 + - - +
200G LEU 4.1 0.2 - - - -
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Residues in contact with THR 199 (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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125G VAL* 3.4 2.3 - - - -
126G HIS* 3.1 43.3 + - + +
166G GLY* 4.6 5.8 - - - +
167G GLU 3.4 6.3 - - - +
168G THR* 2.7 32.7 + - - +
197G GLU 5.5 0.5 + - - -
198G VAL* 1.4 71.3 - - - +
200G LEU* 1.3 66.5 + - - +
201G LYS* 3.2 15.0 + - + +
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Residues in contact with LEU 200 (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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117G PRO* 3.7 19.7 - - + -
123G VAL* 4.0 14.6 - - + -
124G THR 3.9 1.6 - - - +
125G VAL* 3.9 22.4 - - + -
160G VAL* 4.2 7.9 - - + -
163G MET* 3.6 32.8 - - + +
164G ASP 3.6 25.1 - - - +
165G VAL* 3.9 13.7 - - + -
166G GLY* 2.8 32.7 + - - -
167G GLU 2.9 10.3 + - - +
198G VAL* 4.1 1.2 - - - +
199G THR* 1.3 70.4 - - - +
201G LYS* 1.3 59.4 + - - +
202G THR 3.7 19.5 - - - +
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Residues in contact with LYS 201 (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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124G THR* 2.9 24.2 + - + +
125G VAL 4.1 2.9 - - - +
126G HIS* 4.0 24.4 + - + +
141G PRO* 2.8 35.7 + - - +
142G GLU* 3.7 14.5 - - - +
165G VAL* 3.4 14.1 - - - +
166G GLY* 4.6 2.3 + - - -
199G THR* 3.8 18.6 - - + +
200G LEU* 1.3 73.9 - - - +
202G THR* 1.3 70.2 + - + +
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Residues in contact with THR 202 (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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122G VAL 4.6 0.4 - - - -
123G VAL* 3.4 3.7 - - - -
124G THR* 3.1 46.5 + - - +
165G VAL* 3.9 8.1 - - + -
200G LEU* 3.7 6.4 - - - +
201G LYS* 1.3 84.8 - - + +
203G ALA* 1.3 62.1 + - - +
204G VAL* 4.3 10.5 - - + +
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Residues in contact with ALA 203 (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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117G PRO* 3.9 4.7 - - + -
121G GLN* 3.5 24.6 + - - +
122G VAL 3.7 6.7 - - - -
123G VAL* 3.8 15.3 - - + -
165G VAL* 3.7 27.4 - - + +
200G LEU* 5.1 0.4 - - + -
202G THR* 1.3 76.4 - - - +
204G VAL* 1.3 63.2 + - - +
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Residues in contact with VAL 204 (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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121G GLN* 3.3 8.3 - - - +
122G VAL* 2.9 49.7 + - + +
202G THR* 5.0 9.4 - - + +
203G ALA* 1.3 80.8 - - - +
205G ASP* 1.3 68.5 + - - +
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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