Contacts of the strand formed by residues 189 - 196 (chain B) in PDB entry 3GGE
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 GLU 189 (chain B).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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121B TYR* 3.8 9.2 - - - -
122B LYS* 3.2 25.1 + - - +
186B LYS* 3.6 38.4 + - - +
187B LYS 3.3 7.9 - - - +
188B GLU* 1.3 84.1 - - - +
190B LEU* 1.3 69.2 + - - +
191B PHE* 3.7 2.8 + - - -
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Residues in contact with LEU 190 (chain B).
Click here for Legend to table.
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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119B ASN* 3.8 22.4 - - + +
120B VAL* 3.2 36.3 - - - +
121B TYR* 3.7 18.5 - - + +
166B ASN* 4.7 2.1 + - - +
189B GLU* 1.3 79.5 - - - +
191B PHE* 1.3 59.1 + - - +
192B THR* 6.1 1.3 - - + -
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Residues in contact with PHE 191 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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119B ASN* 3.3 4.3 - - - +
120B VAL* 2.8 70.8 + - + +
122B LYS* 4.3 9.6 - - + -
127B LEU* 4.0 30.3 - - + -
150B ILE* 5.0 4.0 - - + -
165B ILE* 4.6 4.0 - - + -
166B ASN* 3.4 23.1 - - - +
182B LEU* 4.2 6.3 - - + -
185B LEU* 3.6 31.4 - - + -
189B GLU 4.3 6.3 - - - -
190B LEU* 1.3 75.9 - - - +
192B THR* 1.3 76.1 + - - +
193B MET* 3.9 27.4 - - + -
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Residues in contact with THR 192 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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117B GLU* 4.9 14.6 - - - +
118B VAL* 3.1 8.1 - - - -
119B ASN* 2.9 25.8 - - - +
165B ILE* 3.7 0.9 - - - -
166B ASN* 3.1 40.1 + - - +
167B GLY 4.5 3.3 + - - -
190B LEU* 5.8 2.5 - - + -
191B PHE* 1.3 81.8 - - - +
193B MET* 1.3 71.6 + - - +
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Residues in contact with MET 193 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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116B LYS 3.7 0.5 - - - +
117B GLU* 3.3 6.7 - - - +
118B VAL* 2.8 49.2 + - + +
120B VAL* 5.6 0.7 - - - -
129B LEU* 5.5 6.3 - - + -
141B ILE* 6.3 0.7 - - + -
150B ILE* 5.9 2.9 - - - -
156B ILE* 5.3 7.2 - - - -
162B ILE* 3.7 35.2 - - + -
164B SER* 3.4 15.0 - - - +
165B ILE* 4.1 6.1 - - + -
182B LEU* 3.7 32.3 - - + -
191B PHE* 3.9 19.1 - - + -
192B THR* 1.3 82.0 - - - +
194B LYS* 1.3 66.8 + - - +
195B LEU* 4.5 12.6 - - + -
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Residues in contact with LYS 194 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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115B GLU* 3.8 25.4 + - + +
116B LYS 3.2 8.3 - - - +
117B GLU* 3.4 29.8 - - + -
162B ILE* 3.9 0.3 - - - -
163B GLU* 3.0 43.0 + - + +
164B SER* 3.4 27.1 + - - +
193B MET* 1.3 78.3 - - - +
195B LEU* 1.3 65.8 + - - +
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Residues in contact with LEU 195 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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114B ILE 3.9 0.3 - - - +
115B GLU* 3.3 5.4 - - - +
116B LYS* 2.8 50.4 + - - +
118B VAL* 4.4 12.8 - - + -
141B ILE* 5.0 4.5 - - + -
156B ILE* 4.0 31.2 - - + -
160B ASP* 3.8 28.7 - - + +
161B HIS 3.2 14.6 - - - +
162B ILE* 3.7 26.0 - - + -
163B GLU 4.6 0.2 - - - +
193B MET* 4.5 14.1 - - + -
194B LYS* 1.3 79.4 - - - +
196B ILE* 1.3 64.1 + - - +
197B GLU 4.3 0.2 + - - -
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Residues in contact with ILE 196 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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113B GLY* 4.6 17.9 - - - +
114B ILE 3.6 5.4 - - - +
115B GLU* 3.8 22.0 - - + +
138B TYR* 3.7 25.1 - - + +
160B ASP* 3.7 2.4 - - - -
161B HIS* 2.9 37.6 + - + +
163B GLU* 3.2 36.1 - - + +
195B LEU* 1.3 80.7 - - - +
197B GLU* 1.3 76.9 + - - +
198B PRO 3.7 0.2 - - - -
169C ASN* 5.1 0.2 - - - +
171C VAL* 4.1 17.9 - - + -
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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