Contacts of the helix formed by residues 133 - 142 (chain J) in PDB entry 5GJQ
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 PRO 133 (chain J).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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111J ASN* 5.8 3.6 - - - +
132J ASP* 1.3 92.7 - - + +
134J LEU* 1.3 72.1 + - + +
135J VAL 3.1 1.8 - - - -
136J SER* 2.1 29.8 + - - +
137J LEU* 2.9 7.6 + - - +
223J PHE* 4.2 24.9 - - + +
224J ILE* 4.6 2.8 - - - +
237J MET* 2.5 30.5 - - + -
240J GLU* 5.7 0.9 - - - +
241J HIS* 5.9 1.6 - - + -
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Residues in contact with LEU 134 (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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132J ASP* 4.5 0.2 - - - +
133J PRO* 1.3 72.9 - - + +
135J VAL* 1.3 69.1 + - + +
137J LEU* 3.2 25.4 + - + -
138J MET* 2.9 33.6 + - + +
210J THR* 4.3 20.9 - - - +
211J PHE 6.2 0.7 - - - +
212J ILE* 4.3 24.7 - - + -
224J ILE* 5.1 0.4 - - + -
234J LEU* 5.9 0.9 - - + -
237J MET* 2.8 45.9 - - + +
241J HIS* 4.2 25.6 - - + +
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Residues in contact with VAL 135 (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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131J VAL* 4.0 27.4 - - + +
132J ASP* 4.4 10.8 - - + +
133J PRO 3.1 0.6 - - - -
134J LEU* 1.3 87.0 - - + +
136J SER* 1.3 59.2 + - - +
138J MET* 3.2 8.2 + - + +
139J MET* 2.9 47.1 + - + +
241J HIS* 5.3 7.4 - - + +
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Residues in contact with SER 136 (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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131J VAL* 5.5 5.5 - - - +
132J ASP 4.2 7.0 + - - -
133J PRO* 2.1 39.8 + - - +
135J VAL* 1.3 79.7 - - - +
137J LEU* 1.3 55.5 + - - -
139J MET* 3.2 8.5 + - - +
140J VAL* 2.9 35.2 + - - +
223J PHE* 3.7 32.9 - - - -
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Residues in contact with LEU 137 (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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133J PRO 2.9 2.8 + - - +
134J LEU* 3.2 26.0 + - + +
136J SER* 1.3 80.5 + - - +
138J MET* 1.3 58.5 + - - +
140J VAL* 3.2 8.1 + - + +
141J GLU* 2.9 32.9 + - + +
212J ILE* 4.1 17.9 - - + -
213J ARG 5.1 6.1 - - - +
214J VAL* 5.3 1.1 - - + -
220J VAL* 2.1 62.8 - - + -
223J PHE* 5.0 3.4 - - + -
224J ILE* 2.4 43.7 - - + -
234J LEU* 5.0 3.8 - - + -
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Residues in contact with MET 138 (chain J).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
134J LEU* 2.9 21.0 + - + +
135J VAL* 3.4 13.5 - - + +
137J LEU* 1.3 78.4 - - - +
139J MET* 1.3 64.0 + - + +
141J GLU* 3.2 5.9 + - + +
142J LYS* 3.0 11.4 + - - +
143J VAL* 2.9 50.5 - - + +
201J ARG* 4.6 16.4 - - - +
211J PHE* 3.6 23.6 - - - +
212J ILE* 5.2 0.9 - - - -
213J ARG 5.1 5.6 - - - +
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Residues in contact with MET 139 (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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135J VAL* 2.9 37.1 + - - +
136J SER* 3.2 10.5 + - - +
138J MET* 1.3 76.9 - - + +
140J VAL* 1.3 64.4 + - + +
142J LYS* 3.2 15.1 + - + +
326K ARG* 3.1 15.6 + - - -
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Residues in contact with VAL 140 (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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136J SER* 2.9 20.4 + - - +
137J LEU* 3.2 8.7 + - - +
139J MET* 1.3 76.5 - - + +
141J GLU* 1.3 64.5 + - - +
219J LEU* 4.2 17.9 - - + -
220J VAL* 4.5 16.4 - - + -
223J PHE* 4.1 26.2 - - + -
290K LEU* 4.3 8.7 - - + -
293K LEU* 4.0 22.2 - - + -
294K ASN* 6.1 0.7 - - - +
320K ALA* 4.2 12.3 - - + +
323K ARG* 4.3 0.3 + - - -
326K ARG* 3.2 19.1 + - - +
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Residues in contact with GLU 141 (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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137J LEU* 2.9 17.2 + - + +
138J MET* 3.6 10.3 - - + +
139J MET 3.2 0.2 - - - -
140J VAL* 1.3 82.3 - - - +
142J LYS* 1.3 70.9 + - - +
143J VAL* 4.1 8.0 - - + +
213J ARG* 3.2 57.5 + - + +
215J SER* 3.8 16.2 + - - -
217J SER* 5.1 2.8 - - - -
220J VAL* 3.8 21.5 - - + +
320K ALA* 5.5 1.6 - - - +
323K ARG* 3.0 44.7 + - - +
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Residues in contact with LYS 142 (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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138J MET* 3.0 14.6 + - - -
139J MET* 3.2 16.0 + - + +
141J GLU* 1.3 81.1 - - - +
143J VAL* 1.3 62.1 + - - +
144J PRO* 3.8 9.6 - - + +
297K ASP* 2.8 28.3 + - - +
323K ARG* 3.7 18.0 - - + +
324K PRO* 2.8 30.5 + - + +
325K GLY* 3.2 15.0 - - - -
326K ARG* 3.6 22.7 - - - +
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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