Contacts of the strand formed by residues 124 - 134 (chain O) in PDB entry 2GTL
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 HIS 124 (chain O).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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109O ILE* 4.7 12.5 - - + +
110O GLY 3.2 14.8 + - - +
111O ASP* 3.5 27.7 + - + -
122O PRO* 3.4 22.7 - - - +
123O GLU* 1.3 95.5 + - + +
125O MET* 1.3 69.7 + - - +
126O THR* 5.8 1.3 - - - +
150O ILE* 4.9 3.6 - - - +
151O GLU 5.6 1.6 + - - -
216O PHE* 4.3 2.0 - - - -
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Residues in contact with MET 125 (chain O).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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109O ILE* 4.8 0.7 - - - -
110O GLY* 2.9 28.0 + - - -
118O THR* 4.6 9.4 - - + -
122O PRO* 4.9 1.1 - - + -
124O HIS* 1.3 85.3 - - - +
126O THR* 1.3 62.8 + - - +
148O ILE* 4.1 25.4 - - + -
149O GLU 3.8 8.5 - - - +
150O ILE* 4.2 22.2 - - + +
188O LEU* 5.3 5.2 - - - -
204O ILE* 3.5 31.2 - - + -
216O PHE* 3.9 25.1 - - + -
218O PHE* 3.7 29.6 - - + -
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Residues in contact with THR 126 (chain O).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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107O LYS* 4.8 17.9 - - + +
108O PHE 3.5 6.3 - - - +
109O ILE* 2.9 29.5 - - + +
124O HIS* 5.8 0.9 - - - +
125O MET* 1.3 73.6 + - - +
127O LEU* 1.3 69.4 + - - +
128O ALA 4.0 2.0 - - - +
148O ILE* 3.6 6.2 - - - +
149O GLU* 2.9 60.3 + - - +
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Residues in contact with LEU 127 (chain O).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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107O LYS* 3.6 0.2 - - - -
108O PHE* 2.7 38.3 + - + +
125O MET* 6.2 0.2 - - - -
126O THR* 1.3 78.1 - - - +
128O ALA* 1.3 58.7 + - - +
129O PHE* 3.6 33.3 - - + -
146O VAL* 4.7 4.7 - - + -
147O HIS 3.9 2.2 - - - +
148O ILE* 3.6 35.9 - - + -
176O LEU* 4.8 0.9 - - + -
178O ILE* 3.9 25.4 - - + -
188O LEU* 4.0 18.4 - - + -
200O PHE* 4.1 20.4 - - + -
218O PHE* 4.0 10.8 - - + -
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Residues in contact with ALA 128 (chain O).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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106O ASP 3.9 4.3 - - - -
107O LYS* 4.2 26.2 - - + -
126O THR* 4.0 2.3 - - + +
127O LEU* 1.3 72.1 - - - +
129O PHE* 1.3 64.3 + - - +
130O GLU 3.6 1.3 + - - -
146O VAL* 3.4 3.9 - - - +
147O HIS* 2.9 49.9 + - + +
149O GLU* 4.7 13.2 - - - +
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Residues in contact with PHE 129 (chain O).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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102O THR* 3.1 55.6 - - + -
103O LYS 4.3 16.2 - - - +
104O ALA* 4.4 1.3 - - - +
105O GLY* 2.9 26.7 + - - -
106O ASP 3.1 20.5 + - - +
108O PHE* 3.8 11.0 - + - -
127O LEU* 3.6 38.6 - - + -
128O ALA* 1.3 72.6 - - - +
130O GLU* 1.3 61.4 + - - +
131O SER 3.8 2.0 - - - +
144O LEU* 3.6 20.9 - - + -
145O HIS 4.0 2.5 - - - +
146O VAL* 3.3 22.2 - - + -
176O LEU* 3.5 17.3 - - + -
200O PHE* 5.8 0.2 - + - -
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Residues in contact with GLU 130 (chain O).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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104O ALA* 3.4 13.1 - - - +
105O GLY 4.3 1.4 + - - -
128O ALA 3.6 4.3 + - - +
129O PHE* 1.3 74.8 - - - +
131O SER* 1.3 60.5 + - - +
145O HIS* 2.9 38.7 + - + +
146O VAL* 5.0 1.6 - - - -
147O HIS* 2.8 39.6 + - + +
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Residues in contact with SER 131 (chain O).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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104O ALA* 4.0 6.9 + - - -
129O PHE* 5.1 2.1 - - - +
130O GLU* 1.3 83.1 + - - +
132O SER* 1.3 64.2 + - - +
144O LEU* 3.5 3.7 - - - +
145O HIS* 3.0 45.7 + - - +
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Residues in contact with SER 132 (chain O).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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100O LEU* 4.5 12.4 - - - +
103O LYS* 4.1 7.2 - - - +
104O ALA* 3.5 27.2 + - - +
129O PHE* 6.2 0.2 - - - -
131O SER* 1.3 78.8 - - - +
133O SER* 1.3 62.0 + - - +
134O ILE* 5.9 0.2 - - - -
142O ALA* 6.0 0.2 - - - -
143O ASP 3.3 7.9 - - - -
144O LEU* 3.4 23.1 - - - -
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Residues in contact with SER 133 (chain O).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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132O SER* 1.3 76.5 - - - +
134O ILE* 1.3 65.1 + - - +
135O ALA 4.1 0.7 + - - -
142O ALA* 4.8 0.4 - - - -
143O ASP* 3.1 37.5 + - - +
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Residues in contact with ILE 134 (chain O).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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100O LEU* 4.8 9.0 - - + -
132O SER 5.9 0.2 - - - -
133O SER* 1.3 76.5 - - - +
135O ALA* 1.3 77.2 + - - +
136O ALA* 3.2 5.0 + - - -
138O PHE 4.1 2.2 - - - +
139O THR* 4.0 29.4 - - + +
141O ILE 4.2 7.0 - - - +
142O ALA* 3.5 28.0 - - + -
171O PHE* 4.1 19.5 - - + -
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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