Contacts of the strand formed by residues 132 - 143 (chain E) in PDB entry 6GJH
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 GLY 132 (chain E).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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128E GLN* 3.2 11.4 - - - +
129E ASP* 2.8 40.8 + - - +
131E HIS* 1.3 80.4 - - - +
133E TYR* 1.3 67.8 + - - -
140F ARG* 4.1 0.9 - - - +
141F LYS 3.6 8.5 - - - -
142F TYR* 5.3 0.9 - - - -
143F THR 6.0 0.9 - - - -
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Residues in contact with TYR 133 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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126E GLU* 3.5 32.5 - - + +
127E ARG* 3.2 16.6 - - - +
128E GLN* 4.0 33.0 + - + -
132E GLY* 1.3 79.1 - - - -
134E ILE* 1.3 62.3 + - - +
139F THR 4.4 0.7 - - - -
140F ARG* 3.2 9.3 - - - +
141F LYS* 2.8 51.3 + - + -
143F THR* 4.7 15.3 - - - -
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Residues in contact with ILE 134 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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124E HIS* 3.6 5.2 - - + -
126E GLU* 3.3 4.0 - - - +
127E ARG* 2.9 47.0 + - + +
129E ASP* 4.1 13.9 - - + +
133E TYR* 1.3 76.6 - - - +
135E SER* 1.3 74.2 + - - +
136E ARG* 3.7 43.3 - - + +
138F PHE* 4.1 11.7 - - + -
139F THR 3.3 14.4 - - - +
140F ARG* 3.5 41.5 - - + +
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Residues in contact with SER 135 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
124E HIS* 3.6 17.5 - - - -
125E GLU* 4.6 0.9 - - - -
126E GLU* 3.8 19.7 + - - +
134E ILE* 1.3 76.5 - - - +
136E ARG* 1.3 64.7 + - - +
137F CYS* 6.2 0.2 - - - -
138F PHE* 3.1 8.5 - - - +
139F THR* 2.9 50.3 + - - -
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Residues in contact with ARG 136 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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103E HIS* 3.4 55.3 + - - +
104E PHE* 3.7 15.8 - - + -
123E LYS* 3.4 2.6 + - - +
124E HIS* 3.2 48.4 + - - +
127E ARG* 4.0 12.1 - - - +
129E ASP* 5.1 4.4 + - - +
134E ILE* 3.7 39.8 - - + +
135E SER* 1.3 80.6 - - - +
137E CYS* 1.3 65.1 + - - +
84F GLY* 5.2 10.3 + - - -
137F CYS* 3.5 6.5 - - - +
138F PHE* 4.5 7.0 - - + -
140F ARG* 4.2 10.1 - - - +
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Residues in contact with CYS 137 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
104E PHE* 4.6 0.9 - - - -
122E GLY 3.2 11.9 - - - +
123E LYS* 4.2 22.2 - - + +
136E ARG* 1.3 76.8 - - - +
138E PHE* 1.3 68.0 + - - +
136F ARG* 3.5 2.8 - - - +
137F CYS* 2.0 78.0 + - - +
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Residues in contact with PHE 138 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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99E LEU* 4.2 16.2 - - + -
101E VAL* 3.9 24.5 - - + -
104E PHE* 3.8 33.0 - + - -
109E LEU* 4.4 2.2 - - + -
120E ILE* 3.7 26.7 - - + -
121E THR* 3.4 2.6 - - - +
122E GLY* 2.9 51.4 + - - +
137E CYS* 1.3 79.2 - - - +
139E THR* 1.3 73.8 + - - +
140E ARG* 3.9 8.7 - - + -
134F ILE* 4.3 13.5 - - + -
135F SER* 3.2 16.4 - - - +
136F ARG* 4.4 9.2 - - + +
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Residues in contact with THR 139 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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119E GLU* 3.7 33.4 - - + +
120E ILE 3.2 5.4 - - - +
121E THR* 3.4 18.4 + - - +
138E PHE* 1.3 80.2 + - - +
140E ARG* 1.3 63.2 + - - +
141E LYS* 4.7 11.2 - - - +
126F GLU* 5.4 3.6 - - - +
133F TYR 4.1 0.5 - - - +
134F ILE* 3.2 4.3 - - - -
135F SER* 3.0 41.4 + - - -
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Residues in contact with ARG 140 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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99E LEU* 4.1 23.2 - - + +
118E VAL 3.8 0.5 - - - +
119E GLU* 3.5 3.3 - - - +
120E ILE* 2.8 36.3 + - + +
138E PHE* 3.9 13.4 - - + -
139E THR* 1.3 74.0 - - - +
141E LYS* 1.3 68.0 + - - +
142E TYR* 3.0 38.6 - - + -
129F ASP* 2.7 42.0 + - - -
131F HIS* 3.5 24.9 - - - +
132F GLY 3.6 12.7 + - - +
133F TYR 3.4 7.0 - - - +
134F ILE* 3.3 29.9 - - + +
136F ARG* 3.7 5.5 - - - +
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Residues in contact with LYS 141 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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117E VAL* 3.9 19.3 - - + -
118E VAL 3.2 9.9 - - - +
119E GLU* 4.0 28.0 - - + -
139E THR* 4.7 8.7 - - + +
140E ARG* 1.3 80.4 - - - +
142E TYR* 1.3 72.1 + - - +
126F GLU* 2.7 35.7 + - - +
132F GLY* 4.6 4.2 - - - -
133F TYR* 3.1 33.8 + - + +
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Residues in contact with TYR 142 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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95E TRP* 4.3 19.5 - + + -
97E VAL* 3.9 40.2 - - + -
98E SER 4.3 6.8 + - - -
99E LEU* 4.3 18.7 - - + +
117E VAL* 3.3 5.8 - - - -
118E VAL* 2.8 38.1 + - + +
120E ILE* 3.7 30.3 - - + -
140E ARG* 3.0 34.3 + - + -
141E LYS* 1.3 77.9 - - - +
143E THR* 1.3 62.8 + - - +
144E LEU 3.7 0.3 + - - -
131F HIS* 4.2 25.3 - - + +
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Residues in contact with THR 143 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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95E TRP* 4.7 7.4 + - - -
116E GLY 3.9 9.4 - - - +
117E VAL* 4.3 13.2 - - + +
142E TYR* 1.3 71.6 - - - +
144E LEU* 1.3 75.3 + - - +
145E PRO* 4.3 2.1 - - - +
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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