Contacts of the strand formed by residues 140 - 152 (chain E) in PDB entry 2IVB
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 140 (chain E).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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132E LYS* 3.4 28.7 + - + +
133E VAL 3.3 13.2 - - - +
134E ALA* 5.1 1.3 - - - -
135E ASP* 3.8 1.9 - - - +
139E GLY* 1.3 82.2 - - - +
141E ARG* 1.3 65.0 + - - +
115G LYS 5.1 0.5 - - - +
116G PHE* 4.2 19.4 - - + +
149G LYS* 3.4 12.7 - - - +
150G TYR* 3.0 51.1 + - + +
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Residues in contact with ARG 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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133E VAL* 2.8 46.3 + - + +
134E ALA 4.7 2.7 - - - -
135E ASP* 3.7 35.2 + - + +
136E PRO* 5.0 3.4 - - - -
140E GLU* 1.3 80.5 - - - +
142E ALA* 1.3 60.3 + - - +
116G PHE* 3.3 11.3 - - - -
125G ASN* 2.9 50.7 + - - +
126G PHE* 4.0 2.4 - - - +
127G LYS* 4.6 3.4 - - - +
147G ASP* 2.8 43.9 + - - +
148G GLY* 3.3 7.3 - - - +
149G LYS* 3.9 11.9 - - - +
150G TYR 4.2 0.9 - - - +
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Residues in contact with ALA 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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130E VAL* 4.8 2.7 - - + -
131E LYS 3.3 5.6 - - - +
141E ARG* 1.3 74.0 - - - +
143E VAL* 1.3 59.9 + - - +
144E ILE* 4.0 13.1 - - + +
116G PHE* 3.5 20.4 - - + -
121G ILE* 3.7 32.5 - - + +
146G LEU 3.6 1.6 - - - +
147G ASP* 3.2 7.5 - - - +
148G GLY 2.9 27.7 + - - +
150G TYR 4.8 0.8 - - - +
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Residues in contact with VAL 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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129E ASP* 3.7 3.6 - - - +
131E LYS* 2.7 49.0 + - + +
133E VAL* 3.9 30.7 - - + -
142E ALA* 1.3 75.9 - - - +
144E ILE* 1.3 57.9 + - - +
145E THR* 4.0 9.9 + - - +
145G THR* 3.5 28.9 - - + -
146G LEU 3.5 2.7 - - - -
147G ASP* 4.2 17.5 - - + +
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Residues in contact with ILE 144 (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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97E PHE* 3.6 34.5 - - + -
100E MET* 5.8 0.2 - - + -
128E LEU* 4.5 5.4 - - + -
129E ASP 3.3 8.7 - - - +
130E VAL* 4.0 23.6 - - + -
142E ALA* 4.3 17.3 - - + +
143E VAL* 1.3 74.1 - - - +
145E THR* 1.3 61.6 + - - +
146E LEU* 4.2 19.5 - - + -
108G LEU* 4.0 19.3 - - + -
112G VAL* 5.3 1.8 - - + -
121G ILE* 4.8 7.6 - - + -
144G ILE 3.7 1.7 - - - +
145G THR* 3.5 2.8 - - - -
146G LEU* 2.7 56.5 + - + +
148G GLY 6.0 0.2 - - - +
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Residues in contact with THR 145 (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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127E LYS* 3.5 1.9 - - + +
128E LEU* 3.3 8.7 - - - +
129E ASP* 3.0 48.2 + - - +
143E VAL* 4.4 12.8 + - - +
144E ILE* 1.3 73.6 + - - +
146E LEU* 1.3 68.8 + - - +
147E ASP* 4.5 6.7 - - + +
143G VAL* 3.4 31.0 - - + -
144G ILE 3.6 3.4 - - - +
145G THR* 4.5 7.1 + - - +
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Residues in contact with LEU 146 (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 PHE* 3.7 20.2 - - + -
127E LYS 3.7 2.9 - - - -
128E LEU* 3.7 30.5 - - + -
144E ILE* 4.2 8.5 - - + +
145E THR* 1.3 76.0 - - - +
147E ASP* 1.3 59.3 + - - +
148E GLY 3.8 0.9 - - - -
97G PHE* 5.0 11.9 - - + -
100G MET* 4.0 28.9 - - + -
142G ALA 3.6 2.9 - - - +
143G VAL* 3.4 3.3 - - - -
144G ILE* 2.9 63.2 + - + +
146G LEU* 4.0 19.5 - - + -
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Residues in contact with ASP 147 (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 PHE* 3.5 5.3 - - - -
127E LYS* 2.8 58.0 + - + +
145E THR* 4.7 10.5 - - + -
146E LEU* 1.3 70.1 - - - +
148E GLY* 1.3 58.5 + - - +
141G ARG* 3.0 39.6 + - - +
142G ALA 3.9 2.0 - - - -
143G VAL* 4.1 19.7 - - - +
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Residues in contact with GLY 148 (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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121E ILE* 4.2 13.2 - - - +
122E ALA 4.4 1.3 - - - -
125E ASN 3.5 11.7 - - - -
126E PHE* 4.2 7.4 - - - -
146E LEU 3.7 2.0 + - - -
147E ASP* 1.3 73.6 - - - +
149E LYS* 1.3 60.3 + - - -
141G ARG* 3.2 19.0 - - - +
142G ALA 2.9 33.1 + - - -
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Residues in contact with LYS 149 (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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121E ILE* 4.3 3.8 - - - +
122E ALA* 2.8 31.8 + - + +
125E ASN* 3.8 29.1 + - + +
148E GLY* 1.3 74.3 - - - -
150E TYR* 1.3 72.0 + - - +
151E LEU* 4.0 15.1 - - + +
135G ASP* 3.4 21.6 + - + +
137G GLU 5.5 0.2 + - - -
138G GLY 3.3 27.2 + - - -
139G GLY* 3.9 3.5 - - - -
140G GLU 3.4 28.0 - - - +
141G ARG* 3.8 12.6 - - + +
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Residues in contact with TYR 150 (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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112E VAL* 4.9 1.6 - - + -
116E PHE* 3.5 49.4 + - + -
117E GLY* 3.2 25.6 - - - -
118E ASP 2.7 25.8 + - - -
119E GLY* 4.0 4.5 - - - -
120E ILE 3.4 17.0 - - - -
121E ILE* 3.9 11.9 - - + +
148E GLY 4.4 0.2 + - - -
149E LYS* 1.3 79.0 - - - +
151E LEU* 1.3 76.0 + - - +
152E PRO* 3.6 29.7 - - + +
140G GLU* 2.8 43.3 + - + +
141G ARG* 4.5 0.8 - - - +
142G ALA 4.6 0.4 - - - +
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Residues in contact with LEU 151 (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 GLY* 3.3 0.7 - - - -
120E ILE* 2.8 51.5 + - + +
122E ALA* 3.4 30.7 - - + -
125E ASN* 5.9 2.2 - - + +
149E LYS* 4.0 21.1 - - + +
150E TYR* 1.3 82.4 - - - +
152E PRO* 1.3 73.4 - - + +
122F ALA* 5.6 2.0 - - + -
124F ILE* 3.6 10.6 - - + +
125F ASN* 6.1 3.1 - - + +
151F LEU* 3.5 38.4 - - + -
1161G AZI 5.0 0.4 - - - +
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Residues in contact with PRO 152 (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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118E ASP 3.4 7.6 - - - +
150E TYR* 3.6 32.5 - - + +
151E LEU* 1.3 89.7 - - + +
153E THR* 1.3 60.0 + - - +
154E LYS* 4.0 33.4 + - + +
124F ILE* 3.5 12.9 - - - +
125F ASN* 4.9 3.3 + - - +
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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