Contacts of the strand formed by residues 140 - 152 (chain I) in PDB entry 2IUO
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 I).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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132I LYS* 3.1 35.1 + - + -
133I VAL 3.6 6.3 - - - +
134I ALA* 5.5 2.9 - - - -
139I GLY* 1.3 79.9 - - - +
141I ARG* 1.3 63.6 + - - +
116J PHE* 3.5 31.2 - - + +
149J LYS* 3.6 10.4 - - - +
150J TYR* 2.9 45.6 + - + +
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Residues in contact with ARG 141 (chain I).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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133I VAL* 2.7 45.2 + - + +
134I ALA 5.2 1.1 - - - -
135I ASP* 3.0 46.6 + - + +
136I PRO* 5.2 3.4 - - - -
137I GLU* 5.0 3.8 + - - -
140I GLU* 1.3 76.8 - - - +
142I ALA* 1.3 59.4 + - - +
143I VAL* 5.0 0.9 - - + -
116J PHE* 3.3 13.9 - - - -
125J ASN* 2.8 43.0 + - - +
126J PHE* 4.0 2.6 - - - +
127J LYS* 4.5 9.5 - - - +
147J ASP* 2.8 54.2 + - - +
148J GLY 3.3 7.6 - - - +
149J LYS* 3.8 8.6 - - + +
150J TYR 4.3 0.4 - - - +
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Residues in contact with ALA 142 (chain I).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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130I VAL* 4.6 4.0 - - + -
131I LYS 3.4 4.9 - - - +
141I ARG* 1.3 73.2 - - - +
143I VAL* 1.3 61.4 - - - +
144I ILE* 3.9 14.7 - - + +
116J PHE* 3.5 14.0 - - + -
121J ILE* 3.4 39.8 - - + +
146J LEU 3.4 1.9 - - - +
147J ASP* 3.4 4.0 - - - +
148J GLY 2.8 31.8 + - - -
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Residues in contact with VAL 143 (chain I).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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129I ASP 3.7 1.6 - - - +
130I VAL* 3.7 1.0 - - - -
131I LYS* 2.7 46.0 + - + +
133I VAL* 3.7 29.2 - - + -
141I ARG* 5.0 1.1 - - + -
142I ALA* 1.3 74.9 - - - +
144I ILE* 1.3 60.2 + - - +
145I THR* 3.9 9.7 + - - +
145J THR* 3.2 33.9 - - + -
146J LEU 3.3 2.5 - - - +
147J ASP* 3.9 21.3 - - + +
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Residues in contact with ILE 144 (chain I).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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97I PHE* 3.5 33.0 - - + -
100I MET* 5.7 0.2 - - + -
128I LEU* 4.6 4.9 - - + -
129I ASP 3.3 9.4 - - - +
130I VAL* 4.1 22.7 - - + -
142I ALA* 3.9 21.1 - - + +
143I VAL* 1.3 75.5 - - - +
145I THR* 1.3 61.7 - - - +
146I LEU* 4.0 20.6 - - + -
108J LEU* 4.1 17.9 - - + -
112J VAL* 5.4 0.9 - - + -
121J ILE* 4.3 9.2 - - + -
144J ILE 3.6 1.4 - - - +
145J THR* 3.5 1.7 - - - -
146J LEU* 2.7 60.3 + - + +
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Residues in contact with THR 145 (chain I).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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127I LYS* 3.7 1.2 - - - +
128I LEU* 3.2 8.1 - - - -
129I ASP* 3.0 48.0 + - - +
131I LYS* 5.8 2.8 - - - +
143I VAL* 3.9 12.5 + - - +
144I ILE* 1.3 72.4 - - - +
146I LEU* 1.3 66.3 + - - +
147I ASP* 4.6 7.4 - - + +
143J VAL* 3.2 34.5 - - + -
144J ILE 3.6 3.1 - - - +
145J THR* 4.3 8.0 + - - +
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Residues in contact with LEU 146 (chain I).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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108I LEU* 6.4 0.2 - - + -
126I PHE* 3.8 26.5 - - + -
127I LYS 3.9 2.5 - - - -
128I LEU* 4.1 11.7 - - + -
144I ILE* 4.0 17.3 - - + -
145I THR* 1.3 76.7 - - - +
147I ASP* 1.3 60.2 + - - +
148I GLY 3.9 1.1 - - - -
97J PHE* 4.4 10.8 - - + -
100J MET* 4.1 20.4 - - + -
108J LEU* 6.0 1.1 - - + -
142J ALA 3.4 3.8 - - - +
143J VAL* 3.4 2.4 - - - +
144J ILE* 2.8 61.4 + - + +
146J LEU* 4.0 28.7 - - + -
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Residues in contact with ASP 147 (chain I).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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126I PHE* 3.1 3.2 - - - -
127I LYS* 2.8 65.8 + - + +
145I THR* 4.7 8.7 - - + +
146I LEU* 1.3 72.1 - - - +
148I GLY* 1.3 56.9 + - - +
141J ARG* 2.7 48.0 + - - +
142J ALA 3.6 3.9 - - - +
143J VAL* 4.1 16.5 - - + +
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Residues in contact with GLY 148 (chain I).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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121I ILE* 3.7 12.9 - - - +
122I GLY 3.6 15.9 - - - -
125I ASN 3.4 8.1 - - - -
126I PHE* 4.0 2.2 - - - -
146I LEU 3.9 1.2 - - - -
147I ASP* 1.3 75.0 + - - +
149I LYS* 1.3 64.1 + - - -
141J ARG* 3.3 6.9 - - - -
142J ALA 2.8 36.9 + - - -
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Residues in contact with LYS 149 (chain I).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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121I ILE* 4.5 1.3 - - - -
122I GLY* 3.0 22.9 + - - +
125I ASN* 3.0 41.3 + - + +
148I GLY* 1.3 72.6 - - - -
150I TYR* 1.3 75.1 + - - +
151I LEU* 3.5 16.3 + - + +
135J ASP* 2.9 28.0 - - - +
138J GLY 3.0 30.3 + - - -
139J GLY* 4.5 3.4 - - - -
140J GLU 3.7 15.3 - - - +
141J ARG* 3.8 7.7 - - + +
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Residues in contact with TYR 150 (chain I).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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112I VAL* 5.0 1.3 - - + -
116I PHE* 3.3 57.0 + + + -
117I GLY* 3.2 23.4 - - - -
118I ASP 2.8 25.9 + - - -
120I ILE 3.4 15.3 - - - -
121I ILE* 3.9 8.0 - - + +
148I GLY 3.7 2.4 + - - -
149I LYS* 1.3 82.7 + - - +
151I LEU* 1.3 78.5 + - - +
152I PRO* 3.5 32.8 - - + +
140J GLU* 2.7 45.9 + - + +
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Residues in contact with LEU 151 (chain I).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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122C GLY* 6.3 0.2 - - - -
124C ILE* 3.4 13.1 - - + +
125C ASN* 5.5 9.0 - - + +
151C LEU* 3.3 40.6 - - + -
1157C BR 4.6 6.3 - - + -
119I GLY* 3.3 1.0 - - - -
120I ILE* 2.9 55.6 + - + -
122I GLY* 4.8 3.4 - - - +
125I ASN* 5.8 2.7 - - + -
149I LYS* 3.5 29.2 - - + +
150I TYR* 1.3 85.2 - - - +
152I PRO* 1.3 69.8 - - + +
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Residues in contact with PRO 152 (chain I).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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124C ILE* 3.3 17.7 - - - +
125C ASN* 4.6 4.5 + - - +
118I ASP 3.5 7.0 - - - +
150I TYR* 3.5 35.6 - - + +
151I LEU* 1.3 83.3 - - - +
153I THR* 1.3 58.7 + - - +
154I LYS* 3.6 43.0 + - + +
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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