Contacts of the strand formed by residues 136 - 146 (chain E) in PDB entry 2IAN
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 LYS 136 (chain E).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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160D MET* 3.7 20.2 - - + -
163D MET* 4.5 15.9 - - + -
165D PHE* 3.6 47.1 - - + -
130E GLU* 3.3 21.0 - - - +
131E ILE* 3.5 4.5 + - - -
134E THR* 3.0 45.1 + - - +
135E GLN* 1.3 83.7 - - + +
137E ALA* 1.3 61.4 + - - +
191E ARG* 3.7 17.4 - - - +
192E VAL 3.8 8.5 - - - +
193E SER* 4.9 2.5 - - - -
194E ALA 4.0 1.3 - - - +
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Residues in contact with ALA 137 (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 PRO* 3.5 24.9 - - + -
130E GLU* 3.5 3.8 - - - -
131E ILE* 3.8 15.5 - - + -
136E LYS* 1.3 75.8 - - - +
138E THR* 1.3 62.4 + - - +
190E LEU 3.9 0.3 - - - +
191E ARG* 3.3 2.4 - - - -
192E VAL* 2.9 38.8 + - + +
194E ALA* 4.4 3.6 - - - -
197E TRP* 3.9 20.0 - - + -
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Residues in contact with THR 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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120D LEU* 3.3 22.7 - - - +
132D LEU* 3.7 26.5 - - + +
134D THR* 5.8 0.7 - - - +
158D LEU* 4.7 3.1 - - + -
169D SER* 5.8 0.9 - - - +
126E PRO* 3.3 12.4 - - - +
130E GLU* 2.4 39.5 + - - -
137E ALA* 1.3 71.0 - - - +
139E LEU* 1.3 64.2 + - - +
189E ARG* 4.1 22.4 - - + -
190E LEU 3.5 6.3 - - - +
191E ARG* 3.2 23.7 + - + -
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Residues in contact with LEU 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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123E VAL* 4.7 7.4 - - + -
124E PHE 3.8 7.0 - - - +
125E GLU* 5.3 0.4 - - - -
126E PRO* 3.8 15.5 - - + -
137E ALA 4.5 0.2 - - - +
138E THR* 1.3 74.5 - - - +
140E VAL* 1.3 59.8 + - - +
141E CYS 4.3 0.2 - - - -
155E TRP* 4.0 22.0 - - + -
189E ARG* 3.2 8.3 - - - +
190E LEU* 2.7 49.0 + - + +
192E VAL* 4.3 18.6 - - + -
197E TRP* 3.7 35.0 - - + -
204E PHE* 3.8 33.7 - - + -
235E ALA* 4.7 7.0 - - + -
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Residues in contact with VAL 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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120D LEU* 4.4 8.9 - - + +
130D VAL* 3.7 32.1 - - + -
132D LEU* 3.6 32.8 - - + -
171D VAL* 4.0 13.5 - - + -
123E VAL* 3.6 2.4 - - - +
124E PHE* 2.8 45.6 + - + +
138E THR* 3.9 0.8 + - + -
139E LEU* 1.3 76.4 - - - +
141E CYS* 1.3 62.8 + - - +
142E LEU* 4.0 22.0 - - + -
155E TRP* 4.5 1.6 - - - -
187E SER* 5.0 0.2 - - - -
188E SER 3.4 10.3 - - - +
189E ARG* 4.5 2.5 - - + -
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Residues in contact with CYS 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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121E VAL* 4.1 14.8 - - - -
122E ALA 3.5 16.4 - - - -
123E VAL* 3.8 1.1 - - + -
140E VAL* 1.3 74.1 - - - +
142E LEU* 1.3 65.6 + - - +
143E ALA 4.1 0.3 + - - -
153E LEU* 4.9 6.2 - - - +
155E TRP* 3.6 16.1 - - + -
186E LEU 3.7 1.0 - - - +
187E SER* 3.4 5.5 - - - -
188E SER* 3.1 32.9 + - - -
206E CYS* 2.0 50.7 - - + -
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Residues in contact with LEU 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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130D VAL* 3.9 17.3 - - + -
171D VAL* 4.1 1.8 - - + -
173D TRP* 3.5 62.8 - - + +
120E GLU 3.7 0.7 - - - +
121E VAL* 3.4 8.2 - - - +
122E ALA* 3.2 29.6 + - + +
124E PHE* 3.7 24.8 - - + -
140E VAL* 4.0 8.3 - - + -
141E CYS* 1.3 75.2 - - - +
143E ALA* 1.3 58.9 + - - +
144E THR* 3.9 16.6 + - + +
186E LEU 3.4 2.2 - - - +
187E SER* 3.9 18.4 - - - -
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Residues in contact with ALA 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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119E PRO* 4.1 8.7 - - + -
120E GLU 3.3 5.2 - - - -
121E VAL* 3.8 15.7 - - + -
141E CYS* 4.1 0.4 + - - -
142E LEU* 1.3 73.2 - - - +
144E THR* 1.3 60.6 + - - +
146E PHE* 3.2 22.1 - - + -
151E VAL* 5.4 0.4 - - + -
153E LEU* 4.9 5.9 - - + +
185E ALA* 3.2 1.7 - - - -
186E LEU* 2.8 43.9 + - + +
208E VAL* 4.4 14.4 - - + -
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Residues in contact with THR 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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173D TRP* 4.4 16.8 - - + +
119E PRO* 3.4 0.7 - - - +
120E GLU* 2.8 64.4 + - - +
142E LEU* 3.9 32.8 - - + +
143E ALA* 1.3 80.2 - - - +
145E GLY* 1.3 62.2 + - - +
146E PHE* 3.4 3.8 - - - -
175E GLU* 3.7 10.1 - - - +
184E TYR 3.8 2.5 - - - -
185E ALA* 4.6 0.2 - - + -
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Residues in contact with GLY 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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117E PHE* 3.3 2.8 - - - +
118E PRO 2.9 9.2 - - - +
120E GLU* 4.5 3.1 - - - -
144E THR* 1.3 75.6 - - - +
146E PHE* 1.3 58.8 + - - +
175E GLU* 3.3 20.8 + - - -
183E ARG* 2.8 43.9 + - - -
184E TYR 2.9 10.0 + - - -
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Residues in contact with PHE 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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117E PHE 3.5 4.9 - - - +
118E PRO 3.4 5.2 - - - -
119E PRO* 3.4 39.7 - - + -
143E ALA* 3.2 35.2 - - + -
144E THR 4.1 0.2 - - - -
145E GLY* 1.3 76.6 - - - +
147E PHE* 1.3 59.7 + - - +
148E PRO 3.6 13.2 - - - -
149E ASP* 3.6 19.5 - - - -
151E VAL* 3.7 27.8 - - + -
172E PRO* 4.9 0.7 - - + -
183E ARG* 4.2 0.7 - - - -
184E TYR* 3.1 51.3 + - + -
185E ALA 4.1 1.1 - - - -
186E LEU* 3.9 19.7 - - + -
210E PHE* 4.1 4.3 - - + -
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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