Contacts of the strand formed by residues 137 - 143 (chain B) in PDB entry 1ILN
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 ARG 137 (chain B).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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98B PHE* 3.9 10.9 - - + -
99B LYS* 2.8 25.8 + - - +
100B PRO 2.6 37.5 + - - -
101B PHE* 3.4 24.7 - - + -
102B GLU* 2.8 21.0 + - - -
127B GLU 5.0 0.4 + - - -
128B ILE* 3.4 4.1 - - - +
129B SER* 2.6 18.8 + - - -
130B GLN* 2.8 24.9 + - - +
132B SER* 2.9 21.2 + - - +
135B PHE* 5.3 0.8 - - + +
136B GLU* 1.3 74.8 - - - +
138B HIS* 1.4 63.5 + - - +
139B LEU* 2.9 5.7 + - - -
160B LEU* 3.0 27.6 + - + +
162B GLN* 3.1 24.0 - - - +
184B VAL* 3.6 15.3 - - + +
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Residues in contact with HIS 138 (chain B).
Click here for Legend to table.
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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136B GLU* 3.3 38.2 - - + +
137B ARG* 1.4 70.8 - - - +
139B LEU* 1.4 57.2 + - - +
156B PRO* 4.2 9.0 - - + +
158B LEU 3.9 11.0 + - - -
159B THR* 4.9 13.9 - - + +
160B LEU* 4.0 1.0 - - - +
184B VAL* 4.4 0.4 - - - +
185B LYS* 2.6 56.8 + - + +
187B LEU* 3.3 46.2 + - + +
188B GLN* 5.5 3.1 + - - -
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Residues in contact with LEU 139 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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101B PHE* 4.0 4.9 - - + -
137B ARG 2.9 10.6 + - - +
138B HIS* 1.4 72.3 - - - +
140B GLU* 1.3 58.4 + - - +
141B PHE* 3.6 20.6 - - + +
155B ALA 4.1 11.7 - - - +
156B PRO* 3.1 19.9 - - + +
157B LEU 4.1 10.3 - - - +
158B LEU* 3.5 38.7 + - + +
160B LEU* 4.6 1.1 - - + -
166B TRP* 3.7 23.1 - - + -
167B ILE* 3.9 12.8 - - + -
182B VAL* 3.7 13.0 - - + -
183B ARG 3.6 17.3 - - - +
184B VAL* 4.3 0.4 - - - +
185B LYS* 2.6 21.7 + - - -
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Residues in contact with GLU 140 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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139B LEU* 1.3 73.4 - - - +
141B PHE* 1.3 65.7 + - - +
142B GLU* 3.2 13.2 + - - +
153B GLU* 3.6 37.9 - - + +
154B GLU 3.2 15.9 - - - +
155B ALA* 4.9 0.3 - - - -
156B PRO* 3.8 8.3 - - - +
182B VAL* 3.7 3.5 - - - +
183B ARG* 3.6 20.5 + - + +
185B LYS* 2.5 46.9 + - - +
194B TRP* 2.8 37.0 + - + +
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Residues in contact with PHE 141 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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124B ILE* 4.2 16.8 - - + -
126B TRP* 4.7 5.2 - + - -
139B LEU* 3.6 10.3 - - + +
140B GLU* 1.3 70.3 - - - +
142B GLU* 1.4 52.3 + - - +
143B ALA* 2.7 25.9 + - + -
152B TRP 3.7 0.3 - - - +
154B GLU* 3.2 57.6 + - - +
167B ILE* 3.7 28.0 - - + -
168B CYS 3.5 22.4 - - - -
169B LEU* 3.6 29.4 - - + -
178B TYR* 4.5 11.0 - + - -
179B GLU 3.8 12.8 - - - -
180B PHE* 5.3 0.4 - - - -
181B GLN 3.5 24.7 - - - -
182B VAL* 4.5 7.9 - - + -
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Residues in contact with GLU 142 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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140B GLU 3.5 14.4 - - - +
141B PHE* 1.4 69.1 - - - +
143B ALA* 1.3 59.8 + - - +
144B ARG 3.2 0.9 + - - -
151B THR* 3.2 20.1 - - + +
152B TRP 3.9 4.0 - - - -
179B GLU* 2.9 32.0 - - - +
181B GLN* 3.3 35.0 + - + +
182B VAL* 3.2 28.0 + - - +
183B ARG* 2.8 44.9 + - - +
197B TRP* 4.0 7.8 - - - +
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Residues in contact with ALA 143 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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141B PHE* 2.7 21.9 + - + +
142B GLU* 1.3 69.3 - - - +
144B ARG* 1.3 64.5 + - - +
151B THR* 3.7 0.4 - - - -
152B TRP* 3.2 39.1 + - + -
154B GLU* 4.1 23.3 - - + +
178B TYR* 4.6 13.7 - - - +
179B GLU* 5.0 0.2 - - - -
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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