Contacts of the strand formed by residues 147 - 153 (chain E) in PDB entry 5IJ7
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 PRO 147 (chain E).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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65A ILE* 4.3 10.5 - - + -
66A GLN 3.2 27.6 - - - +
68A VAL* 3.7 23.8 - - + -
88E ASN* 4.1 20.6 - - - +
138E TRP* 4.2 10.3 - - + -
139E THR 3.4 10.5 - - - +
140E TYR* 4.3 1.3 - - - -
145E SER 4.3 1.1 - - - +
146E HIS* 1.4 88.4 - - - +
148E LEU* 1.3 64.2 + - - +
162E ASN* 4.1 0.7 - - - +
163E PRO* 3.1 24.6 - - + +
164E ILE* 3.6 14.1 - - + -
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Residues in contact with LEU 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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138E TRP* 3.3 8.8 - - - -
139E THR* 2.8 52.1 + - + +
140E TYR 4.3 0.7 - - - +
141E ASP* 4.1 27.4 - - + +
146E HIS* 4.1 7.6 - - + +
147E PRO* 1.3 81.5 - - - +
149E LEU* 1.3 60.4 + - - +
150E ALA 4.2 0.4 - - - -
160E ILE* 4.0 18.6 - - + -
161E ILE 3.4 14.8 - - - +
162E ASN* 3.8 27.1 - - + +
163E PRO* 4.2 1.1 - - - -
169E ILE* 4.4 15.3 - - + -
170E LYS* 6.3 1.8 - - - -
206E ILE* 5.2 8.7 - - + -
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Residues in contact with LEU 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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100E ALA* 3.6 24.9 - - + -
107E VAL* 3.6 27.6 - - + -
109E LEU* 4.1 11.4 - - + -
136E CYS* 4.1 4.7 - - + -
137E ALA 3.5 24.5 - - - +
138E TRP* 3.6 40.6 - - + +
148E LEU* 1.3 75.0 - - - +
150E ALA* 1.3 60.8 + - - +
151E VAL* 4.0 6.0 + - + -
159E ARG 3.7 1.2 - - - +
160E ILE* 4.5 2.2 - - - -
161E ILE* 2.7 50.3 + - + +
163E PRO* 4.6 4.2 - - + +
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Residues in contact with ALA 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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136E CYS* 3.0 7.6 - - - +
137E ALA 2.8 31.2 + - - +
148E LEU 4.2 0.4 - - - -
149E LEU* 1.3 72.0 - - - +
151E VAL* 1.3 59.6 + - - +
158E ILE* 4.6 0.7 - - + -
159E ARG 3.1 7.0 - - - +
160E ILE* 3.6 22.2 - - + +
182E LEU* 3.6 17.7 - - + +
184E PHE* 3.6 27.5 - - + -
192E LEU* 4.3 4.0 - - + -
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Residues in contact with VAL 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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102E VAL* 3.8 4.7 - - + -
107E VAL* 3.6 39.0 - - + -
133E PHE* 3.8 25.5 - - + -
135E THR 3.4 7.9 - - - +
136E CYS* 3.7 16.6 - - + -
149E LEU* 4.1 6.7 - - + -
150E ALA* 1.3 79.5 - - - +
152E ALA* 1.3 62.6 + - - +
157E ILE 3.8 0.2 - - - +
158E ILE* 3.5 1.6 - - - -
159E ARG* 2.9 48.3 + - + +
161E ILE* 4.0 11.9 - - + -
182E LEU* 3.6 4.5 - - - +
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Residues in contact with ALA 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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133E PHE* 3.7 11.4 - - - -
134E TYR 3.0 17.3 + - - -
135E THR* 3.1 20.6 + - + +
151E VAL* 1.3 77.8 - - - +
153E GLY* 1.3 58.4 + - - +
157E ILE 3.3 19.7 - - - +
158E ILE* 4.1 1.3 - - - -
179E ILE* 3.9 29.2 - - + -
182E LEU* 3.9 15.5 - - + +
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Residues in contact with GLY 153 (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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131E GLU* 3.9 3.7 + - - -
132E ASN 3.0 15.0 - - - -
133E PHE* 3.9 3.6 - - - -
134E TYR* 3.6 14.8 - - - -
152E ALA* 1.3 75.7 - - - +
154E SER* 1.3 61.4 + - - -
155E ARG 3.4 2.9 - - - -
156E GLY* 3.3 7.3 + - - -
157E ILE 4.3 3.8 + - - -
179E ILE* 2.9 31.6 + - - +
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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