Contacts of the strand formed by residues 123 - 133 (chain E) in PDB entry 5J0Z
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 SER 123 (chain E).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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115E ASP* 4.6 2.6 - - - +
122E ASP* 1.3 73.0 + - - +
124E GLN* 1.3 79.7 + - - +
160E TRP* 4.8 0.2 - - - -
163E GLU* 5.1 0.2 + - - -
189E ARG* 6.5 0.2 - - - -
190E ILE 3.2 9.4 - - - -
191E SER* 3.0 28.9 - - - +
192E ARG 4.6 0.4 - - - +
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Residues in contact with GLN 124 (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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113E PRO 4.6 1.3 - - - +
114E LEU* 3.4 30.2 - - + +
115E ASP* 2.9 46.8 + - - +
116E PHE* 4.9 0.8 - - - +
122E ASP* 2.7 24.5 + - - -
123E SER* 1.3 82.6 + - - +
125E THR* 1.3 65.1 + - - +
126E LEU* 3.9 1.6 - - + -
160E TRP* 3.8 22.4 - - + -
189E ARG* 3.2 8.0 - - - +
190E ILE* 2.7 49.8 + - + +
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Residues in contact with THR 125 (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 SER* 3.7 4.5 + - - -
113E PRO 4.6 4.8 - - - +
124E GLN* 1.3 73.1 + - - +
126E LEU* 1.3 68.1 + - - +
127E HIS* 3.3 34.7 + - + +
187E GLN* 4.2 9.9 - - + +
188E LEU 3.6 4.0 - - - +
189E ARG* 3.4 39.8 + - + +
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Residues in contact with LEU 126 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
30E LEU* 4.1 11.4 - - + -
37E PHE* 3.7 43.5 - - + -
112E SER* 3.6 8.5 - - - +
114E LEU* 3.6 31.6 - - + -
124E GLN* 4.7 1.6 - - + -
125E THR* 1.3 79.1 - - - +
127E HIS* 1.3 61.3 + - - +
128E ILE* 4.4 0.4 - - - -
157E LEU* 4.8 3.8 - - + -
187E GLN* 3.4 6.9 - - - -
188E LEU* 2.6 64.2 + - + +
190E ILE* 3.8 24.0 - - + -
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Residues in contact with HIS 127 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
80E ASN* 2.6 32.5 + - - +
110E VAL* 3.3 9.2 - - - +
112E SER* 3.5 15.0 + - - +
113E PRO* 5.5 5.8 - - + -
125E THR* 3.3 39.5 + - + +
126E LEU* 1.3 74.7 + - - +
128E ILE* 1.3 59.4 + - - +
129E TYR* 3.4 31.1 + - + -
185E ASP* 3.2 31.6 + - - -
186E TYR 3.4 2.2 - - - -
187E GLN* 3.7 15.2 - - + +
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Residues in contact with ILE 128 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
22E ILE* 4.1 10.5 - - + +
24E LEU* 4.4 4.5 - - + -
37E PHE* 4.1 23.1 - - + -
39E VAL* 4.3 26.2 - - + -
78E PHE* 3.4 37.2 - - + -
80E ASN* 3.8 3.6 - - - +
81E VAL* 5.9 0.7 - - + -
106E PHE* 5.3 2.2 - - + -
110E VAL* 4.4 11.7 - - + -
126E LEU 5.7 0.4 - - - -
127E HIS* 1.3 76.9 - - - +
129E TYR* 1.3 60.7 + - - +
130E LEU 3.7 1.6 + - - -
165E PHE* 4.4 22.9 - - + -
186E TYR* 2.9 42.1 + - + +
188E LEU* 5.8 3.6 - - + -
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Residues in contact with TYR 129 (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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154D ASP* 3.7 21.8 - - - -
78E PHE* 3.4 8.0 - - - -
79E VAL* 2.8 50.4 + - + -
80E ASN* 2.9 23.3 + - + +
127E HIS* 3.4 50.2 + + + -
128E ILE* 1.3 74.9 - - - +
130E LEU* 1.3 59.7 + - - +
183E LYS* 3.6 25.6 - - - -
184E LEU 3.6 6.5 - - - +
185E ASP* 3.4 27.8 + - + -
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Residues in contact with LEU 130 (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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20E THR* 4.1 19.1 - - + -
22E ILE* 3.9 13.2 - - + -
43E LEU* 4.0 16.2 - - + -
76E ILE* 3.3 29.4 - - + -
77E ARG 3.9 5.2 - - - +
78E PHE* 3.7 32.1 - - + -
79E VAL* 4.4 0.4 - - - -
128E ILE 3.7 1.8 + - - -
129E TYR* 1.3 73.3 - - - +
131E ILE* 1.3 61.0 + - - +
142E LEU* 3.6 7.4 - - + +
183E LYS* 3.3 4.2 - - - +
184E LEU* 2.7 45.7 + - + +
186E TYR* 3.6 26.2 - - + -
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Residues in contact with ILE 131 (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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76E ILE* 3.5 9.2 - - - +
77E ARG* 2.9 47.5 + - + +
79E VAL* 3.8 15.9 - - + -
130E LEU* 1.3 72.3 - - - +
132E VAL* 1.3 68.8 + - - +
142E LEU* 3.8 2.9 - - - +
174E PHE* 4.9 6.1 - - + -
176E LEU* 5.6 1.1 - - + -
181E GLU* 3.5 32.3 - - + +
182E SER 3.4 13.0 - - - +
183E LYS* 3.8 23.3 - - + -
403E ACT 3.5 39.7 - - + +
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Residues in contact with VAL 132 (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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74E PRO* 4.6 1.8 - - + -
75E GLU 3.3 26.0 - - - +
76E ILE* 3.8 11.0 - - + -
131E ILE* 1.3 78.1 - - - +
133E ARG* 1.3 73.0 + - - +
134E SER* 3.8 1.2 + - - -
140E ILE* 4.1 33.4 - - + +
142E LEU* 3.3 33.4 - - + -
181E GLU* 3.5 6.8 - - - -
182E SER* 3.1 34.0 + - - +
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Residues in contact with ARG 133 (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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42D PHE* 4.4 6.3 - - - -
90D VAL* 3.7 23.8 - - + -
91D ASP* 5.5 4.6 - - - +
103D LEU* 3.6 22.9 - - - +
75E GLU* 3.9 12.9 + - - +
77E ARG* 4.2 15.8 - - - +
131E ILE* 4.8 0.2 - - - +
132E VAL* 1.3 85.7 - - - +
134E SER* 1.3 72.2 + - - +
135E VAL* 3.8 5.5 + - - +
140E ILE* 4.3 5.7 - - - +
176E LEU* 3.1 21.8 + - - +
177E GLU* 3.1 31.1 + - - +
179E ARG* 3.7 29.5 + - - +
180E LEU 4.0 2.4 + - - +
181E GLU* 2.8 43.2 + - - +
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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