Contacts of the strand formed by residues 122 - 132 (chain E) in PDB entry 4LML
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 122 (chain E).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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114E ASP* 5.2 2.4 - - - +
117E ARG* 5.2 12.3 + - - +
120E PHE 3.6 2.9 + - - -
121E ASP* 1.3 75.0 - - - +
123E GLN* 1.3 73.4 + - - +
162E GLU* 5.1 0.9 + - - -
188E ARG* 4.7 15.7 + - - -
189E ILE 3.5 8.7 - - - -
190E SER* 3.5 18.2 - - - -
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Residues in contact with GLN 123 (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 PRO 4.3 1.9 - - - +
113E LEU* 3.2 25.8 - - + +
114E ASP* 2.5 56.7 + - - +
121E ASP* 2.7 23.7 + - - +
122E SER* 1.3 84.8 + - - +
124E THR* 1.3 65.5 + - - +
125E LEU* 4.1 0.4 - - + -
159E TRP* 3.7 17.3 - - + -
188E ARG* 3.5 9.6 + - - +
189E ILE* 2.8 50.2 + - + +
191E ARG* 5.5 0.2 - - - +
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Residues in contact with THR 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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111E SER* 4.4 2.9 + - - -
112E PRO* 4.7 6.5 - - - +
123E GLN* 1.3 79.7 + - - +
125E LEU* 1.3 63.8 + - - +
126E HIS* 3.4 32.9 + - - +
186E GLN* 4.4 10.1 + - - +
187E LEU 3.6 4.3 - - - -
188E ARG* 3.5 42.0 - - - +
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Residues in contact with LEU 125 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
29E LEU* 3.8 10.8 - - + -
34E GLU 6.5 0.2 - - - -
36E PHE* 3.4 55.4 - - + -
111E SER* 3.9 10.3 - - - +
112E PRO 4.8 0.7 - - - +
113E LEU* 3.6 30.5 - - + -
123E GLN* 5.1 0.7 - - + -
124E THR* 1.3 75.9 + - - +
126E HIS* 1.3 60.6 + - - +
156E LEU* 4.6 7.6 - - + -
186E GLN* 3.4 5.5 - - - -
187E LEU* 2.9 45.7 + - + +
189E ILE* 3.7 29.2 - - + -
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Residues in contact with HIS 126 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
79E ASN* 2.7 25.0 + - - +
109E VAL* 3.2 13.2 - - - +
111E SER* 3.2 15.8 + - - +
112E PRO* 5.4 10.1 - - + -
124E THR* 3.4 30.6 + - + +
125E LEU* 1.3 78.8 + - - +
127E ILE* 1.3 60.3 + - - +
128E TYR* 3.1 36.6 + + + +
184E ASP* 3.3 14.4 + - - -
185E TYR 3.6 0.7 - - - -
186E GLN* 3.5 28.7 - - + +
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Residues in contact with ILE 127 (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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21E ILE* 4.1 12.1 - - + -
23E LEU* 5.1 7.0 - - + -
36E PHE* 4.3 9.2 - - + -
38E VAL* 4.2 23.6 - - + -
77E PHE* 3.4 33.4 - - + -
79E ASN* 3.9 2.5 - - - +
80E VAL* 6.2 0.2 - - + -
105E PHE* 5.4 0.9 - - + -
109E VAL* 3.7 29.2 - - + -
126E HIS* 1.3 77.1 - - - +
128E TYR* 1.3 64.2 + - - +
129E LEU* 4.0 9.2 - - + -
164E PHE* 5.3 7.6 - - + -
183E LEU 3.6 1.2 - - - +
185E TYR* 2.9 48.4 + - + +
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Residues in contact with TYR 128 (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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153B ASP* 5.8 4.0 - - - -
77E PHE* 3.3 9.2 - - - +
78E VAL* 2.9 47.1 + - + -
79E ASN* 3.1 36.6 + - + -
126E HIS* 3.1 42.3 + - + -
127E ILE* 1.3 75.0 - - - +
129E LEU* 1.3 65.1 + - - +
182E LYS* 4.0 26.9 - - + -
183E LEU 3.1 14.6 - - - +
184E ASP* 3.2 33.8 + - + -
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Residues in contact with LEU 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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19E THR* 3.7 34.5 - - + -
21E ILE* 3.6 15.9 - - + -
42E LEU* 3.8 21.3 - - + -
75E ILE* 3.9 15.5 - - + -
76E ARG 3.5 2.9 - - - -
77E PHE* 3.5 36.8 - - + -
127E ILE* 4.0 3.8 - - + -
128E TYR* 1.3 77.2 - - - +
130E ILE* 1.3 60.3 + - - +
140E VAL* 3.6 5.7 - - + +
181E SER 3.4 1.6 - - - +
182E LYS* 3.3 1.6 - - - -
183E LEU* 2.8 42.6 + - + -
185E TYR* 4.0 13.2 - - + +
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Residues in contact with ILE 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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24B ILE* 6.5 1.1 - - + -
41B PHE* 5.6 2.2 - - + -
104B ARG* 5.9 0.2 - - - -
75E ILE* 3.7 4.3 - - - +
76E ARG* 2.8 67.8 + - - +
78E VAL* 3.5 33.5 - - + +
129E LEU* 1.3 73.4 - - - +
131E VAL* 1.3 63.4 + - - +
140E VAL* 5.0 0.4 - - - -
173E PHE* 5.6 3.1 - - + -
175E LEU* 6.0 2.7 - - + -
180E GLU* 3.2 28.0 - - + +
181E SER 3.0 6.7 - - - +
182E LYS* 3.4 33.0 - - + -
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Residues in contact with VAL 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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17E VAL* 5.0 0.9 - - + -
73E PRO* 4.4 4.5 - - + -
74E GLU 3.4 19.3 - - - +
75E ILE* 3.4 21.1 - - + -
76E ARG* 5.5 1.6 - - - +
130E ILE* 1.3 74.4 - - - +
132E ARG* 1.3 69.3 + - - +
138E ASN* 3.8 33.0 - - + +
139E ILE 4.5 0.2 - - - -
140E VAL* 3.4 26.9 - - + +
179E LEU 4.2 0.2 - - - +
180E GLU* 3.2 8.0 - - - -
181E SER* 3.0 42.9 + - - +
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Residues in contact with ARG 132 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
41B PHE* 5.0 2.8 - - - -
89B VAL* 3.8 24.2 - - + +
90B ASP* 4.9 7.0 + - - +
102B LEU* 3.5 27.6 - - - +
74E GLU* 4.3 7.9 + - - +
76E ARG* 4.5 11.5 - - - +
131E VAL* 1.3 85.3 - - - +
133E SER* 1.3 70.5 + - - +
134E VAL* 5.4 1.2 - - - +
138E ASN* 4.1 4.8 - - - +
175E LEU* 2.7 26.1 + - - +
176E GLU* 3.1 22.2 + - - +
178E ARG* 3.2 30.8 - - + +
179E LEU 4.5 1.1 - - - +
180E GLU* 3.2 34.6 + - + +
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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