Contacts of the strand formed by residues 143 - 153 (chain E) in PDB entry 4KJQ
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 MET 143 (chain E).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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141E ALA* 3.9 20.4 + - - +
142E SER* 1.3 92.6 + - - +
144E VAL* 1.3 61.7 + - - +
170E GLY* 6.5 0.2 - - - -
190E THR* 3.4 40.8 - - + +
191E VAL 3.3 13.5 - - - -
192E PRO* 4.1 20.6 - - + -
193E SER* 4.3 2.0 - - - -
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Residues in contact with VAL 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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134E PRO* 4.1 20.4 - - + -
140E ALA* 6.1 2.9 - - + -
141E ALA 6.1 0.2 - - - +
143E MET* 1.3 74.8 - - - +
145E THR* 1.3 68.1 + - - +
146E LEU* 3.9 3.5 + - + -
189E VAL 3.8 0.3 - - - +
190E THR* 3.3 1.4 - - - -
191E VAL* 2.6 56.3 + - + +
192E PRO 3.4 16.4 - - - +
193E SER* 3.6 16.4 - - - +
196E TRP* 4.0 30.7 - - + +
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Residues in contact with THR 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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134E PRO* 4.2 4.5 - - - +
144E VAL* 1.3 73.7 - - - +
146E LEU* 1.3 73.6 + - - +
188E SER* 4.7 0.7 - - - -
189E VAL 3.3 6.3 - - - +
190E THR* 2.3 32.2 + - - +
113F THR* 5.6 4.9 - - - +
115F SER* 3.5 26.6 + - - +
117F PHE* 2.9 33.6 - - + -
134F PHE* 4.2 10.8 - - + -
136F ASN* 4.5 10.8 + - - +
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Residues in contact with LEU 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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132E LEU 3.8 5.4 - - - +
134E PRO* 3.5 31.9 - - + -
144E VAL* 4.6 5.8 - - + +
145E THR* 1.3 80.7 - - - +
147E GLY* 1.3 60.1 + - - +
188E SER* 3.7 3.1 - - - -
189E VAL* 2.7 39.2 + - + +
191E VAL* 4.5 6.7 - - + -
196E TRP* 3.6 55.2 - - + +
201E VAL* 3.9 23.1 - - + -
218E ILE* 3.7 18.4 - - + -
117F PHE* 4.5 3.4 - - - -
134F PHE* 4.0 0.9 - - - -
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Residues in contact with GLY 147 (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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132E LEU* 2.8 34.2 + - - +
146E LEU* 1.3 78.4 - - - +
148E CYS* 1.3 63.7 + - - +
162E TRP* 3.4 11.0 - - - -
187E SER 3.1 14.6 - - - -
218E ILE* 3.4 7.1 - - - +
134F PHE* 4.0 10.1 - - - -
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Residues in contact with CYS 148 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
129E VAL* 4.3 3.8 - - + -
130E TYR 3.2 15.0 - - - +
132E LEU* 4.0 4.4 - - - +
147E GLY* 1.3 76.7 - - - +
149E LEU* 1.3 61.9 + - - +
150E VAL* 3.9 5.2 + - - +
160E VAL* 4.7 5.2 - - - -
162E TRP* 3.5 6.5 - - + -
186E SER* 3.3 4.9 - - - -
187E SER* 3.1 29.2 + - - -
203E CYS* 2.0 55.2 - - - -
205E VAL* 4.2 11.7 - - - -
218E ILE* 4.1 5.2 - - + -
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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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128E SER 3.7 0.7 - - - +
129E VAL* 3.3 3.8 - - - +
130E TYR* 2.6 68.4 + - + +
132E LEU* 3.8 18.9 - - + +
148E CYS* 1.3 73.5 - - - +
150E VAL* 1.3 63.8 + - - +
151E LYS* 4.0 13.2 - - + -
184E THR* 4.3 14.6 - - + -
185E LEU 4.2 2.9 - - - +
186E SER* 3.9 17.0 - - - +
123F GLN* 4.3 3.1 - - - +
130F SER* 3.7 29.4 - - - +
132F VAL* 3.7 23.3 - - + -
177F THR* 4.5 7.4 - - + +
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Residues in contact with VAL 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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127E PRO* 3.6 27.6 - - + -
128E SER 3.5 3.1 - - - -
129E VAL* 4.0 5.2 - - + -
148E CYS* 4.1 9.4 - - - +
149E LEU* 1.3 78.2 - - - +
151E LYS* 1.3 58.1 + - - +
153E TYR* 3.9 13.0 - - + -
158E VAL* 4.7 6.1 - - + -
160E VAL* 4.4 4.9 - - + -
184E THR* 3.3 2.4 - - - -
185E LEU* 2.6 57.0 + - + +
187E SER 5.6 0.2 - - - +
205E VAL* 3.8 37.5 - - + -
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Residues in contact with LYS 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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127E PRO* 3.6 0.5 - - - +
128E SER* 2.9 38.1 + - - +
130E TYR* 3.6 34.1 - - + +
149E LEU* 4.0 12.5 - - + +
150E VAL* 1.3 75.3 - - - +
152E GLY* 1.3 64.1 + - - +
153E TYR* 3.5 3.4 - - - -
183E TYR 3.7 1.3 - - - -
184E THR* 3.3 31.5 + - + +
123F GLN* 4.1 7.4 - - - +
130F SER* 3.3 19.0 + - - -
177F THR* 5.7 1.0 - - - +
179F THR* 3.7 21.1 + - - +
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Residues in contact with GLY 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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125E THR* 3.1 25.8 - - - +
126E PRO 3.1 6.2 - - - +
151E LYS* 1.3 79.5 - - - +
153E TYR* 1.3 60.1 + - - +
182E LEU* 3.7 29.3 - - - +
183E TYR 3.1 8.6 + - - -
184E THR* 4.0 2.0 + - - -
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Residues in contact with TYR 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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125E THR 3.2 12.3 - - - +
127E PRO* 3.5 33.2 - - + -
150E VAL* 3.9 19.1 - - + -
151E LYS 4.5 0.4 - - - -
152E GLY* 1.3 80.0 - - - +
154E PHE* 1.3 63.4 + - - +
155E PRO 3.6 20.2 - - - -
156E GLU* 2.8 28.0 + - + -
158E VAL* 3.5 25.0 - - + +
176E ALA* 3.3 16.6 - - - +
182E LEU* 3.7 2.0 - - - +
183E TYR* 2.9 65.5 + + + +
184E THR* 4.3 1.6 - - - -
185E LEU* 3.4 12.4 - - - +
207E HIS* 3.7 8.7 - + + -
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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