Contacts of the strand formed by residues 142 - 152 (chain E) in PDB entry 2GJ6
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 LYS 142 (chain E).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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168D MET* 3.9 20.0 - - + -
171D MET* 6.2 3.1 - - - -
173D PHE* 3.7 53.4 - - + -
136E GLU* 3.4 16.3 - - - +
137E ILE* 3.8 6.8 + - - -
140E THR* 2.9 40.2 + - - +
141E GLN* 1.3 84.5 + - - +
143E ALA* 1.3 61.3 + - - +
197E ARG* 3.8 19.7 - - - +
198E VAL 3.7 5.4 - - - +
199E SER* 4.6 3.4 - - - -
200E ALA* 3.9 5.7 - - - +
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Residues in contact with ALA 143 (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 PRO* 3.9 17.0 - - + -
136E GLU* 3.8 3.1 - - - -
137E ILE* 4.3 8.5 - - + -
142E LYS* 1.3 74.7 - - - +
144E THR* 1.3 62.5 + - - +
145E LEU* 3.6 0.9 + - - +
196E LEU 3.4 4.9 - - - +
197E ARG* 4.0 2.4 - - - +
198E VAL* 2.7 40.7 + - + +
199E SER 4.3 3.6 - - - +
200E ALA* 4.4 1.8 - - - -
203E TRP* 3.8 29.4 - - + -
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Residues in contact with THR 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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128D LEU* 4.1 8.1 - - - +
140D LEU* 3.8 23.8 - - + +
142D THR* 5.7 0.9 - - - +
166D LEU* 5.2 1.8 - - + -
177D SER* 5.9 0.9 - - - -
132E PRO* 3.4 22.5 - - - +
136E GLU* 2.4 36.0 + - - +
143E ALA* 1.3 70.7 - - - +
145E LEU* 1.3 61.3 + - - +
146E VAL* 4.0 3.9 + - + -
195E ARG* 3.7 31.6 - - + -
196E LEU 3.6 4.9 - - - +
197E ARG* 3.3 27.3 + - + +
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Residues in contact with LEU 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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129E VAL* 4.0 20.4 - - + -
130E PHE 4.0 8.7 - - - +
132E PRO* 3.8 11.7 - - + -
143E ALA 4.2 2.7 - - - +
144E THR* 1.3 72.9 - - - +
146E VAL* 1.3 60.2 + - - +
161E TRP* 3.7 15.1 - - + -
195E ARG* 3.3 2.8 - - - +
196E LEU* 2.6 59.8 + - + +
198E VAL* 4.0 13.7 - - + -
203E TRP* 3.7 27.8 - - + -
210E PHE* 3.9 44.4 - - + -
241E ALA* 4.6 0.7 - - + -
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Residues in contact with VAL 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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128D LEU* 3.8 15.7 - - + +
138D VAL* 3.8 27.8 - - + -
140D LEU* 4.2 8.7 - - + -
179D VAL* 4.2 15.3 - - + -
129E VAL* 3.6 4.0 - - - +
130E PHE* 2.8 50.6 + - + +
144E THR* 4.0 4.4 + - + -
145E LEU* 1.3 78.1 - - - +
147E CYS* 1.3 63.5 + - - +
148E LEU* 5.4 1.6 - - + -
161E TRP* 4.1 2.5 - - - -
193E SER* 5.9 1.6 - - - -
194E SER 3.3 8.3 - - - +
195E ARG* 3.8 26.0 - - + -
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Residues in contact with CYS 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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127E VAL* 3.9 15.7 - - - -
128E ALA 3.4 10.1 - - - -
129E VAL* 4.5 1.3 - - + +
146E VAL* 1.3 75.8 - - - +
148E LEU* 1.3 67.0 + - - +
149E ALA 4.7 0.2 - - - -
159E LEU* 4.4 5.1 - - + +
161E TRP* 3.6 15.9 - - + -
192E LEU 3.8 0.5 - - - +
193E SER* 3.3 9.7 - - - -
194E SER* 2.8 32.5 + - - +
212E CYS* 2.0 49.8 - - + -
214E VAL* 4.9 0.4 - - - -
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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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136D LYS* 4.1 15.7 + - - -
138D VAL* 3.9 22.4 - - + -
179D VAL* 5.5 0.7 - - + -
181D TRP* 3.7 58.8 - - + -
126E GLU 3.3 2.4 - - - +
127E VAL* 3.3 4.0 - - - -
128E ALA* 2.8 36.0 + - + +
130E PHE* 3.9 21.5 - - + -
146E VAL* 5.4 1.8 - - + -
147E CYS* 1.3 76.8 - - - +
149E ALA* 1.3 60.0 + - - +
150E THR* 3.8 9.8 + - + +
192E LEU 3.7 14.6 - - - +
193E SER* 3.8 10.8 - - - -
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Residues in contact with ALA 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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125E PRO* 4.4 5.2 - - + -
126E GLU 3.2 6.5 - - - +
127E VAL* 4.3 4.7 - - + -
147E CYS* 4.0 2.6 - - - -
148E LEU* 1.3 72.3 - - - +
150E THR* 1.3 59.0 + - - +
152E PHE* 3.6 16.3 - - + -
159E LEU* 4.8 3.8 - - + +
191E ALA* 3.3 4.0 - - - +
192E LEU* 2.8 48.6 + - + +
214E VAL* 4.0 28.9 - - + -
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Residues in contact with THR 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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136D LYS* 3.2 33.8 + - - +
181D TRP* 4.4 10.3 - - + +
124E PRO 4.3 0.2 - - - +
125E PRO* 3.4 2.9 - - - +
126E GLU* 2.6 58.5 + - - +
148E LEU* 4.3 17.4 + - + -
149E ALA* 1.3 78.3 - - - +
151E GLY* 1.3 60.3 - - - +
152E PHE* 3.6 4.3 - - - -
181E GLU* 3.4 14.4 - - - +
190E TYR 3.6 2.5 - - - -
191E ALA* 3.9 8.3 - - + -
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Residues in contact with GLY 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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123E PHE* 3.3 13.0 - - - +
124E PRO 3.8 3.9 - - - +
126E GLU* 6.5 0.2 - - - -
150E THR* 1.3 72.1 - - - +
152E PHE* 1.3 56.5 - - - -
181E GLU* 2.9 25.8 + - - -
189E ARG* 2.8 41.0 + - - -
190E TYR 2.9 6.0 + - - -
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Residues in contact with PHE 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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123E PHE 3.4 13.0 - - - +
125E PRO* 3.6 31.2 - - + -
149E ALA* 3.6 24.7 - - + -
150E THR 4.1 3.8 - - - -
151E GLY* 1.3 77.2 - - - +
153E TYR* 1.3 62.2 + - - +
154E PRO 3.5 17.9 - - - -
155E ASP* 3.8 12.8 - - - -
157E VAL* 3.7 29.4 - - + -
178E PRO* 4.0 15.0 - - + -
189E ARG* 4.3 0.4 - - - -
190E TYR* 2.6 68.9 + - + +
191E ALA* 3.7 6.7 - - - -
192E LEU* 3.8 9.0 - - + -
216E PHE* 4.2 6.3 - + + -
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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