Contacts of the strand formed by residues 149 - 159 (chain E) in PDB entry 4JRX
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 149 (chain E).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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158D ASP* 5.3 0.7 - - - -
183D MET* 3.8 24.2 - - + -
186D MET* 3.8 25.5 - - + +
188D PHE* 3.6 37.3 - - + -
143E GLU* 3.3 17.5 - - - +
144E ILE* 3.5 15.4 + - - -
147E THR* 3.1 35.7 + - - +
148E GLN* 1.4 77.6 - - - +
150E ALA* 1.3 62.0 + - - +
204E ARG* 3.7 27.6 - - + +
205E VAL 3.4 5.8 - - - +
207E ALA 4.2 1.8 - - - +
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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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139E PRO* 3.6 24.5 - - + -
143E GLU* 3.6 2.7 - - - -
144E ILE* 3.9 9.9 - - + -
149E LYS* 1.3 74.8 - - - +
151E THR* 1.3 62.7 + - - +
152E LEU* 3.8 2.1 + - + +
203E LEU 3.5 2.6 - - - +
204E ARG* 3.5 1.5 - - - -
205E VAL* 2.7 41.6 + - + +
206E SER 4.4 3.4 - - - +
210E TRP* 3.7 25.6 - - + -
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Residues in contact with THR 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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143D LEU* 3.4 18.4 - - - +
155D LEU* 3.8 30.9 - - + +
157D THR* 5.3 0.2 + - - -
181D LEU* 4.9 2.7 - - + -
192D SER* 5.7 1.3 - - - +
139E PRO* 3.4 13.3 - - - +
143E GLU* 2.7 36.1 + - - +
150E ALA* 1.3 71.5 - - - +
152E LEU* 1.3 62.9 + - - +
153E VAL* 4.5 0.7 - - + -
202E ARG* 3.6 29.6 - - + -
203E LEU 3.4 8.1 - - - +
204E ARG* 3.1 20.9 + - + +
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Residues in contact with LEU 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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136E VAL* 3.9 21.1 - - + -
137E PHE 3.6 7.2 - - - +
138E GLU* 5.4 0.2 - - - -
139E PRO* 3.7 26.0 - - + -
150E ALA 4.3 5.6 - - - +
151E THR* 1.3 73.6 - - - +
153E VAL* 1.3 62.9 + - - +
168E TRP* 3.9 17.5 - - + -
202E ARG* 3.2 5.2 - - - -
203E LEU* 2.7 43.2 + - + +
205E VAL* 5.1 3.8 - - + -
210E TRP* 4.0 16.6 - - + -
217E PHE* 3.8 43.5 - - + -
248E ALA* 4.2 9.4 - - + -
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Residues in contact with VAL 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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143D LEU* 3.8 24.6 - - + +
153D VAL* 3.9 19.3 - - + -
155D LEU* 3.9 27.1 - - + -
194D VAL* 4.1 10.5 - - + -
136E VAL* 3.4 4.5 - - - +
137E PHE* 2.7 43.0 + - + -
151E THR* 4.5 1.8 - - + -
152E LEU* 1.3 78.2 - - - +
154E CYS* 1.3 62.4 + - - +
155E LEU* 4.0 22.9 - - + -
168E TRP* 4.3 2.5 - - - -
200E SER* 5.1 0.7 - - - -
201E SER 3.4 6.5 - - - +
202E ARG* 4.1 9.4 - - + -
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Residues in contact with CYS 154 (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 VAL* 3.7 18.8 - - - -
135E ALA 3.5 6.5 - - - -
136E VAL* 4.5 1.1 - - + -
153E VAL* 1.3 73.4 - - - +
155E LEU* 1.3 67.7 + - - +
166E LEU* 4.3 8.2 - - - +
168E TRP* 3.5 18.3 - - + -
199E LEU 3.9 0.4 - - - +
200E SER* 3.3 5.2 - - - -
201E SER* 2.7 38.1 + - - +
219E CYS* 2.1 50.7 - - + -
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Residues in contact with LEU 155 (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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151D LYS* 3.7 19.3 - - + -
153D VAL* 3.7 17.7 - - + -
194D VAL* 4.4 1.8 - - + -
196D TRP* 3.6 49.4 - - + +
133E GLU 3.2 5.4 - - - +
134E VAL* 3.4 1.2 - - - +
135E ALA* 3.0 31.0 + - + +
137E PHE* 3.7 18.2 - - + -
153E VAL* 4.0 11.4 - - + -
154E CYS* 1.3 78.7 - - - +
156E ALA* 1.3 60.1 + - - +
157E THR* 3.9 9.9 + - + +
199E LEU 3.5 1.8 - - - +
200E SER* 3.7 26.0 - - - -
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Residues in contact with ALA 156 (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* 4.1 9.6 - - + -
133E GLU 3.2 6.7 - - - -
134E VAL* 4.3 1.8 - - + -
154E CYS* 4.2 0.6 - - - -
155E LEU* 1.3 70.8 - - - +
157E THR* 1.4 59.8 + - - +
159E PHE* 3.3 16.7 - - + -
164E VAL* 5.8 0.2 - - + -
166E LEU* 4.5 4.7 - - + -
198E ALA* 3.2 2.3 - - - -
199E LEU* 2.7 48.2 + - + +
221E VAL* 3.9 29.6 - - + -
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Residues in contact with THR 157 (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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151D LYS* 3.6 23.5 + - - +
196D TRP* 3.9 26.2 - - + +
132E PRO* 3.3 2.4 - - - +
133E GLU* 2.7 51.9 + - - +
155E LEU* 4.3 13.2 + - + +
156E ALA* 1.4 77.6 - - - +
158E GLY* 1.3 64.5 + - - +
159E PHE* 3.3 3.1 - - - -
188E GLU* 3.5 8.3 - - - +
197E TYR 3.6 4.5 - - - -
198E ALA* 3.9 15.3 - - + -
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Residues in contact with GLY 158 (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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130E PHE* 3.2 14.9 - - - +
131E PRO 3.6 4.3 - - - +
133E GLU* 5.5 2.5 - - - -
157E THR* 1.3 71.1 - - - +
159E PHE* 1.3 59.3 + - - +
188E GLU* 3.0 25.6 + - - -
196E ARG* 3.0 36.0 + - - -
197E TYR 3.0 6.6 + - - -
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Residues in contact with PHE 159 (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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130E PHE 3.4 5.4 - - - +
131E PRO 4.1 0.2 - - - -
132E PRO* 3.5 41.3 - - + -
156E ALA* 3.3 32.1 - - + -
157E THR 3.3 0.6 - - - -
158E GLY* 1.3 78.0 - - - +
160E TYR* 1.3 59.8 + - - +
161E PRO 3.6 13.5 - - - -
162E ASP* 3.8 12.3 - - + -
164E VAL* 3.5 33.4 - - + -
185E PRO* 4.2 4.9 - - + -
196E ARG* 4.3 0.2 - - - -
197E TYR* 2.6 69.6 + - + +
198E ALA 4.1 1.3 - - - -
199E LEU* 3.7 17.3 - - + -
223E PHE* 4.4 2.9 - - + -
302E IOD 4.5 1.6 - - + -
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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