Contacts of the strand formed by residues 190 - 199 (chain E) in PDB entry 4MJI
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 TYR 190 (chain E).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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151E GLY 3.3 23.6 + - - -
152E PHE* 2.9 45.4 + - + +
153E TYR* 4.1 15.7 - + - -
154E PRO* 4.8 1.6 - - + -
155E ASP* 3.7 39.9 - - + -
178E PRO* 4.1 13.7 - - + -
179E LEU* 4.1 4.9 - - + -
180E LYS* 4.0 47.2 + - + +
181E GLU* 3.4 2.3 - - - +
186E ASN* 3.8 13.9 + - - +
188E SER 3.3 22.7 - - - -
189E ARG* 1.3 74.5 - - - +
191E ALA* 1.3 59.4 + - - +
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Residues in contact with ALA 191 (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 TYR* 5.8 3.4 - - + -
176D TRP* 4.4 24.0 - - + +
148E LEU* 5.5 4.0 - - + -
149E ALA 3.9 6.1 - - - +
150E THR* 5.5 0.7 - - - -
175E ASP* 5.1 0.9 - - - +
178E PRO* 3.4 1.9 - - - +
179E LEU 3.0 40.7 + - - +
181E GLU* 3.7 21.1 - - + +
190E TYR* 1.3 77.2 - - - +
192E LEU* 1.3 59.0 - - - +
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Residues in contact with LEU 192 (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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41D ARG* 4.4 15.0 - - - +
147E CYS 4.0 0.2 - - - +
148E LEU* 4.8 2.9 - - - +
149E ALA* 3.0 42.2 + - + +
152E PHE* 4.0 6.7 - - + -
157E VAL* 4.2 19.5 - - + -
159E LEU* 3.7 29.7 - - + +
174E THR* 4.0 7.6 - - + -
175E ASP* 3.7 28.0 - - - +
176E PRO 4.8 0.2 - - - +
177E GLN 4.3 0.7 - - - +
178E PRO* 3.6 38.1 - - + -
191E ALA* 1.3 74.7 - - - +
193E SER* 1.3 65.8 + - - +
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Residues in contact with SER 193 (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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156D THR* 3.2 16.3 + - - -
174D VAL* 4.2 9.8 - - - +
146E VAL* 4.8 3.1 - - - -
147E CYS 2.9 15.7 - - - -
148E LEU* 4.2 16.4 - - - -
159E LEU* 4.4 1.3 - - - -
174E THR* 3.1 20.1 - - - +
175E ASP* 3.0 20.9 + - - +
192E LEU* 1.3 72.8 - - - +
194E SER* 1.3 62.0 + - - +
195E ARG* 2.7 23.2 + - - -
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Residues in contact with SER 194 (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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146E VAL* 3.4 1.0 - - - -
147E CYS* 2.6 37.0 + - - -
159E LEU* 3.5 28.5 - - - -
161E TRP* 2.6 31.5 + - - -
173E CYS 2.7 18.8 + - - -
174E THR* 3.4 12.0 + - - +
193E SER* 1.3 79.1 - - - +
195E ARG* 1.3 64.1 + - - +
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Residues in contact with ARG 195 (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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135D LEU* 4.6 3.6 - - - -
156D THR* 3.1 23.4 + - - +
159D CYS* 2.9 23.4 - - - +
161D LEU* 4.2 11.4 - - + -
172D SER* 2.8 45.2 + - - +
174D VAL* 4.1 19.4 - - - +
144E THR* 4.0 14.1 - - + -
145E LEU 3.1 14.4 - - - +
146E VAL* 4.5 3.6 - - + -
161E TRP* 4.2 1.6 - - - -
171E GLY 4.5 0.7 - - - -
172E VAL* 3.3 6.8 - - - +
173E CYS* 2.8 45.8 + - - +
175E ASP* 2.8 14.8 + - - -
193E SER* 2.7 33.9 + - - -
194E SER* 1.3 75.9 - - - +
196E LEU* 1.3 60.8 + - - +
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Residues in contact with LEU 196 (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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161D LEU* 5.3 0.2 - - - -
143E ALA 3.7 1.2 - - - +
144E THR* 3.4 2.5 - - - -
145E LEU* 2.9 44.5 + - + +
161E TRP* 3.8 37.2 - - + -
163E VAL* 4.4 24.5 - - + -
168E VAL* 5.1 3.4 - - + -
170E SER 3.7 14.8 - - - +
171E GLY 3.4 7.4 - - - -
172E VAL* 3.6 27.8 - - + -
195E ARG* 1.3 76.2 - - - +
197E ARG* 1.3 76.8 + - - +
198E VAL* 4.6 8.3 - - + -
210E PHE* 4.5 8.5 - - + -
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Residues in contact with ARG 197 (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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137D THR* 3.4 6.9 + - - -
138D ASP* 2.0 38.0 + - - -
161D LEU* 3.7 22.9 - - + +
163D MET* 3.5 39.0 - - + +
168D PHE* 4.1 4.6 - - - -
170D SER* 3.1 25.4 + - - -
136E GLU* 3.3 19.2 + - - -
140E THR* 3.8 10.9 + - - -
142E LYS* 3.5 38.5 - - - +
143E ALA 3.3 3.6 - - - -
144E THR* 3.1 21.8 + - - +
170E SER 4.9 0.9 - - - +
171E GLY* 3.2 9.1 + - - +
196E LEU* 1.3 80.6 - - - +
198E VAL* 1.3 65.7 + - - +
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Residues in contact with VAL 198 (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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163D MET* 4.5 7.6 - - - -
142E LYS* 3.4 11.5 - - - +
143E ALA* 2.8 46.9 + - + +
145E LEU* 4.8 2.7 - - + -
163E VAL* 5.6 3.1 - - + -
196E LEU* 4.6 18.4 - - + -
197E ARG* 1.3 80.2 - - - +
199E SER* 1.3 72.7 + - - +
202E PHE* 3.9 25.8 - - + -
203E TRP* 3.9 15.0 - - + +
210E PHE* 4.5 12.6 - - + -
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Residues in contact with SER 199 (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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163D MET* 5.2 0.8 - - - -
166D MET* 4.4 26.1 - - - +
141E GLN 4.4 3.1 - - - -
142E LYS* 4.4 6.3 - - - +
143E ALA 4.2 0.7 - - - -
198E VAL* 1.3 83.6 - - - +
200E ALA* 1.3 65.3 + - - +
201E THR* 3.8 19.3 + - - -
202E PHE* 3.0 20.8 + - - +
203E TRP* 3.3 9.4 + - - +
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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