Contacts of the strand formed by residues 176 - 185 (chain D) in PDB entry 4MXW
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 GLU 176 (chain D).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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110B GLN* 2.4 36.4 + - - +
233B ARG* 5.3 2.0 - - - +
162D SER* 3.3 4.0 - - - -
163D LEU* 2.7 51.9 + - + +
170D TYR* 3.2 41.3 - - + +
175D PRO* 1.3 73.8 - - - +
177D LEU* 1.3 66.4 + - - +
178D LEU* 3.6 8.0 + - + +
217D GLU* 5.4 0.2 - - - +
95R LEU* 4.8 10.2 - - - +
99R GLN* 5.0 13.4 - - - +
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Residues in contact with LEU 177 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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110B GLN* 4.7 5.0 + - - +
232B ALA 5.1 0.7 - - - +
233B ARG* 3.8 48.7 + - + +
234B GLY 5.3 0.2 - - - +
160D ARG* 3.6 36.3 - - + +
161D SER 3.9 0.2 - - - +
162D SER* 3.5 20.2 - - - +
175D PRO 4.2 1.8 + - - -
176D GLU* 1.3 79.2 - - - +
178D LEU* 1.3 69.0 + - - +
179D LEU 3.8 7.0 - - - +
180D GLU* 3.4 30.1 - - + +
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Residues in contact with LEU 178 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
110B GLN* 3.2 41.2 - - - +
234B GLY* 3.3 21.9 + - - -
135D LEU* 3.9 25.8 - - + -
161D SER* 3.2 11.1 + - - +
162D SER 4.1 4.5 - - - -
163D LEU* 3.8 39.0 - - + +
176D GLU* 3.8 12.1 - - + +
177D LEU* 1.3 77.0 - - - +
179D LEU* 1.3 78.6 + - + +
211D VAL* 3.9 19.5 - - + -
219D VAL* 4.3 3.8 - - + -
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Residues in contact with LEU 179 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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91B HIS* 5.0 6.7 - - + +
234B GLY* 4.0 1.8 - - - -
237B PHE* 3.5 37.9 - - + -
135D LEU* 3.7 20.4 - - + +
160D ARG* 3.1 6.9 - - - +
161D SER* 2.9 32.6 + - - +
177D LEU* 3.8 1.1 - - - +
178D LEU* 1.3 95.1 - - + +
180D GLU* 1.3 61.0 + - - +
207D PHE* 3.4 29.8 - - + -
208D GLY 3.8 0.2 - - - -
209D GLY* 3.5 35.7 - - - +
211D VAL* 4.9 5.8 - - + -
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Residues in contact with GLU 180 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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138B LEU* 4.1 6.4 - - - +
232B ALA* 3.7 14.2 - - - +
234B GLY 2.5 30.7 + - - +
235B LYS* 3.4 38.7 + - - +
237B PHE* 5.6 0.4 - - - -
158D THR* 5.0 9.0 - - - +
159D LEU 3.2 17.7 - - - +
160D ARG* 3.8 18.4 + - + -
177D LEU* 3.4 29.1 - - + +
179D LEU* 1.3 78.3 - - - +
181D GLY* 1.3 60.8 + - - +
207D PHE* 4.1 8.0 - - - -
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Residues in contact with GLY 181 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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138B LEU* 5.3 2.7 - - - -
204B SER* 3.5 16.8 - - - -
235B LYS* 4.5 1.8 - - - -
158D THR* 4.0 0.9 - - - -
159D LEU* 2.9 31.4 + - - +
180D GLU* 1.3 78.8 - - - +
182D ALA* 1.3 62.2 + - - +
205D VAL* 4.1 9.6 - - - -
206D GLY 5.8 0.2 - - - -
207D PHE* 3.7 15.0 - - - -
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Residues in contact with ALA 182 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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202B TYR* 4.3 19.3 - - + -
203B THR* 3.1 28.9 + - - -
204B SER* 3.2 10.3 + - - -
235B LYS* 4.5 13.2 - - - +
157D VAL 3.6 4.7 - - - -
158D THR* 3.1 33.7 - - + +
181D GLY* 1.3 72.6 - - - -
183D GLU* 1.3 58.3 + - - +
184D THR 4.3 0.4 - - - -
205D VAL* 4.2 7.4 - - - +
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Residues in contact with GLU 183 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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153A LYS* 3.9 16.9 + - - -
183B GLU* 3.5 18.9 - - - +
202B TYR 3.2 5.6 - - - +
203B THR* 3.4 22.3 + - - +
204B SER 5.2 2.7 - - - +
157D VAL* 2.5 47.5 + - + +
182D ALA* 1.3 75.1 - - - +
184D THR* 1.3 65.0 + - - +
185D VAL* 4.0 18.6 - - + +
203D THR* 4.4 9.2 - - - +
204D SER 4.2 7.6 - - - +
205D VAL* 3.7 26.8 - - + +
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Residues in contact with THR 184 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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201B TRP* 3.2 13.9 - - - +
202B TYR* 2.5 65.4 + - + +
154D GLY 5.8 0.9 - - - -
155D ARG 3.1 7.2 - - - +
156D SER* 3.4 31.2 - - - -
158D THR* 5.9 0.4 - - + -
183D GLU* 1.3 76.2 - - - +
185D VAL* 1.3 66.2 + - - +
186D THR* 5.9 2.2 - - - -
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Residues in contact with VAL 185 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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153A LYS* 4.8 3.1 - - - +
154D GLY* 4.3 0.2 - - - -
155D ARG* 2.9 34.8 + - + +
157D VAL* 5.4 3.3 - - + +
183D GLU* 3.9 22.7 + - + +
184D THR* 1.3 80.2 - - - +
186D THR* 1.3 63.6 + - - +
187D PRO* 3.5 30.8 - - + +
201D TRP* 5.0 12.3 - - + -
203D THR* 4.2 23.3 - - + +
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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