Contacts of the strand formed by residues 177 - 185 (chain E) in PDB entry 3QAZ
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 GLN 177 (chain E).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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146E LEU 4.2 1.4 - - - +
147E SER 4.6 0.2 - - - -
148E PRO* 3.4 28.9 - - + +
175E ASP 5.2 0.4 - - - +
176E THR* 1.3 73.3 - - - +
178E TYR* 1.3 60.4 + - - +
179E GLU* 5.8 0.4 - - - -
203E PHE 4.0 6.1 - - - +
204E ARG* 3.3 32.8 - - + +
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Residues in contact with TYR 178 (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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145E THR* 3.7 22.2 - - + -
146E LEU 3.5 3.4 - - - -
147E SER* 3.6 29.4 - - - -
172E LEU* 3.2 33.0 - - + +
173E THR* 3.2 26.1 + - - -
176E THR* 3.5 35.3 - - + +
177E GLN* 1.3 73.7 - - - +
179E GLU* 1.3 63.4 + - - +
202E ALA* 3.3 4.5 - - - +
203E PHE* 3.0 71.1 + + + +
205E THR* 3.9 4.7 - - + -
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Residues in contact with GLU 179 (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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145E THR* 3.6 3.6 - - - -
146E LEU* 2.7 56.0 + - + +
152E TRP* 3.2 32.1 + - + -
177E GLN 5.8 0.2 - - - -
178E TYR* 1.3 74.3 - - - +
180E PHE* 1.3 60.5 + - - +
200E PRO* 4.0 11.9 - - - +
201E LEU 3.3 5.6 - - - +
202E ALA* 3.4 25.9 - - + +
203E PHE* 4.8 1.6 - - - -
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Residues in contact with PHE 180 (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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112E LEU* 3.8 15.9 - - + -
124E ILE* 3.3 46.7 - - + -
126E TRP* 3.5 29.8 - + - -
143E ALA* 3.4 30.7 - - + -
144E ARG 3.6 10.8 - - - -
145E THR* 5.0 1.3 - - + -
152E TRP* 4.2 1.1 - - - -
158E LEU* 4.7 1.8 - - + -
167E ILE* 3.6 17.3 - - + -
169E LEU* 4.4 16.4 - - + -
179E GLU* 1.3 76.6 - - - +
181E GLN* 1.3 67.0 + - - +
182E VAL* 4.1 4.7 - - + -
198E SER* 4.5 0.7 + - - -
199E GLN 4.4 0.9 - - - +
200E PRO* 3.2 5.7 - - - +
201E LEU* 2.5 45.0 + - + +
203E PHE* 4.5 6.1 - - + -
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Residues in contact with GLN 181 (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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143E ALA* 3.1 7.1 - - - +
144E ARG* 3.1 42.1 + - + -
152E TRP* 3.5 35.7 - - + +
180E PHE* 1.3 80.0 - - - +
182E VAL* 1.3 60.1 + - - +
197E TRP* 3.3 39.2 - - + +
198E SER* 3.1 28.2 + - - +
200E PRO* 4.0 18.3 - - + +
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Residues in contact with VAL 182 (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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109E PRO* 3.4 28.1 - - + +
112E LEU* 3.8 9.0 - - + -
126E TRP* 3.7 44.2 - - + +
141E PHE* 4.3 4.9 - - + -
142E GLU 3.1 16.8 - - - +
143E ALA* 4.2 3.4 - - + -
180E PHE* 4.1 8.5 - - + -
181E GLN* 1.3 76.8 - - - +
183E ARG* 1.3 76.9 + - - +
197E TRP* 3.7 3.1 - - - -
198E SER* 2.9 33.9 + - - +
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Residues in contact with ARG 183 (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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109E PRO* 3.8 5.2 - - - -
141E PHE* 2.9 32.4 - - - -
142E GLU* 2.7 44.1 + - + +
144E ARG* 5.6 0.2 - - - +
157E LEU* 4.4 6.1 - - - +
182E VAL* 1.3 77.0 - - - +
184E VAL* 1.3 62.3 + - - +
194E TRP* 3.3 45.3 - - + +
195E SER* 3.0 29.0 + - - +
196E PRO 4.2 0.9 - - - +
197E TRP* 3.2 50.9 - - + +
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Residues in contact with VAL 184 (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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106E LEU* 3.9 19.7 + - + +
107E MET 3.8 13.0 - - - +
109E PRO* 4.5 6.7 - - + -
128E ILE* 4.3 6.3 - - + -
139E LEU* 3.8 24.2 - - + -
140E GLU 3.5 15.0 - - - +
141E PHE* 3.7 15.9 - - + -
183E ARG* 1.3 77.3 - - - +
185E LYS* 1.3 72.7 + - - +
193E THR 4.2 0.5 - - - +
194E TRP* 3.1 11.3 - - - -
195E SER* 2.7 53.9 + - - +
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Residues in contact with LYS 185 (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 LEU* 3.7 3.7 - - - +
140E GLU* 3.1 47.2 + - - +
184E VAL* 1.3 80.8 - - - +
186E PRO* 1.3 85.8 + - + +
187E LEU* 5.4 5.1 + - - +
192E THR* 3.6 27.6 - - + +
193E THR* 4.0 17.0 - - - +
194E TRP* 3.3 35.1 - - + +
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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