Contacts of the strand formed by residues 182 - 188 (chain A) in PDB entry 1EXB
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 ALA 182 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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140A LEU* 4.3 5.2 - - + -
151A TYR* 4.4 1.1 - - - -
152A VAL* 3.1 18.8 - - + +
155A VAL* 3.8 28.9 - - + -
176A VAL* 3.5 4.1 + - + -
177A ILE* 3.3 34.6 - - + +
180A GLY* 3.3 3.5 - - - -
181A MET* 1.3 83.3 + - - +
183A MET* 1.3 64.1 + - - +
184A TYR 4.0 6.3 - - - +
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Residues in contact with MET 183 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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151A TYR* 3.6 39.7 - - + +
152A VAL 3.2 12.4 + - - +
153A ASP* 3.3 24.7 - - - +
177A ILE* 3.8 15.8 - - - +
180A GLY* 6.6 0.4 - - - -
182A ALA* 1.3 76.5 - - - +
184A TYR* 1.3 88.4 + - + +
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Residues in contact with TYR 184 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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45A SER* 4.4 12.8 - - - -
46A GLY* 4.4 6.5 + - - -
47A LEU* 3.9 46.7 + - + +
153A ASP 2.9 18.3 + - - +
154A VAL* 3.2 6.6 - - + -
155A VAL* 3.0 24.6 + - - +
177A ILE* 3.8 9.6 - - - -
182A ALA* 3.6 2.8 - - - +
183A MET* 1.3 98.4 - - + +
185A TRP* 1.3 63.4 + - - +
208A ILE* 6.0 1.6 - - + -
211A ILE* 3.5 38.1 - - + -
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Residues in contact with TRP 185 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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154A VAL* 4.1 5.4 - - - -
155A VAL* 3.1 24.9 - - + +
169A THR* 4.9 2.7 - - + -
170A VAL* 4.2 22.2 - - + -
173A MET* 3.4 50.1 - - + +
174A THR* 4.8 1.0 + - - -
177A ILE* 3.7 17.7 - - + -
184A TYR* 1.3 77.7 - - - +
186A GLY* 1.3 88.5 + - - +
187A THR* 3.9 13.9 - - + -
190A TRP* 4.4 12.8 - + - -
198A ALA* 4.1 12.1 - - + -
208A ILE* 2.8 29.4 + - + +
209A PRO 3.7 8.4 + - - +
210A PRO* 3.3 31.9 - - + +
211A ILE* 3.0 26.7 + - - +
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Residues in contact with GLY 186 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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154A VAL* 4.1 2.5 - - - +
155A VAL 2.9 8.7 + - - -
156A PHE* 3.4 14.5 - - - -
157A ALA* 3.2 19.1 + - - +
185A TRP* 1.3 90.1 - - - +
187A THR* 1.3 63.4 + - - -
210A PRO* 4.2 4.5 - - - -
212A CYS* 3.1 16.6 - - - -
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Residues in contact with THR 187 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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156A PHE* 3.4 5.3 - - - -
157A ALA 3.7 5.4 - - - +
185A TRP* 3.9 12.3 - - + -
186A GLY* 1.3 80.1 - - - +
188A SER* 1.3 62.4 + - - +
190A TRP* 3.6 43.3 - - + +
195A ILE* 3.8 12.9 - - + +
210A PRO* 4.1 14.1 - - + -
212A CYS 2.7 11.4 + - - -
213A GLU* 2.7 29.4 + - - +
214A GLN 2.8 23.0 + - - -
238A VAL* 5.7 0.2 - - - +
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Residues in contact with SER 188 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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118A LYS* 5.0 0.4 - - - -
156A PHE* 4.7 5.6 - - - -
157A ALA 3.0 17.1 + - - -
158A ASN* 3.7 9.4 + - - -
159A ARG* 3.1 11.6 - - - -
187A THR* 1.3 77.2 - - - +
189A ARG* 1.3 68.5 + - - +
190A TRP* 3.1 15.0 - - - -
213A GLU* 3.5 2.2 - - - -
214A GLN* 3.1 17.3 + - - -
1000A NDP 2.9 36.5 + - - -
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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