Contacts of the strand formed by residues 183 - 191 (chain A) in PDB entry 5EQX
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 SER 183 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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154A PRO* 3.9 10.9 - - - +
181A ALA* 3.2 4.4 - - - +
182A SER* 1.3 87.1 + - - +
184A TYR* 1.3 70.1 + - - +
206A ILE 3.2 14.1 - - - -
207A LYS* 4.3 9.9 - - - -
208A VAL* 4.0 4.0 - - - -
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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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152A GLN* 3.2 30.3 - - + -
154A PRO* 3.3 29.6 - - + -
155A ALA* 4.9 7.5 - - + +
159A MET* 3.6 24.9 - - + +
160A PHE* 3.7 25.6 - + + -
175A SER 5.5 0.2 + - - -
176A LEU* 4.0 12.8 - - + +
177A ASP 5.1 5.6 + - - -
180A GLN* 5.9 0.5 - - - +
181A ALA* 3.3 30.5 - - + +
183A SER* 1.3 75.0 - - - +
185A ARG* 1.3 59.9 + - - +
186A LEU* 3.9 3.8 - - + -
205A ASN* 3.5 2.5 - - - +
206A ILE* 2.6 49.9 + - + +
208A VAL* 3.4 26.7 - - + -
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Residues in contact with ARG 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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151A SER 4.2 0.2 - - - +
152A GLN* 4.1 0.5 - - - -
153A GLU* 2.5 58.6 + - + +
154A PRO* 3.1 28.2 - - + +
184A TYR* 1.3 70.3 - - - +
186A LEU* 1.3 67.7 + - - +
203A GLU* 3.2 29.5 + - - +
204A CYS 3.3 4.7 - - - +
205A ASN* 3.6 13.9 - - - +
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Residues in contact with LEU 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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149A ILE* 3.5 36.1 - - + -
151A SER 3.4 16.8 - - - +
152A GLN* 3.6 26.9 - - + +
160A PHE* 3.5 36.1 - - + -
169A VAL* 5.1 2.5 - - + -
184A TYR* 3.9 3.3 - - + -
185A ARG* 1.3 75.6 - - - +
187A VAL* 1.3 66.3 + - - +
188A VAL* 5.1 0.2 - - + -
203A GLU* 3.6 8.0 - - - +
204A CYS* 2.6 43.6 + - + +
206A ILE* 3.5 22.2 - - + -
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Residues in contact with VAL 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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149A ILE* 4.0 3.2 - - - -
150A VAL* 3.1 39.6 + - + +
151A SER* 3.2 38.0 + - - +
153A GLU* 4.5 13.0 - - - +
186A LEU* 1.3 79.4 - - - +
188A VAL* 1.3 66.7 - - - +
201A GLN* 4.4 15.0 - - + +
202A CYS 3.4 12.1 - - - +
203A GLU* 4.3 4.3 - - + +
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Residues in contact with VAL 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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108A PHE* 3.8 20.2 - - + -
130A LEU* 3.8 11.0 - - + -
147A PHE* 4.1 13.9 - - + -
148A LYS 3.8 4.7 - - - +
149A ILE* 4.4 9.6 - - + -
162A LEU* 3.9 27.1 - - + -
186A LEU* 5.1 0.2 - - + -
187A VAL* 1.3 79.3 - - - +
189A SER* 1.3 63.5 + - - +
190A GLY 4.0 0.7 - - - -
201A GLN* 3.2 9.6 - - - +
202A CYS* 2.7 42.9 + - - -
204A CYS* 3.7 29.4 - - + -
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Residues in contact with SER 189 (chain A).
Click here for Legend to table.
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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146A ALA 3.2 12.3 - - - +
148A LYS* 3.1 35.8 + - - +
150A VAL* 4.6 7.2 - - - -
188A VAL* 1.3 76.7 - - - +
190A GLY* 1.3 61.2 + - - +
191A ALA* 3.7 3.6 + - - +
199A SER* 4.7 8.8 + - - -
200A THR 3.9 5.6 + - - -
201A GLN* 3.9 24.1 + - - +
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Residues in contact with GLY 190 (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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106A PRO* 3.8 4.7 - - - +
108A PHE* 3.5 21.1 - - - -
145A ILE* 4.2 9.0 - - - -
146A ALA 3.4 6.1 - - - -
147A PHE* 4.1 10.8 - - - -
189A SER* 1.3 71.8 - - - +
191A ALA* 1.3 59.6 + - - -
199A SER* 3.3 3.5 - - - -
200A THR* 3.0 36.4 + - - +
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Residues in contact with ALA 191 (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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106A PRO* 4.0 3.4 - - - -
145A ILE* 3.4 2.9 - - - +
146A ALA* 2.6 42.4 + - - +
189A SER* 4.7 5.2 - - - +
190A GLY* 1.3 73.9 - - - -
192A ASP* 1.3 60.6 + - - +
195A GLY* 3.6 27.8 + - - +
197A GLY 4.8 0.9 - - - +
198A LEU 3.1 15.7 - - - +
199A SER* 3.4 11.9 - - - +
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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