Contacts of the strand formed by residues 181 - 186 (chain A) in PDB entry 4ER3
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 HIS 181 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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158A LEU* 3.8 12.6 - - + +
159A PHE 3.1 22.8 + - - -
179A CYS* 3.2 5.3 - - - +
180A LYS* 1.3 84.5 + - + +
182A HIS* 1.3 92.5 + - - +
183A TYR* 3.4 39.5 + + + +
215A GLU* 3.6 29.1 - - + +
216A TYR* 3.6 5.7 - - - -
217A THR* 2.8 28.0 + - - -
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Residues in contact with HIS 182 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
159A PHE* 3.5 20.9 - + + -
170A VAL* 4.0 10.1 - - + -
173A VAL* 3.4 21.6 + - + +
174A ALA* 3.5 29.3 - - + -
177A THR* 2.8 29.4 + - - -
179A CYS* 3.4 19.6 - - + +
181A HIS* 1.3 78.2 - - - +
183A TYR* 1.3 63.0 + - - +
214A ALA* 3.7 16.1 - - + +
215A GLU 3.1 20.7 + - - +
216A TYR* 3.1 11.5 - - + -
217A THR 3.0 24.9 + - - -
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Residues in contact with TYR 183 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
158A LEU* 4.4 7.3 - - + +
159A PHE* 2.8 21.5 + - - +
160A VAL* 3.3 13.9 - - + -
161A ASP 2.9 24.6 + - - -
170A VAL* 3.5 10.4 - - - +
181A HIS* 3.4 47.8 + + + +
182A HIS* 1.3 75.2 - - - +
184A GLY* 1.3 60.8 + - - +
217A THR* 3.5 11.7 - - - +
219A GLU* 3.4 11.4 - - - -
228A TRP* 4.5 6.3 - - + -
231A ARG* 3.3 26.9 + - - -
407A EDO 3.5 34.9 - - - -
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Residues in contact with GLY 184 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
161A ASP 3.8 2.0 - - - -
164A SER* 3.1 25.8 - - - -
170A VAL* 3.5 9.9 - - - +
183A TYR* 1.3 76.1 - - - +
185A VAL* 1.3 61.1 + - - +
217A THR 3.0 10.4 + - - +
218A LEU* 4.2 3.8 - - - -
219A GLU* 3.1 30.8 + - - +
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Residues in contact with VAL 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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160A VAL* 4.5 1.1 - - + -
161A ASP 3.5 7.5 + - - +
162A LEU* 4.0 10.1 - - + -
163A GLY* 2.9 23.6 + - - +
164A SER* 2.8 23.4 + - - -
184A GLY* 1.3 73.1 - - - +
186A GLU* 1.3 63.5 + - - +
219A GLU* 3.8 6.5 - - + +
220A ARG 4.9 0.9 - - - -
221A GLY* 3.7 26.0 - - - +
222A ASP 4.2 0.9 - - - +
223A PHE* 3.7 28.0 - - + +
228A TRP* 3.6 42.8 - - + +
401A 0QK 3.8 0.8 + - - -
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Residues in contact with GLU 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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164A SER* 3.8 10.0 + - - +
165A GLY 2.8 33.6 + - - +
185A VAL* 1.3 76.2 - - - +
187A LYS* 1.3 57.2 + - - +
188A ALA* 3.0 32.6 + - - +
191A PRO* 4.0 9.2 - - + -
192A ALA* 4.1 8.2 - - + +
219A GLU 3.3 10.6 + - - +
220A ARG* 3.2 10.4 - - - +
221A GLY 2.8 28.4 + - - -
401A 0QK 2.4 56.2 + - - -
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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