Contacts of the strand formed by residues 185 - 191 (chain E) in PDB entry 4F2N
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 ARG 185 (chain E).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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23E TYR* 3.5 66.6 - - + +
25E THR* 4.8 0.2 - - - -
160E CYS* 4.2 2.0 - - - -
161E VAL* 2.8 43.4 + - - +
163E PRO* 3.6 32.1 - - + +
183E GLY 5.0 0.4 - - - +
184E LEU* 1.3 76.2 - - - +
186E PRO* 1.3 69.7 - - - +
187E ILE* 4.0 1.6 - - - +
227E ARG 4.5 1.6 + - - -
228E ALA* 2.9 52.2 + - + -
230E LYS 5.2 5.1 + - - -
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Residues in contact with PRO 186 (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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23E TYR* 5.2 0.3 + - - -
25E THR* 3.5 22.6 + - + +
106E PHE* 4.3 16.4 - - + -
110E PHE* 3.5 14.6 - - + -
158E TRP* 3.5 39.0 - - + -
159E LEU 3.8 5.8 - - - +
160E CYS* 4.0 7.2 - - - -
179E PRO* 4.6 10.1 - - + -
180E LEU* 5.1 5.8 - - + +
184E LEU 3.7 9.4 - - - +
185E ARG* 1.3 86.5 - - - +
187E ILE* 1.3 62.8 + - - +
224E MET* 3.8 15.1 - - - +
228E ALA* 5.4 0.2 - - - +
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Residues in contact with ILE 187 (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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110E PHE* 3.4 13.5 - - - -
114E CYS* 4.2 1.4 - - - -
126E LEU* 4.3 5.2 - - + -
159E LEU* 2.9 36.2 + - + +
160E CYS 4.7 0.2 - - - +
161E VAL* 4.0 15.5 - - + -
168E LEU* 3.6 27.4 - - + -
185E ARG 3.6 2.9 + - - +
186E PRO* 1.3 77.9 - - - +
188E PHE* 1.3 63.7 + - - +
220E PHE* 4.5 0.3 - - - -
221E VAL* 3.4 37.1 - - + +
224E MET* 3.7 19.5 - - + +
225E TYR* 3.6 37.5 - - + +
228E ALA* 4.4 2.0 - - + -
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Residues in contact with PHE 188 (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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110E PHE* 3.6 7.5 - - - -
114E CYS* 3.8 22.0 - - + -
115E LEU* 4.9 2.5 - - + -
140E PHE* 5.1 2.7 - + - -
144E PHE* 3.5 38.1 - + - -
158E TRP* 3.4 6.6 - - - -
159E LEU* 2.9 41.3 + - + +
187E ILE* 1.3 81.6 - - - +
189E THR* 1.3 87.2 + - - +
190E ALA 4.4 0.2 - - - -
212E LEU* 4.4 13.5 - - + -
213E TRP* 3.8 19.7 - + - -
216E VAL* 3.7 37.5 - - + -
218E TRP* 5.0 3.1 - + + -
221E VAL* 3.8 22.4 - - + -
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Residues in contact with THR 189 (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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107E ASN 4.2 1.1 - - - +
110E PHE* 3.8 18.8 - - + -
111E PHE* 3.4 38.6 - - + +
114E CYS* 3.8 2.7 - - - +
156E TRP* 3.4 23.7 - - + +
157E THR 3.2 11.8 + - - -
158E TRP* 3.3 31.1 - - + -
188E PHE* 1.3 98.3 - - - +
190E ALA* 1.3 61.3 + - - +
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Residues in contact with ALA 190 (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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111E PHE* 3.9 6.1 - - - -
144E PHE* 3.6 28.2 - - + -
156E TRP* 3.5 2.3 - - - -
157E THR* 2.8 32.8 + - - -
189E THR* 1.3 77.0 - - - +
191E ASP* 1.3 63.7 + - - +
192E VAL* 3.4 3.0 + - + +
209E LEU* 3.8 14.1 - - + -
212E LEU* 3.7 21.3 - - + -
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Residues in contact with ASP 191 (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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58E HIS* 2.8 30.5 + - - -
108E HIS* 3.4 9.2 + - - -
111E PHE* 3.6 19.7 - - + -
155E GLY 3.6 0.9 - - - +
156E TRP* 3.4 31.8 - - + -
190E ALA* 1.3 71.2 - - - +
192E VAL* 1.3 60.1 + - - +
193E TRP* 3.1 36.4 + - - +
195E HIS* 3.6 3.8 + - - -
196E ALA* 3.5 16.6 - - + +
208E TYR* 2.7 32.4 + - - -
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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