Contacts of the strand formed by residues 168 - 174 (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 LEU 168 (chain E).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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126E LEU* 5.2 0.7 - - + -
129E ALA* 3.7 41.3 - - + +
130E ILE* 4.0 18.6 - - + +
133E GLN* 3.0 32.3 + - + +
134E PHE* 3.8 18.0 - - + -
159E LEU* 4.2 6.5 - - + -
160E CYS 3.2 12.3 - - - +
161E VAL* 3.7 14.1 - - + -
166E LYS 3.9 1.1 + - - +
167E GLU* 1.3 75.5 - - - +
169E LEU* 1.3 62.7 + - - +
187E ILE* 3.6 29.8 - - + -
225E TYR* 4.0 12.1 - - + -
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Residues in contact with LEU 169 (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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134E PHE* 4.0 6.0 - - - -
159E LEU* 3.5 6.1 - - - -
160E CYS* 2.9 37.8 + - + +
162E ASP* 3.8 34.5 - - + +
167E GLU* 4.2 2.5 - - + +
168E LEU* 1.3 78.8 - - - +
170E ILE* 1.3 68.7 + - - +
171E ASP* 3.8 27.5 + - + +
184E LEU* 4.1 22.9 - - + -
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Residues in contact with ILE 170 (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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134E PHE* 3.8 25.6 - - + -
140E PHE* 3.9 21.5 - - + -
143E SER* 3.7 17.5 - - - +
144E PHE* 3.6 29.4 - - + +
147E ALA* 3.8 27.8 - - + -
157E THR* 4.1 11.0 - - + -
158E TRP 3.2 10.1 - - - +
159E LEU* 4.6 0.4 - - + -
169E LEU* 1.3 82.4 - - - +
171E ASP* 1.3 63.4 + - - +
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Residues in contact with ASP 171 (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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157E THR* 3.6 0.7 - - - +
158E TRP* 2.7 43.0 + - + +
160E CYS* 4.6 8.7 - - - -
169E LEU* 3.8 15.6 - - + +
170E ILE* 1.3 76.7 - - - +
172E SER* 1.3 68.0 + - - +
173E THR* 3.9 18.7 - - - +
179E PRO* 4.5 8.0 - - - +
182E SER* 5.5 1.2 + - - -
184E LEU* 3.9 22.0 - - + +
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Residues in contact with SER 172 (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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147E ALA* 3.7 18.1 + - - +
151E ASN* 3.7 22.2 - - - -
156E TRP 3.4 4.0 - - - -
157E THR* 2.9 22.9 + - - +
171E ASP* 1.3 81.5 + - - +
173E THR* 1.3 66.2 + - - +
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Residues in contact with THR 173 (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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151E ASN* 3.1 12.9 + - - -
155E GLY* 3.3 0.3 - - - -
156E TRP* 2.9 33.1 + - - +
158E TRP* 3.0 23.3 + - - +
171E ASP* 3.9 13.9 - - - +
172E SER* 1.3 78.4 - - - +
174E SER* 1.3 60.2 + - - +
177E GLY* 2.7 39.5 + - - +
178E CYS 4.0 3.6 - - - +
179E PRO* 4.5 7.4 - - + -
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Residues in contact with SER 174 (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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151E ASN* 4.7 4.7 - - - -
152E PHE 5.1 3.0 + - - -
154E SER 3.6 7.6 + - - -
173E THR* 1.3 74.8 - - - +
175E ASN* 1.3 80.1 + - - +
176E ALA 3.2 0.7 + - - -
177E GLY* 3.0 21.9 + - - -
175F ASN* 4.5 12.5 + - - -
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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