Contacts of the strand formed by residues 171 - 177 (chain E) in PDB entry 3FFC
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 VAL 171 (chain E).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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10E TYR* 4.6 7.7 + - - -
139E PRO* 4.5 1.6 - - + -
166E PHE* 3.6 48.0 - - + -
169E ASP* 3.5 12.0 + - - +
170E HIS* 1.3 83.2 - - - +
172E GLU* 1.3 63.0 + - - +
206E LEU* 4.1 19.9 - - + +
228E VAL* 3.7 21.3 - - + -
229E GLN 3.1 6.5 - - - +
230E PHE* 3.5 22.4 - - + -
231E TYR* 4.9 1.1 - - - -
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Residues in contact with GLU 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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10E TYR* 3.8 20.1 + - - +
171E VAL* 1.3 73.8 - - - +
173E LEU* 1.3 64.1 + - - +
174E SER* 3.9 3.7 + - - -
227E GLN* 3.7 2.9 + - - +
228E VAL* 4.4 0.9 - - - -
229E GLN* 2.9 50.5 + - + +
231E TYR* 2.7 30.9 + - + -
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Residues in contact with LEU 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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161E CYS* 4.3 10.8 - - + -
163E ALA* 4.2 10.5 - - + -
171E VAL 4.1 1.2 - - - -
172E GLU* 1.3 72.8 - - - +
174E SER* 1.3 67.7 + - - +
175E TRP* 4.1 6.1 - - + +
188E THR* 4.2 17.4 + - + +
206E LEU* 4.0 37.6 - - + +
208E SER* 3.4 38.8 - - - +
226E CYS* 3.9 15.5 - - - -
227E GLN 3.3 5.6 - - - +
228E VAL* 4.0 26.6 - - + +
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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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172E GLU 4.8 3.2 + - - -
173E LEU* 1.3 79.9 - - - +
175E TRP* 1.3 63.5 + - - +
176E TRP* 2.9 24.1 + - - -
181E GLU* 3.5 24.7 + - - -
227E GLN* 2.8 44.7 + - - -
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Residues in contact with TRP 175 (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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143E VAL* 4.5 8.1 - - + -
159E LEU* 3.8 34.5 - - + -
160E VAL 4.1 1.6 - - - -
161E CYS* 3.4 33.9 - - + -
173E LEU* 4.1 4.0 - - + +
174E SER* 1.3 77.6 - - - +
176E TRP* 1.3 62.2 + - - +
181E GLU* 3.5 7.1 - - - +
182E VAL* 3.0 45.4 + - + -
186E VAL* 3.4 25.2 - - + +
188E THR* 5.6 1.1 - - - -
208E SER* 2.5 38.1 + - - -
209E ARG 3.8 5.3 - - - -
210E LEU* 3.5 33.4 - - + -
224E PHE* 5.0 2.9 - - + -
225E ARG 3.6 11.4 - - - -
226E CYS* 3.8 25.4 - - + -
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Residues in contact with TRP 176 (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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174E SER* 2.9 29.9 + - - -
175E TRP* 1.3 79.3 - - - +
177E VAL* 1.3 62.8 + - - +
178E ASN 3.9 0.8 + - - -
179E GLY* 3.9 22.8 + - - +
180E LYS 3.4 8.1 - - - +
181E GLU* 3.5 43.2 - - + +
210E LEU* 6.0 0.2 - - - -
223E HIS 3.4 3.1 - - - +
224E PHE* 3.7 0.9 - - - -
225E ARG* 2.6 69.2 + - + +
227E GLN* 3.4 38.2 - - + -
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Residues in contact with VAL 177 (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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176E TRP* 1.3 74.1 - - - +
178E ASN* 1.3 80.8 + - - +
180E LYS* 2.8 27.3 + - - +
182E VAL* 3.7 33.1 - - + +
210E LEU* 3.7 23.8 - - + -
212E VAL* 5.4 2.9 - - + -
216E PHE* 3.4 35.0 - - + -
223E HIS 3.3 8.3 - - - +
224E PHE* 4.0 9.9 - - + -
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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