Contacts of the strand formed by residues 171 - 179 (chain C) in PDB entry 3FUX
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 ALA 171 (chain C).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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131C LEU* 4.0 17.9 - - + -
167C VAL* 2.8 23.8 + - + +
168C ALA* 3.6 17.6 + - - +
170C HIS* 1.3 81.9 - - - +
172C VAL* 1.3 68.6 + - - +
173C ALA* 3.8 1.9 + - - +
197C LEU* 4.1 6.5 - - + -
198C THR 3.4 22.0 - - - +
199C PRO* 3.8 3.4 - - + -
200C THR* 4.3 5.8 - - - +
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Residues in contact with VAL 172 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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171C ALA* 1.3 73.5 - - - +
173C ALA* 1.3 68.3 + - - +
174C GLU* 4.7 12.3 - - + +
196C ARG 3.7 1.3 - - - +
197C LEU* 3.2 5.4 - - - -
198C THR* 2.8 46.8 + - + +
200C THR* 4.6 9.6 - - + +
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Residues in contact with ALA 173 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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151C MET 3.5 24.9 - - - +
152C THR* 3.9 13.7 - - + +
167C VAL* 3.7 8.5 - - + -
168C ALA* 6.3 0.4 - - - -
171C ALA 3.8 1.9 + - - +
172C VAL* 1.3 77.2 - - - +
174C GLU* 1.3 67.3 + - - +
196C ARG 3.7 3.6 - - - -
197C LEU* 3.6 18.2 - - + -
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Residues in contact with GLU 174 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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152C THR* 4.0 5.6 - - - -
172C VAL* 4.7 13.1 - - + +
173C ALA* 1.3 80.2 - - - +
175C ARG* 1.3 61.1 + - - +
176C LEU* 3.6 17.4 + - + +
195C VAL* 3.3 6.2 - - - +
196C ARG* 2.7 83.4 + - + +
197C LEU* 4.7 0.4 - - - +
198C THR* 4.5 6.4 + - - -
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Residues in contact with ARG 175 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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145C LYS* 3.1 26.6 - - - +
148C ALA* 3.9 17.9 - - + -
149C GLU* 4.8 9.0 - - - +
152C THR* 3.9 24.2 - - + +
174C GLU* 1.3 71.1 - - - +
176C LEU* 1.3 63.6 + - - +
177C PHE* 4.7 2.9 - - - +
178C ASP* 2.7 39.0 + - - +
193C SER* 3.5 24.2 + - - -
194C LEU 3.7 3.8 - - - -
195C VAL* 4.6 2.2 - - + +
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Residues in contact with LEU 176 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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42C ALA* 3.6 31.4 - - + -
174C GLU* 3.6 33.2 - - + +
175C ARG* 1.3 75.4 - - - +
177C PHE* 1.3 76.6 + - + +
194C LEU* 2.8 26.0 + - + +
196C ARG* 3.7 38.4 - - + +
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Residues in contact with PHE 177 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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35C HIS* 3.9 12.3 - + - -
38C ARG* 3.4 61.9 - - + +
39C ILE* 4.5 6.5 - - + -
42C ALA* 5.5 0.2 - - + -
175C ARG* 3.7 1.9 - - - -
176C LEU* 1.3 89.4 - - + +
178C ASP* 1.3 71.7 + - - +
179C LEU* 3.6 31.0 - - + -
193C SER* 3.2 5.0 - - - -
194C LEU* 2.9 59.7 + - + -
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Residues in contact with ASP 178 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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35C HIS* 4.7 3.3 + - - -
38C ARG* 5.5 0.9 + - - -
145C LYS* 4.0 13.3 + - + +
175C ARG* 2.7 36.4 + - - -
177C PHE* 1.3 86.4 - - - +
179C LEU* 1.3 63.8 + - - +
180C PRO* 4.3 3.1 - - - +
191C TRP* 3.8 21.6 - - + -
192C SER 3.3 7.6 - - - +
193C SER* 2.8 26.4 + - - -
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Residues in contact with LEU 179 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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30C LEU* 4.6 2.9 - - + -
35C HIS* 3.5 37.9 - - + -
39C ILE* 5.0 2.7 - - + -
142C LEU* 3.4 44.0 - - + -
177C PHE* 3.6 15.9 - - + -
178C ASP* 1.3 78.3 - - - +
180C PRO* 1.3 70.9 - - + +
183C ALA* 4.2 15.0 - - + -
184C PHE* 4.3 10.0 - - + -
191C TRP* 3.3 7.9 - - - -
192C SER* 2.8 36.2 + - - +
193C SER* 3.9 4.0 - - - -
194C LEU 3.7 12.6 - - - +
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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