Contacts of the strand formed by residues 166 - 173 (chain C) in PDB entry 3F78
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 TYR 166 (chain C).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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128C GLY 5.0 1.8 - - - -
130C VAL* 3.4 40.1 - - + +
132C LEU* 5.3 1.6 - - + -
161C LEU* 3.4 46.4 - - + +
163C ASN* 3.0 34.4 + - - +
164C THR* 4.3 3.7 - - - +
165C SER* 1.3 88.9 - - - +
167C GLN* 1.3 63.5 + - - +
168C PHE* 3.8 24.7 - + + -
186C TYR* 3.7 14.0 + - - -
190C LYS* 5.7 1.2 - - - -
306C ILE* 2.6 30.9 + - + -
307C TYR* 3.3 16.1 - - - +
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Residues in contact with GLN 167 (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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130C VAL 3.0 5.8 + - - +
131C ASP* 3.1 19.6 - - - +
132C LEU* 2.9 26.0 + - - +
164C THR 5.3 1.1 - - - +
166C TYR* 1.3 75.1 - - - +
168C PHE* 1.3 68.2 + - - +
183C PHE* 3.7 17.7 - - + +
186C TYR* 3.9 9.0 - - + -
187C VAL* 3.4 31.3 - - + +
225C GLY 3.0 25.4 + - - +
227C ARG* 3.4 34.4 + - - +
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Residues in contact with PHE 168 (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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132C LEU* 3.2 30.1 - - + -
134C PHE* 3.5 31.4 - + + -
157C VAL* 4.3 7.0 - - + -
158C MET* 3.7 39.5 - - + -
161C LEU* 3.8 34.3 - - + -
166C TYR* 3.8 22.7 - + + -
167C GLN* 1.3 79.3 - - - +
169C ALA* 1.3 59.9 + - - +
181C PHE* 3.3 5.5 - - + -
182C ASP 3.7 0.2 - - - +
183C PHE* 3.4 13.6 - - - -
186C TYR* 3.2 51.4 - + + +
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Residues in contact with ALA 169 (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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132C LEU 3.0 5.1 + - - -
133C VAL* 3.3 5.4 - - + -
134C PHE* 2.9 31.0 + - - -
168C PHE* 1.3 74.5 - - - +
170C ALA* 1.3 61.8 + - - +
181C PHE* 3.4 21.8 - - - +
182C ASP* 3.9 9.4 - - - -
183C PHE* 3.6 13.0 - - + +
219C VAL* 3.8 27.8 - - + -
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Residues in contact with ALA 170 (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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134C PHE* 3.3 16.8 - - + +
136C PHE* 4.2 15.5 - - + -
154C MET* 4.8 1.6 - - - -
169C ALA* 1.3 75.6 - - - +
171C VAL* 1.3 61.4 + - - +
179C THR* 3.7 0.5 - - - -
180C GLU* 2.8 31.7 + - + -
181C PHE* 3.0 39.7 + - + +
196C LEU* 4.2 7.4 - - + -
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Residues in contact with VAL 171 (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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133C VAL* 4.2 6.7 - - + -
134C PHE 2.8 9.3 + - - +
135C LEU* 3.3 26.3 - - + +
136C PHE* 2.9 30.1 + - - -
170C ALA* 1.3 79.8 - - - +
172C GLN* 1.3 69.2 + - - +
177C TYR* 4.4 3.1 - - + -
178C LYS 3.3 12.1 - - - +
179C THR* 4.1 9.2 - - + +
214C TYR* 3.8 22.9 - - + -
215C VAL* 4.0 8.7 - - + -
219C VAL* 3.6 32.3 - - + -
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Residues in contact with GLN 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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136C PHE* 3.3 28.2 - - + +
138C GLY* 3.4 17.4 - - - -
147C PHE* 3.7 8.5 - - - -
171C VAL* 1.3 74.3 - - - +
173C PHE* 1.3 63.5 + - - +
177C TYR* 3.4 3.5 - - - -
178C LYS* 2.9 33.0 + - - +
180C GLU* 3.0 26.9 + - - +
199C VAL* 3.7 6.9 - - - +
200C LYS 2.9 21.4 + - - +
201C HIS* 3.6 3.1 - - - -
202C MET* 2.9 49.8 + - + +
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Residues in contact with PHE 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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135C LEU* 3.7 32.1 - - + -
136C PHE 2.9 17.4 + - - -
137C ASP* 3.4 32.1 - - + +
138C GLY 2.8 27.6 + - - -
139C SER 4.4 0.2 + - - -
172C GLN* 1.3 75.6 - - - +
174C SER* 1.3 62.3 + - - +
176C SER 3.4 4.3 - - - -
177C TYR* 3.9 9.4 - - + -
202C MET* 4.0 1.8 - - - -
206C THR* 3.8 16.6 - - + -
207C ASN 3.9 13.0 - - - -
208C THR* 3.5 37.7 - - + -
211C ALA* 3.4 27.6 - - + -
236C ILE* 4.6 3.8 - - + -
237C ILE 4.1 1.8 - - - -
238C THR* 4.3 8.1 - - - -
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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