Contacts of the helix formed by residues 163 - 173 (chain C) in PDB entry 3FZ7
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 GLN 163 (chain C).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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317B PHE* 3.7 18.5 - - - -
162C VAL* 1.3 77.8 - - - +
164C ILE* 1.3 87.3 + - - +
165C CYS* 2.8 44.1 + - - +
166C TRP* 3.0 17.2 + - - +
167C HIS* 3.9 4.7 - - - -
208C THR* 5.0 3.6 + - + +
212C THR* 3.3 27.8 + - + +
213C TYR* 4.2 4.0 - - - -
243C ASP* 4.4 16.5 + - - +
245C ALA* 6.1 5.8 - - + -
276C LYS* 5.9 3.5 - - - +
465C HIS* 3.0 26.9 + - - +
466C THR* 4.7 1.4 - - - -
467C PO4 4.4 12.6 + - - +
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Residues in contact with ILE 164 (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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301B PHE* 4.0 35.2 - - + -
302B ASN 5.8 0.9 - - - +
303B VAL* 3.8 29.8 - - + -
312B THR* 6.1 0.9 - - - +
317B PHE* 3.8 28.0 - - + -
163C GLN* 1.3 94.4 + - - +
165C CYS* 1.3 68.1 + - + +
167C HIS* 2.8 26.8 + - + +
168C LYS* 2.9 20.3 + - + +
213C TYR* 4.6 4.0 + - - -
465C HIS* 4.1 19.5 + - + +
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Residues in contact with CYS 165 (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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126C SER* 4.9 4.0 - - - -
127C SER* 3.9 32.5 - - - +
130C CYS* 3.1 40.1 - - + +
131C MET* 4.4 4.3 - - + +
163C GLN* 2.8 24.3 + - - +
164C ILE* 1.3 75.3 - - + +
166C TRP* 1.3 71.5 + - - +
168C LYS* 3.4 9.9 + - - +
169C PHE* 2.8 28.6 + - - +
243C ASP* 4.1 4.9 - - - -
467C PO4 5.7 0.2 - - - +
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Residues in contact with TRP 166 (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 CYS* 3.5 41.1 - - + -
134C GLY* 4.1 8.3 - - - -
137C MET* 4.2 7.0 - - + -
157C LEU* 4.6 6.7 - - + -
159C CYS* 5.4 0.9 - - + -
162C VAL* 3.8 38.1 - - + -
163C GLN 3.0 10.0 + - - +
165C CYS* 1.3 84.2 - - - +
167C HIS* 1.3 61.4 + - - +
169C PHE* 3.9 30.4 - + + +
170C ALA* 3.0 31.0 + - - +
177C LEU* 4.2 11.3 - - + +
206C VAL* 3.8 28.4 - - + +
241C HIS* 3.5 32.5 - + - -
243C ASP* 2.9 31.1 + - + +
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Residues in contact with HIS 167 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
301B PHE* 3.4 23.0 - - + -
162C VAL* 3.8 18.4 + - + +
163C GLN 3.9 16.6 - - - -
164C ILE* 2.8 17.8 + - + +
166C TRP* 1.3 77.1 - - - +
168C LYS* 1.3 61.7 + - - +
170C ALA* 4.0 2.7 - - - +
171C ARG* 3.2 24.9 + - - +
177C LEU* 3.6 19.4 - - + +
179C GLU* 3.2 30.1 + - - -
213C TYR* 5.2 3.5 + - - -
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Residues in contact with LYS 168 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
301B PHE* 3.8 35.2 - - + -
312B THR* 5.2 7.3 + - - -
314B ALA* 3.2 28.0 + - - +
315B ILE 4.1 2.4 + - - -
316B ASN 3.0 27.9 + - - -
317B PHE* 3.7 21.7 - - - -
127C SER* 4.1 4.9 + - - +
131C MET* 4.3 11.0 - - + -
164C ILE* 2.9 30.0 + - - +
165C CYS* 3.8 7.4 - - - +
167C HIS* 1.3 75.0 - - - +
169C PHE* 1.3 60.7 + - - +
172C TYR* 2.7 52.3 + - + +
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Residues in contact with PHE 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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130C CYS 5.5 0.2 - - - -
131C MET* 4.2 17.0 - - - +
134C GLY* 3.3 44.2 - - - -
135C MET* 3.4 6.1 - - - -
138C LYS* 4.8 3.1 - - + -
157C LEU* 4.4 9.6 - - + -
165C CYS 2.8 21.3 + - - +
166C TRP* 3.9 27.6 - + + +
167C HIS 3.4 0.2 - - - -
168C LYS* 1.3 72.6 - - - +
170C ALA* 1.3 62.6 + - + +
173C TRP* 2.9 75.8 + + + +
175C VAL* 4.1 30.5 - - + -
177C LEU* 6.3 0.2 - - + -
203C ILE* 4.1 11.4 - - + -
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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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166C TRP 3.0 18.0 + - - +
167C HIS* 4.0 4.7 - - - +
169C PHE* 1.3 84.8 - - + +
171C ARG* 1.3 58.5 + - - +
174C ASP* 3.1 8.3 + - - -
175C VAL* 2.8 51.3 + - + +
177C LEU* 3.8 28.0 - - + +
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Residues in contact with ARG 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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139B TRP* 3.4 23.8 - - + +
298B GLU* 2.9 36.1 + - - +
299B LEU* 5.2 0.4 - - + -
300B VAL 4.5 5.3 + - - -
301B PHE* 3.5 38.1 - - + +
167C HIS 3.2 16.6 + - - +
168C LYS 3.8 2.2 - - - +
170C ALA* 1.3 82.5 - - - +
172C TYR* 1.3 75.7 + - + +
173C TRP 3.4 0.7 + - - -
174C ASP* 3.6 7.6 + - - +
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Residues in contact with TYR 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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135B MET* 3.5 32.1 - - + -
139B TRP* 3.7 13.2 - - - -
173B TRP* 2.9 25.9 + - - +
299B LEU* 2.7 48.9 + - + -
301B PHE* 3.7 24.6 - + - -
312B THR 4.6 0.7 + - - -
313B PHE* 3.3 16.0 - + - -
314B ALA 3.9 20.9 + - - -
315B ILE* 4.9 3.1 - - + -
131C MET* 4.8 4.3 - - + -
168C LYS* 2.7 40.3 + - + +
171C ARG* 1.3 78.9 - - + +
173C TRP* 1.3 79.4 + + + +
174C ASP* 3.5 1.8 - - - +
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Residues in contact with TRP 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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172B TYR 2.8 30.4 + - - -
173B TRP* 3.3 39.1 - + - -
315B ILE* 5.1 2.9 - - + -
131C MET* 3.5 44.6 - - + -
135C MET* 3.5 37.4 - - + +
138C LYS* 3.0 34.0 + - + +
139C TRP* 5.1 2.5 - + - -
169C PHE* 2.9 56.2 + + + +
172C TYR* 1.3 99.1 - + + +
174C ASP* 1.3 70.1 + - - +
175C VAL* 3.2 6.8 + - + +
315C ILE* 4.2 5.4 - - + -
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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