Contacts of the helix formed by residues 163 - 173 (chain F) 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 F).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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317A PHE* 3.7 26.7 - - - +
162F VAL* 1.3 81.0 - - - +
164F ILE* 1.3 81.2 + - - +
165F CYS* 3.0 35.6 + - - +
166F TRP* 3.1 17.3 + - - +
167F HIS* 4.0 1.0 - - - -
208F THR* 5.0 5.2 + - + +
212F THR* 3.3 28.1 + - + +
213F TYR* 3.8 5.8 - - - +
243F ASP* 4.4 15.3 + - - +
276F LYS* 5.9 3.0 - - - +
465F HIS* 3.0 27.3 + - + +
466F THR* 4.9 0.6 - - - -
467F PO4 4.2 12.5 + - - -
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Residues in contact with ILE 164 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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301A PHE* 4.0 35.0 - - + -
302A ASN 5.4 0.4 - - - +
303A VAL* 3.7 28.3 - - + -
312A THR* 6.0 0.7 - - - +
317A PHE* 4.0 27.1 - - + -
162F VAL 3.9 0.2 + - - -
163F GLN* 1.3 93.0 + - - +
165F CYS* 1.3 59.1 + - + +
167F HIS* 2.8 32.5 + - + -
168F LYS* 2.9 19.2 + - + +
213F TYR* 4.1 4.0 + - - -
465F HIS* 4.0 18.5 + - + +
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Residues in contact with CYS 165 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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317A PHE* 6.2 0.4 - - + -
126F SER* 4.5 4.7 - - - -
127F SER* 3.5 30.1 - - - +
130F CYS* 3.3 40.6 - - + +
131F MET* 4.4 4.4 - - - +
163F GLN* 3.0 21.0 + - - +
164F ILE* 1.3 77.7 - - - +
166F TRP* 1.3 70.8 + - - +
168F LYS* 3.5 13.3 + - - +
169F PHE* 2.9 27.4 + - - +
243F ASP* 4.4 2.9 - - - -
467F PO4 5.8 0.2 - - - -
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Residues in contact with TRP 166 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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130F CYS* 3.4 48.5 - - + -
134F GLY* 4.1 7.4 - - - -
137F MET* 4.1 15.3 - - + -
157F LEU* 4.8 8.5 - - + -
162F VAL* 3.8 36.8 - - + -
163F GLN 3.1 10.2 + - - +
164F ILE 3.0 0.8 - - - -
165F CYS* 1.3 82.7 - - - +
167F HIS* 1.3 59.5 + - - +
169F PHE* 3.8 23.8 - + + +
170F ALA* 3.1 28.8 + - - +
177F LEU* 4.2 11.0 - - + +
206F VAL* 3.8 27.1 - - + +
241F HIS* 3.5 30.5 - + - -
243F ASP* 2.7 31.3 + - - +
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Residues in contact with HIS 167 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
301A PHE* 3.4 28.9 - + + -
162F VAL* 3.9 17.2 + - + +
163F GLN 4.0 15.0 - - - -
164F ILE* 2.8 19.6 + - + +
166F TRP* 1.3 76.8 - - - +
168F LYS* 1.3 62.8 + - - +
170F ALA* 3.6 3.8 + - - +
171F ARG* 3.1 20.7 + - - +
177F LEU* 3.8 15.7 - - + +
179F GLU* 3.1 29.3 + - - -
213F TYR* 5.3 1.7 + - - -
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Residues in contact with LYS 168 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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301A PHE* 3.8 33.4 - - + -
312A THR* 4.9 11.3 + - - -
314A ALA* 2.8 33.4 + - - +
315A ILE 4.1 3.8 + - - +
316A ASN 3.3 20.4 + - - -
317A PHE* 4.0 19.9 - - + -
127F SER* 4.4 6.7 + - - +
131F MET* 5.0 5.4 - - + -
164F ILE* 2.9 25.6 + - + +
165F CYS* 3.7 15.3 - - - +
167F HIS* 1.3 74.9 - - - +
169F PHE* 1.3 56.8 + - - +
171F ARG 3.4 0.3 + - - -
172F TYR* 2.7 57.4 + - + -
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Residues in contact with PHE 169 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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130F CYS 5.6 0.2 - - - -
131F MET* 4.1 16.3 - - - +
134F GLY* 3.4 43.7 - - - -
135F MET* 3.5 5.6 - - - -
138F LYS* 4.8 2.7 - - + -
157F LEU* 4.9 6.3 - - + -
165F CYS 2.9 18.3 + - - +
166F TRP* 4.0 29.6 - + + +
167F HIS 3.4 0.2 - - - -
168F LYS* 1.3 75.8 - - - +
170F ALA* 1.3 59.8 + - + +
173F TRP* 2.8 75.2 + + + +
175F VAL* 4.0 32.3 - - + -
203F ILE* 4.1 11.9 - - + -
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Residues in contact with ALA 170 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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157F LEU* 6.0 0.2 - - + -
166F TRP 3.1 19.3 + - - +
167F HIS* 4.0 4.0 - - - +
169F PHE* 1.3 82.2 - - + +
171F ARG* 1.3 61.6 + - - +
174F ASP* 3.1 4.5 + - - -
175F VAL* 3.0 49.1 + - + +
177F LEU* 3.8 28.0 - - + +
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Residues in contact with ARG 171 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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139A TRP* 3.3 29.3 - - + +
298A GLU* 3.5 40.7 + - - +
299A LEU* 4.9 0.7 - - + -
300A VAL 5.4 2.8 + - - -
301A PHE* 3.2 38.1 - - + -
167F HIS* 3.1 16.5 + - - +
168F LYS 3.9 2.2 - - - +
170F ALA* 1.3 80.6 - - - +
172F TYR* 1.3 73.2 + - + +
173F TRP 3.4 0.2 + - - -
174F ASP* 3.4 7.7 + - - +
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Residues in contact with TYR 172 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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135A MET* 3.5 35.9 - - + -
139A TRP* 3.5 13.4 - - - -
173A TRP* 3.1 24.1 + - - +
299A LEU* 2.7 48.7 + - + -
301A PHE* 3.6 25.0 - + - -
312A THR 4.6 0.2 + - - -
313A PHE* 3.2 17.9 - + - -
314A ALA 3.8 20.8 + - - -
315A ILE* 4.9 2.5 - - + -
131F MET* 4.8 5.6 - - + -
168F LYS* 2.7 40.7 + - + +
171F ARG* 1.3 77.3 - - + +
173F TRP* 1.3 78.5 + + + +
174F ASP* 4.6 1.6 - - - +
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Residues in contact with TRP 173 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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172A TYR 2.9 29.9 + - - -
173A TRP* 3.3 38.0 - + - -
315A ILE* 5.3 0.9 - - + -
131F MET* 3.7 42.4 - - + -
135F MET* 3.4 38.8 - - + -
138F LYS* 2.7 40.4 + - + +
139F TRP* 5.0 3.8 - + - -
169F PHE* 2.8 59.5 + + + +
170F ALA 3.9 0.2 - - - -
172F TYR* 1.3 87.0 - + + +
174F ASP* 1.3 65.0 + - - +
175F VAL* 3.3 6.5 + - + +
315F ILE* 3.9 9.4 - - + -
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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