Contacts of the helix formed by residues 163 - 173 (chain A) 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 A).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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126A SER* 6.1 0.2 - - - -
127A SER* 5.8 0.2 - - - -
161A PRO 4.0 0.2 + - - -
162A VAL* 1.3 86.0 - - - +
164A ILE* 1.3 79.1 + - - +
165A CYS* 2.9 39.3 + - - +
166A TRP* 3.0 15.3 + - - +
167A HIS* 4.0 1.3 - - - -
208A THR* 4.9 5.5 + - + +
212A THR* 3.6 26.5 + - + +
213A TYR* 4.2 5.4 - - - -
243A ASP* 4.4 14.9 + - - +
276A LYS* 5.6 4.8 - - - +
465A HIS* 2.9 27.9 + - + +
466A THR* 4.7 1.0 - - - -
467A PO4 4.3 13.6 + - - -
317F PHE* 3.8 24.9 - - - +
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Residues in contact with ILE 164 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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163A GLN* 1.3 93.1 + - - +
165A CYS* 1.3 61.3 + - - +
166A TRP 3.1 0.4 - - - -
167A HIS* 2.9 30.2 + - + +
168A LYS* 3.0 22.2 + - - +
213A TYR* 4.6 1.3 + - - -
465A HIS* 3.6 25.2 + - + +
301F PHE* 4.0 35.2 - - + -
302F ASN 5.6 1.3 - - - +
303F VAL* 4.0 25.6 - - + -
317F PHE* 3.9 23.3 - - + -
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Residues in contact with CYS 165 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
126A SER* 4.6 2.5 - - - -
127A SER* 4.0 28.7 - - - +
130A CYS* 2.9 42.0 - - + +
131A MET* 4.3 5.0 - - + +
163A GLN* 2.9 18.9 + - - +
164A ILE* 1.3 81.4 - - + +
166A TRP* 1.3 73.1 + - - +
168A LYS* 3.6 11.8 + - - +
169A PHE* 2.9 27.0 + - - +
243A ASP* 4.2 3.4 - - - -
467A PO4 5.7 0.2 - - - +
317F PHE* 6.3 0.2 - - + -
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Residues in contact with TRP 166 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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130A CYS* 3.5 40.6 - - + -
134A GLY* 4.2 9.4 - - - -
137A MET* 4.2 11.7 - - + -
157A LEU* 4.9 6.5 - - + -
159A CYS* 5.4 0.2 - - - -
162A VAL* 3.7 42.0 - - + -
163A GLN 3.0 7.0 + - - -
165A CYS* 1.3 84.2 - - - +
167A HIS* 1.3 66.9 + - - +
169A PHE* 3.7 23.4 - + + +
170A ALA* 3.0 25.5 + - - +
177A LEU* 4.1 12.5 - - + +
206A VAL* 3.8 26.9 - - + +
241A HIS* 3.5 34.8 - + - -
243A ASP* 2.7 31.5 + - + +
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Residues in contact with HIS 167 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
162A VAL* 3.9 17.0 + - + +
163A GLN 4.0 14.1 - - - -
164A ILE* 2.9 19.8 + - + +
166A TRP* 1.3 74.4 - - - +
168A LYS* 1.3 65.4 + - - +
170A ALA* 3.3 4.3 + - - +
171A ARG* 3.0 24.4 + - - +
177A LEU* 3.4 19.4 - - + +
179A GLU* 3.2 28.8 + - - -
213A TYR* 5.4 2.4 + - - -
301F PHE* 3.8 22.3 - + + -
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Residues in contact with LYS 168 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
127A SER* 4.2 2.2 + - - +
131A MET* 4.3 12.3 - - + -
164A ILE* 3.0 29.0 + - + +
165A CYS* 3.8 11.0 - - - +
167A HIS* 1.3 75.3 - - - +
169A PHE* 1.3 57.5 + - - +
171A ARG* 4.4 0.2 - - - -
172A TYR* 2.8 48.8 + - + +
301F PHE* 3.6 37.9 - - + -
312F THR* 5.0 8.2 + - - -
314F ALA* 2.8 33.7 + - - +
315F ILE 3.9 3.0 + - - -
316F ASN 3.1 21.6 + - - -
317F PHE* 4.1 19.1 - - - -
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Residues in contact with PHE 169 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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130A CYS 5.6 0.2 - - - -
131A MET* 4.1 17.7 - - - +
134A GLY* 3.4 43.7 - - - -
135A MET* 3.5 5.6 - - - -
138A LYS* 4.8 3.4 - - + -
157A LEU* 4.9 8.3 - - + -
165A CYS 2.9 19.0 + - - +
166A TRP* 3.7 28.9 - + + +
167A HIS 3.2 0.2 - - - -
168A LYS* 1.3 75.6 - - - +
170A ALA* 1.3 68.3 + - + +
173A TRP* 3.0 64.1 + + + +
175A VAL* 4.0 30.1 - - + -
203A ILE* 4.2 12.8 - - + -
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Residues in contact with ALA 170 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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157A LEU* 6.0 0.4 - - + -
166A TRP 3.0 16.9 + - - +
167A HIS* 3.7 4.5 - - - +
169A PHE* 1.3 83.3 - - + +
171A ARG* 1.3 58.7 + - - +
174A ASP* 3.0 11.3 + - - -
175A VAL* 2.9 49.2 + - + +
177A LEU* 3.8 27.1 - - + +
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Residues in contact with ARG 171 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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167A HIS 3.0 15.3 + - - +
168A LYS 3.8 2.5 - - - +
170A ALA* 1.3 80.2 - - - +
172A TYR* 1.3 78.7 + - + +
173A TRP 3.4 0.5 + - - -
174A ASP* 3.5 6.1 + - - +
139F TRP* 3.4 30.5 - - + +
298F GLU* 3.1 43.2 + - - +
299F LEU* 5.1 0.2 - - + -
300F VAL 5.0 3.4 + - - -
301F PHE* 3.3 36.8 - - + -
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Residues in contact with TYR 172 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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131A MET* 4.9 4.5 - - + -
168A LYS* 2.8 39.3 + - + +
171A ARG* 1.3 82.1 - - + +
173A TRP* 1.3 78.5 + + + +
174A ASP* 3.5 1.3 - - - +
135F MET* 3.6 25.4 - - + -
138F LYS* 5.8 0.2 + - - -
139F TRP* 3.8 12.6 - - - -
173F TRP* 2.9 26.3 + - - -
299F LEU* 2.5 54.7 + - + -
301F PHE* 3.5 24.2 - + - -
312F THR 4.7 0.2 + - - -
313F PHE* 3.2 21.9 - + - -
314F ALA 3.8 19.3 + - - -
315F ILE* 5.0 2.0 - - + -
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Residues in contact with TRP 173 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
131A MET* 3.7 43.5 - - + -
135A MET* 3.3 37.9 - - + -
138A LYS* 3.0 33.5 + - + +
139A TRP* 4.9 3.8 - + - -
169A PHE* 3.0 49.2 + + + +
170A ALA 3.7 0.2 - - - -
172A TYR* 1.3 101.3 - + + +
174A ASP* 1.3 70.7 + - - +
175A VAL* 3.3 5.7 + - + +
315A ILE* 4.4 5.2 - - + -
172F TYR 3.1 29.4 + - - -
173F TRP* 3.3 39.2 - + - -
315F ILE* 5.1 3.1 - - + -
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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