Contacts of the helix formed by residues 158 - 172 (chain A) in PDB entry 5Z66
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 158 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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61A LYS* 3.9 0.7 - - - -
148A VAL 5.1 0.4 + - - -
150A PRO* 3.5 14.9 - - + +
154A PHE* 3.3 28.4 - + + -
156A GLU* 2.6 58.1 + - + -
157A VAL* 1.3 76.1 - - - +
159A TYR* 1.3 64.1 + - - +
161A ASP* 3.5 24.8 - - + +
162A SER* 2.7 30.4 + - - -
185A PHE* 3.7 3.8 - - - -
197A ASN* 3.4 25.4 - - - -
203A TYR* 2.8 27.3 + + - -
208A GLN* 4.3 0.2 - - - +
609A VDM 3.5 40.2 - - + -
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Residues in contact with TYR 159 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
158A TYR* 1.3 76.9 - - - +
160A TRP* 1.3 67.7 + - - +
162A SER 3.1 6.8 + - - -
185A PHE* 4.3 7.6 - + - -
195A ILE* 3.6 39.0 - - + -
196A PRO 4.1 6.2 + - - +
197A ASN 3.2 8.3 + - - -
207A SER* 3.5 22.9 - - - -
208A GLN* 3.2 25.7 + - + +
209A PRO 3.8 3.1 - - - -
210A PRO* 3.2 12.1 - - + +
211A PHE* 3.1 14.4 + - - -
212A PHE* 2.9 35.8 + - - +
215A MET* 3.3 22.2 - - + +
237A GLU* 2.6 30.8 + - - -
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Residues in contact with TRP 160 (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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159A TYR* 1.3 75.4 - - - +
161A ASP* 1.3 76.0 + - - +
162A SER 3.1 0.7 + - - -
163A TYR* 3.2 11.7 + - - +
164A PHE* 3.2 24.5 - + - -
208A GLN* 3.1 40.0 + - - +
209A PRO* 3.6 43.3 - - + +
211A PHE* 3.8 24.5 - + + -
310A GLY* 3.8 14.9 - - - -
311A TRP* 4.0 16.6 - + - -
336A ASP* 6.0 0.7 - - - -
407A PHE* 4.9 14.1 - + - -
447A TRP* 3.4 39.9 - + - -
455A PRO* 4.4 14.8 - - + -
456A LEU* 4.9 4.0 - - + -
520A TRP* 3.4 9.9 - + - -
609A VDM 3.0 25.4 + - - -
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Residues in contact with ASP 161 (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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150A PRO* 3.7 15.0 - - + +
158A TYR* 3.5 17.7 - - + +
159A TYR 3.3 0.2 - - - -
160A TRP* 1.3 79.8 - - - +
162A SER* 1.3 59.9 + - - +
164A PHE* 3.2 5.7 + - - +
165A THR* 3.0 33.0 + - - +
518A PHE* 4.2 1.4 - - - -
520A TRP* 3.6 34.0 + - + +
609A VDM 2.5 53.2 + - - -
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Residues in contact with SER 162 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
148A VAL 4.4 3.3 + - - -
157A VAL* 3.4 19.4 - - - +
158A TYR 2.7 23.5 + - - -
159A TYR 3.1 6.4 + - - -
160A TRP 3.1 1.4 - - - -
161A ASP* 1.3 75.5 - - - +
163A TYR* 1.3 61.1 + - - +
165A THR* 3.7 8.4 - - - -
166A MET* 2.8 36.3 + - - +
181A MET* 4.0 12.3 - - - +
185A PHE* 3.6 20.4 - - - -
215A MET* 3.9 2.2 - - - -
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Residues in contact with TYR 163 (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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160A TRP 3.2 11.4 + - - +
162A SER* 1.3 77.5 - - - +
164A PHE* 1.3 70.1 + + + +
166A MET* 3.2 6.0 + - - +
167A LEU* 3.0 58.5 + - + +
211A PHE* 3.5 37.7 - + + -
214A MET* 3.5 37.0 + - + +
215A MET* 3.6 33.1 - - + +
218A LEU* 4.5 13.3 - - + +
410A TYR* 3.4 25.7 + - - -
458A TRP* 5.0 1.7 + - - -
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Residues in contact with PHE 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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160A TRP* 3.2 28.5 - + - -
161A ASP 3.2 0.6 + - - +
163A TYR* 1.3 77.7 - + - +
165A THR* 1.3 66.6 + - - +
167A LEU* 3.3 33.7 + - + +
211A PHE* 3.7 37.7 - + - -
410A TYR* 4.8 0.4 - - - -
455A PRO* 3.5 49.8 - - + -
458A TRP* 3.9 15.7 - + - -
459A VAL* 4.3 7.4 - - + -
520A TRP* 3.6 26.9 - + + -
523A GLY* 3.4 16.9 - - - -
524A VAL* 4.0 12.8 - - + -
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Residues in contact with THR 165 (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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123A TRP* 3.6 17.5 - - + -
148A VAL* 3.5 38.4 + - + +
149A VAL 5.5 0.7 + - - -
150A PRO* 5.9 0.3 - - - +
161A ASP* 3.0 20.8 + - - +
162A SER* 3.7 8.6 - - - -
164A PHE* 1.3 76.5 - - - +
166A MET* 1.3 62.5 + - - +
168A GLY* 3.1 4.5 + - - -
169A LEU* 3.0 27.2 + - + +
181A MET* 4.7 2.2 - - + -
519A GLY* 3.5 28.0 - - - +
520A TRP* 3.8 1.1 + - - +
523A GLY* 4.6 1.6 - - - -
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Residues in contact with MET 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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162A SER 2.8 26.8 + - - +
163A TYR* 3.4 5.8 - - - +
165A THR* 1.3 69.6 - - - +
167A LEU* 1.3 60.4 + - - +
169A LEU* 4.2 7.2 - - - -
170A ALA* 2.8 32.7 + - - +
178A ILE* 3.5 27.1 - - + +
181A MET* 3.5 40.4 - - + -
182A VAL* 3.7 22.0 - - + +
185A PHE* 4.2 5.4 - - + -
215A MET* 3.6 43.5 - - - -
218A LEU* 3.7 15.7 - - + +
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Residues in contact with LEU 167 (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 TYR* 3.0 47.6 + - + +
164A PHE* 3.4 21.3 - - + +
165A THR 3.2 0.4 - - - -
166A MET* 1.3 77.0 - - - +
168A GLY* 1.3 56.5 + - - +
170A ALA* 3.7 4.0 - - - +
171A GLU* 3.0 26.3 + - - +
218A LEU* 4.4 17.9 - - + -
458A TRP* 3.4 43.3 - - + +
523A GLY 4.7 0.9 - - - +
524A VAL* 5.0 3.4 - - + -
527A LYS* 3.6 35.0 + - + +
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Residues in contact with GLY 168 (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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123A TRP* 3.8 6.7 - - - -
164A PHE 3.4 4.4 + - - -
165A THR 3.1 5.5 + - - -
167A LEU* 1.3 77.0 - - - +
169A LEU* 1.3 62.5 + - - +
171A GLU* 3.2 6.3 + - - +
172A SER* 2.8 27.4 + - - -
523A GLY* 3.6 26.8 - - - -
526A LEU* 3.5 12.0 - - - +
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Residues in contact with LEU 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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123A TRP* 3.5 36.1 - - + -
148A VAL* 4.1 5.8 - - + -
165A THR* 3.0 26.8 + - + +
166A MET* 3.7 7.4 - - - +
168A GLY* 1.3 74.6 - - - +
170A ALA* 1.3 58.4 + - - +
172A SER* 3.3 5.0 + - - -
173A ASP 3.0 8.5 + - - -
174A HIS* 2.8 46.2 + - + +
177A LYS* 4.0 17.9 - - + -
178A ILE* 3.7 20.9 - - + -
181A MET* 3.5 32.5 - - + -
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Residues in contact with ALA 170 (chain A).
Click here for Legend to table.
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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166A MET 2.8 20.3 + - - +
167A LEU* 3.7 4.9 - - - +
169A LEU* 1.3 70.5 - - - +
171A GLU* 1.3 66.1 + - - +
173A ASP* 3.2 12.1 + - - -
175A TRP* 3.6 41.9 + - + -
178A ILE* 3.4 9.5 - - + +
218A LEU* 4.2 12.8 - - + -
527A LYS* 6.0 2.0 - - - +
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Residues in contact with GLU 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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116A ARG* 3.0 25.5 + - - -
120A ASP* 4.6 0.5 - - - +
167A LEU 3.0 15.2 + - - +
168A GLY* 3.2 10.5 + - - +
170A ALA* 1.3 79.1 - - - +
172A SER* 1.3 64.0 + - - +
173A ASP* 3.6 1.4 + - - +
526A LEU* 3.5 32.5 - - + +
527A LYS* 4.1 16.1 - - + +
530A ASP* 2.6 33.4 - - - +
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Residues in contact with SER 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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120A ASP* 3.8 21.1 - - - -
123A TRP* 3.3 10.5 + - - -
168A GLY 2.8 16.1 + - - -
171A GLU* 1.3 86.9 + - - +
173A ASP* 1.3 70.3 + - - +
174A HIS* 3.2 32.4 + - - -
526A LEU* 3.9 1.0 - - - +
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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