Contacts of the helix formed by residues 164 - 176 (chain A) in PDB entry 1EZF
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 SER 164 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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162A VAL* 4.0 2.3 - - - +
163A THR* 1.3 86.4 + - - +
165A GLU* 1.3 64.7 + - - +
166A GLN* 3.1 30.1 - - - +
167A GLU* 3.0 29.1 + - - +
168A TRP* 3.0 10.7 + - - +
232A PRO* 4.4 1.6 - - - -
234A GLU* 3.4 27.8 + - - -
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Residues in contact with GLU 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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164A SER* 1.3 72.9 - - - +
166A GLN* 1.3 71.6 + - - +
168A TRP* 2.9 26.4 + - + +
169A ASP* 3.0 18.8 + - - +
232A PRO* 4.6 4.7 - - + +
234A GLU* 4.9 2.1 + - + +
235A VAL* 3.7 30.3 - - + +
238A ARG* 5.5 4.0 + - - -
261A GLU* 4.5 10.4 - - - +
262A LEU* 5.5 1.5 - - + +
265A ASN* 3.1 32.8 - - - +
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Residues in contact with GLN 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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164A SER* 3.1 20.0 - - - +
165A GLU* 1.3 102.3 + - - +
167A GLU* 1.3 57.1 + - + +
169A ASP* 3.4 13.1 + - - +
170A LYS* 3.0 23.6 + - - +
234A GLU* 4.9 2.4 - - - +
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Residues in contact with GLU 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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157A PHE* 3.4 24.4 - - + -
160A LYS* 3.4 27.5 + - - -
161A HIS 5.2 0.9 - - - +
162A VAL* 3.9 2.2 - - - +
163A THR* 3.3 31.7 + - - +
164A SER* 3.0 22.6 + - - +
166A GLN* 1.3 75.2 - - + +
168A TRP* 1.3 59.6 + - - +
170A LYS* 3.3 24.0 + - - +
171A TYR* 2.9 23.6 + - - +
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Residues in contact with TRP 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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162A VAL* 3.5 12.5 - - + +
164A SER 3.0 4.2 + - - +
165A GLU* 2.9 16.5 + - + +
167A GLU* 1.3 74.9 - - - +
169A ASP* 1.3 57.3 + - - +
171A TYR* 3.3 3.7 + - + +
172A CYS* 2.9 40.2 + - - -
213A LYS* 3.6 39.3 - - + -
216A ILE* 3.8 33.4 - - + +
217A ILE* 4.1 14.4 - - + -
230A PHE 3.3 26.6 + - - -
231A TRP* 5.3 0.2 - + - -
232A PRO* 3.4 31.4 - - + -
262A LEU* 3.8 30.1 - - + -
265A ASN* 3.5 39.3 - - - -
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Residues in contact with ASP 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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165A GLU* 3.0 17.1 + - - +
166A GLN* 3.4 13.4 + - - +
168A TRP* 1.3 78.8 - - - +
170A LYS* 1.3 52.1 + - - +
172A CYS* 3.6 5.5 - - - +
173A HIS* 2.7 37.0 + - - +
209A LEU* 3.8 18.1 - - + +
213A LYS* 2.7 33.7 + - - +
265A ASN* 5.2 0.9 - - - +
269A HIS* 5.1 1.9 + - - -
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Residues in contact with LYS 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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156A GLU* 2.8 27.7 + - - -
157A PHE* 3.7 9.6 - - + -
160A LYS* 5.3 0.2 - - - +
166A GLN 3.0 14.1 + - - +
167A GLU* 3.3 26.5 + - - +
168A TRP 3.2 0.2 - - - -
169A ASP* 1.3 77.1 - - - +
171A TYR* 1.3 61.7 + - - +
173A HIS* 3.3 11.6 + - + +
174A TYR* 3.1 58.8 + - + -
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Residues in contact with TYR 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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83A GLU* 2.6 35.9 + - - -
153A GLY 4.9 4.7 - - - -
154A MET* 5.1 1.1 - - - -
157A PHE* 3.6 46.9 - + + -
162A VAL* 4.5 10.8 - - + -
167A GLU 2.9 14.5 + - - +
168A TRP* 3.7 7.9 - + - +
170A LYS* 1.3 76.2 - - - +
172A CYS* 1.3 67.1 + - - +
174A TYR* 2.9 16.1 + - + +
175A VAL* 3.0 42.0 + - + +
212A GLN* 5.1 1.8 - - + -
216A ILE* 4.1 22.2 - - + -
230A PHE* 3.1 39.2 - + + -
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Residues in contact with CYS 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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168A TRP* 2.9 37.7 + - - +
169A ASP* 3.7 2.5 - - - +
171A TYR* 1.3 76.3 - - - +
173A HIS* 1.3 57.3 + - - +
175A VAL* 4.3 0.7 - - - -
176A ALA* 2.8 30.5 + - - +
177A GLY 2.9 5.2 + - - -
209A LEU* 3.5 22.4 - - + -
212A GLN* 3.8 29.8 - - + -
213A LYS* 3.7 27.4 - - + -
216A ILE* 4.2 7.2 - - - -
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Residues in contact with HIS 173 (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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169A ASP 2.7 23.0 + - - +
170A LYS* 3.4 12.3 - - + +
171A TYR 3.1 0.2 - - - -
172A CYS* 1.3 72.3 - - - +
174A TYR* 1.3 81.9 + + - +
177A GLY 3.0 2.2 + - - +
178A LEU* 2.7 64.6 + - + +
181A ILE* 5.1 5.6 - - + -
205A ASN* 2.8 30.4 + - + +
209A LEU* 3.4 10.0 - - + +
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Residues in contact with TYR 174 (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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149A ARG* 3.6 18.4 - - + -
150A MET* 3.0 27.0 - - - +
152A ILE* 5.0 6.6 - - + +
153A GLY* 3.4 32.8 - - - -
156A GLU* 2.9 27.3 + - - -
157A PHE* 3.8 16.8 - + - -
170A LYS* 3.1 52.4 + - + -
171A TYR* 2.9 9.0 + - + +
173A HIS* 1.3 94.0 - + - +
175A VAL* 1.3 65.2 + - + +
178A LEU* 3.6 13.8 - - + +
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Residues in contact with VAL 175 (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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80A ASP* 5.3 4.6 - - - +
83A GLU* 4.1 8.3 - - - +
150A MET* 4.0 12.1 - - + +
154A MET* 4.2 20.0 - - + -
171A TYR* 3.0 53.3 + - + +
172A CYS 4.0 0.4 - - - +
174A TYR* 1.3 84.5 - - + +
176A ALA* 1.3 60.4 + - - +
179A VAL* 3.4 18.1 - - - +
212A GLN* 3.6 31.4 - - + +
991A IN0 4.1 9.5 - - + +
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Residues in contact with ALA 176 (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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172A CYS 2.8 6.9 + - - +
173A HIS 3.7 0.2 + - - -
174A TYR 3.7 0.4 - - - -
175A VAL* 1.3 75.0 - - - +
177A GLY* 1.3 68.5 + - - +
178A LEU 3.3 1.3 - - - -
179A VAL* 3.1 11.8 + - - +
180A GLY 3.1 16.8 + - - -
208A GLY* 3.2 27.2 - - - +
212A GLN* 3.4 28.9 - - + +
991A IN0 3.4 18.6 - - + -
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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