Contacts of the helix formed by residues 165 - 171 (chain A) in PDB entry 4EJX
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 ASP 165 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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164A ILE* 1.3 78.2 - - + +
166A ALA* 1.3 70.2 + - - +
167A PRO* 3.3 1.3 - - - +
168A LYS* 2.9 37.1 + - - +
169A ASP* 3.6 10.8 + - - -
211A TRP* 4.1 19.3 - - + -
740A GLN* 3.4 19.6 + - + +
742A GLN* 3.8 13.4 - - - +
1027A ILE* 5.8 1.7 - - - +
1028A HIS* 2.7 40.3 + - - -
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Residues in contact with ALA 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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161A HIS* 5.0 5.8 - - + -
162A SER 3.9 10.2 - - - +
163A HIS* 4.3 27.8 + - + +
164A ILE 3.8 4.4 + - - +
165A ASP* 1.3 72.6 + - - +
167A PRO* 1.3 74.9 - - + +
168A LYS 3.4 0.3 + - - -
169A ASP* 3.4 12.1 + - - +
170A ILE* 3.5 20.7 + - + +
1020A HIS* 5.4 2.9 - - + -
1022A HIS* 5.3 3.8 - - + +
1027A ILE* 4.3 19.7 - - + -
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Residues in contact with PRO 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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165A ASP* 3.3 6.5 - - - +
166A ALA* 1.3 95.1 - - + +
168A LYS* 1.3 51.2 + - + +
170A ILE* 3.1 12.3 + - + +
171A ALA* 2.8 36.8 + - - +
209A PHE* 5.6 1.8 - - + -
269A MET* 6.1 1.3 - - - -
1022A HIS* 6.5 0.2 - - + -
1024A THR* 3.2 40.4 - - + +
1027A ILE* 3.7 16.4 - - + -
1028A HIS* 3.2 34.3 - - + +
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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
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165A ASP* 2.9 35.0 + - - +
167A PRO* 1.3 73.1 - - - +
169A ASP* 1.3 51.2 + - - +
171A ALA 4.1 0.9 - - - -
172A SER* 2.6 34.1 + - - -
208A ASN 5.4 1.7 + - - -
209A PHE* 3.3 43.9 - - + +
210A SER 4.6 6.5 + - - -
211A TRP* 3.4 49.3 - - + +
742A GLN* 4.7 6.8 + - - +
1028A HIS* 4.4 9.6 - - + +
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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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96A ARG* 3.9 3.0 + - - -
98A TYR* 3.6 18.0 - - + -
162A SER* 2.8 49.6 + - - +
164A ILE* 3.5 18.5 + - - +
165A ASP 3.6 6.9 + - - -
166A ALA 3.4 2.3 + - - +
167A PRO 3.2 0.4 - - - -
168A LYS* 1.3 74.6 - - - +
170A ILE* 1.3 60.8 + - - +
171A ALA 3.3 0.4 - - - -
172A SER* 3.1 9.3 + - - -
173A GLY 3.0 9.0 + - - -
174A LEU* 3.0 25.4 + - + +
211A TRP* 2.6 36.6 + - - -
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Residues in contact with ILE 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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73A PHE* 4.7 0.9 - - - -
161A HIS* 3.5 35.0 - - + +
162A SER 5.1 0.2 - - - +
166A ALA 3.5 16.3 + - - +
167A PRO* 3.1 10.9 + - + +
169A ASP* 1.3 77.6 - - - +
171A ALA* 1.3 58.4 + - - +
173A GLY* 2.9 21.7 + - - -
174A LEU 3.9 18.2 - - - +
175A ILE* 4.2 15.8 - - + +
203A SER* 5.6 1.3 - - - +
205A VAL* 4.3 8.4 - - + +
269A MET* 3.5 54.1 - - + -
270A GLY* 5.9 1.1 - - - -
1022A HIS* 4.1 5.4 - - + -
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Residues in contact with ALA 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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50A LYS* 2.8 17.7 + - - -
167A PRO 2.8 19.2 + - - +
170A ILE* 1.3 74.5 - - - +
172A SER* 1.3 57.7 + - - +
173A GLY 3.1 0.7 - - - -
205A VAL* 3.6 12.7 - - + +
206A ASP* 3.3 26.4 - - + +
207A GLU* 2.8 11.6 - - - +
209A PHE* 3.7 24.0 - - + +
210A SER* 3.7 5.0 - - - -
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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