Contacts of the helix formed by residues 160 - 168 (chain A) in PDB entry 4UAL
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 160 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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158A GLY 5.1 0.3 - - - +
159A GLY* 1.3 75.2 - - - +
161A LEU* 1.3 65.5 + - - +
162A LEU* 4.0 8.6 - - - +
163A THR* 2.8 40.5 + - - -
164A LEU* 3.0 21.3 + - - +
203A PRO 4.1 1.1 - - - +
204A ASP* 3.7 23.7 - - - +
206A VAL 3.3 12.3 - - - +
207A LEU* 4.0 14.4 - - + +
208A LEU* 4.4 7.9 - - - +
369A ASN 4.1 2.5 + - - +
370A PHE* 4.3 8.7 - - - +
501A 3FV 5.2 9.1 + - + -
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Residues in contact with LEU 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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160A ASP* 1.3 70.4 - - - +
162A LEU* 1.3 66.7 + - - +
164A LEU* 3.1 21.0 + - + +
165A LEU* 2.9 35.1 + - + +
172A LEU* 4.8 1.6 - - + -
180A TYR* 4.2 27.4 - - + -
184A MET* 4.0 14.6 - - - -
203A PRO* 3.3 26.9 + - + +
206A VAL* 2.8 36.8 + - + +
208A LEU* 4.8 6.9 - - + +
270A CYS* 6.1 0.7 - - + -
274A MET* 3.8 25.6 - - + -
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Residues in contact with LEU 162 (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 ASP* 3.9 5.4 - - - +
161A LEU* 1.3 80.3 - - - +
163A THR* 1.3 71.1 + - - +
165A LEU* 3.5 6.6 + - - +
166A SER* 3.2 23.5 + - - -
203A PRO* 3.3 15.8 + - + -
204A ASP* 3.6 43.7 - - + +
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Residues in contact with THR 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 ASP* 2.8 26.8 + - - -
162A LEU* 1.3 83.5 - - - +
164A LEU* 1.3 66.4 + - - +
166A SER* 3.2 7.5 + - - -
167A LYS* 3.1 40.6 + - + +
369A ASN 3.3 24.7 - - - +
370A PHE* 3.6 17.9 - - - +
371A ASP* 4.1 7.2 + - + +
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Residues in contact with LEU 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 ASP 3.0 14.0 + - - +
161A LEU* 3.1 19.9 + - + +
163A THR* 1.3 78.5 - - - +
165A LEU* 1.3 62.0 + - - +
167A LYS* 3.1 10.9 + - + +
168A PHE* 3.1 47.1 + - + -
172A LEU* 4.6 6.1 - - + -
176A MET* 4.5 6.5 - - + -
180A TYR* 3.3 40.8 - - + +
208A LEU* 4.3 12.1 - - + -
357A TYR* 3.5 35.9 - - + -
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Residues in contact with LEU 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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161A LEU* 2.9 31.3 + - + +
162A LEU* 3.8 5.6 - - - +
164A LEU* 1.3 76.4 - - - +
166A SER* 1.3 62.3 + - - +
168A PHE* 3.1 11.0 + - - +
170A ASP* 2.7 51.7 + - - +
171A LYS 4.3 0.2 - - - +
172A LEU* 3.6 32.5 - - + -
203A PRO* 4.4 22.7 - - + -
270A CYS 5.8 0.2 - - - +
273A GLU* 5.6 5.8 - - + +
274A MET* 4.3 24.2 - - + +
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Residues in contact with SER 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 LEU* 3.2 17.7 + - - -
163A THR* 3.6 8.5 - - - -
164A LEU 3.2 0.4 - - - -
165A LEU* 1.3 81.4 - - - +
167A LYS* 1.3 59.2 + - - +
169A GLU* 3.2 13.3 + - - +
170A ASP* 4.0 14.2 + - - +
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Residues in contact with LYS 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 THR* 3.1 37.2 + - + +
164A LEU* 3.1 11.9 + - + +
166A SER* 1.3 78.3 - - - +
168A PHE* 1.3 66.2 + - + +
169A GLU* 3.2 8.4 + - - +
357A TYR* 4.0 25.8 + - + +
368A SER 4.8 4.8 + - - -
369A ASN* 4.2 23.0 + - - +
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Residues in contact with PHE 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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164A LEU* 3.1 37.8 + - + -
165A LEU 3.1 8.6 + - - +
167A LYS* 1.3 79.6 - - + +
169A GLU* 1.3 72.3 + - - +
170A ASP 3.2 1.1 - - - -
171A LYS* 3.2 26.2 + - - +
172A LEU* 3.7 18.2 - - + -
173A PRO* 4.5 9.0 - - + -
176A MET* 3.8 30.5 - - + -
356A PRO 6.1 0.2 - - - -
357A TYR* 4.1 18.4 - + - -
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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