Contacts of the helix formed by residues 159 - 169 (chain A) in PDB entry 5PLF
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 THR 159 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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157A LEU 4.3 7.0 - - - +
158A GLY* 1.3 76.3 - - - -
160A ILE* 1.3 64.0 + - - +
161A GLN* 3.6 16.3 + - - +
162A ASP* 3.0 39.4 + - - +
163A LEU* 3.0 21.7 + - - +
175A VAL* 6.1 0.9 - - - -
176A ASN* 3.5 22.0 - - + +
296A ALA 6.0 0.2 - - - -
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Residues in contact with ILE 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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158A GLY 3.9 0.2 + - - -
159A THR* 1.3 72.2 - - - +
161A GLN* 1.4 63.4 + - - +
163A LEU* 3.3 6.9 + - - +
164A LEU* 3.0 27.9 + - + +
176A ASN* 3.1 30.1 + - + +
198A LEU* 3.7 31.9 - - + -
294A ASN* 3.9 11.7 - - + +
295A PHE* 4.0 16.2 - - - -
296A ALA* 4.0 19.5 - - + +
300A TRP* 4.4 9.9 - - + -
324A PHE* 3.5 34.8 - - + -
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Residues in contact with GLN 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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159A THR* 3.6 18.2 - - - +
160A ILE* 1.4 79.3 - - - +
162A ASP* 1.3 62.4 + - - +
164A LEU* 3.5 2.4 + - - +
165A GLU* 3.0 24.3 + - - +
172A ILE* 3.8 31.2 + - + +
173A GLU 3.7 16.3 + - - +
174A GLY* 3.5 27.0 - - - +
175A VAL* 3.3 9.9 + - - -
176A ASN* 3.6 13.5 - - - +
320A SER* 3.1 26.9 + - - -
324A PHE* 3.7 14.4 - - + -
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Residues in contact with ASP 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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158A GLY* 5.9 0.9 - - - -
159A THR* 3.0 32.5 + - - +
161A GLN* 1.3 74.9 - - - +
163A LEU* 1.4 61.0 + - - +
165A GLU* 3.4 18.7 + - - +
166A LYS* 2.9 44.4 + - + +
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Residues in contact with LEU 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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159A THR 3.0 13.7 + - - +
160A ILE* 3.6 8.3 - - - +
162A ASP* 1.4 72.2 - - - +
164A LEU* 1.3 67.3 + - - +
166A LYS* 3.2 21.2 + - - +
167A GLU* 2.9 48.5 + - + +
296A ALA* 3.8 31.2 - - + +
297A THR* 3.7 31.2 - - - +
298A PRO* 4.0 9.2 - - + -
300A TRP* 4.2 2.7 - - + -
301A ILE* 4.0 15.3 - - + -
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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 ILE* 3.0 15.2 + - + +
161A GLN 3.7 4.5 - - - +
163A LEU* 1.3 76.2 - - - +
165A GLU* 1.3 59.3 + - - +
168A CYS* 2.7 49.9 + - + +
169A GLY 3.7 0.2 + - - -
170A VAL* 4.4 8.4 + - + +
172A ILE* 3.9 15.3 - - + -
300A TRP* 4.1 18.4 - - + -
301A ILE* 3.4 26.7 - - + -
323A ALA 5.8 0.2 - - - +
324A PHE* 3.6 39.3 - - + -
327A ILE* 5.4 8.1 - - + -
328A LEU* 4.0 18.2 - - + -
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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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161A GLN 3.0 14.4 + - - +
162A ASP* 3.7 19.7 - - - +
163A LEU 3.2 0.2 - - - -
164A LEU* 1.3 80.7 - - - +
166A LYS* 1.3 58.5 + - + +
169A GLY* 2.8 30.8 + - - -
170A VAL 3.3 24.5 - - - +
171A VAL* 3.7 36.8 - - + +
172A ILE 5.1 0.6 + - - +
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Residues in contact with LYS 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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32A ASP* 4.9 10.1 + - - -
158A GLY* 6.1 3.2 - - - -
162A ASP* 2.9 32.8 + - + +
163A LEU* 3.7 23.6 - - - +
165A GLU* 1.3 75.1 - - + +
167A GLU* 1.3 71.3 + - + +
169A GLY 4.7 0.5 + - - -
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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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163A LEU* 2.9 41.5 + - + +
166A LYS* 1.3 85.8 - - - +
168A CYS* 1.3 73.7 + - - +
298A PRO* 3.4 39.2 - - + +
301A ILE* 4.3 9.6 - - + +
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Residues in contact with CYS 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* 2.7 40.1 + - + +
167A GLU* 1.3 79.5 - - - +
169A GLY* 1.3 59.6 + - - +
170A VAL* 3.4 15.2 + - + +
301A ILE* 4.0 23.3 - - - -
305A LYS* 5.9 1.8 - - - -
327A ILE* 5.7 3.1 - - + -
328A LEU* 4.9 6.1 - - - -
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Residues in contact with GLY 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* 2.8 20.5 + - - +
166A LYS 4.6 0.4 - - - -
167A GLU 3.7 0.8 - - - -
168A CYS* 1.3 76.6 - - - +
170A VAL* 1.3 59.6 + - - +
171A VAL* 3.9 6.2 + - - +
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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