Contacts of the helix formed by residues 159 - 169 (chain N) in PDB entry 5L4K
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 ARG 159 (chain N).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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108N TYR* 3.5 12.4 + - - +
123N LYS* 6.0 1.3 - - - +
131N GLU* 5.7 3.5 - - - +
134N VAL* 4.2 16.6 - - - +
135N ASN* 3.5 32.2 + - - +
138N PHE* 5.5 2.4 - - - +
154N ALA 3.7 8.4 + - - +
157N THR* 3.0 31.5 + - + +
158N ARG* 1.3 79.1 - - - +
160N LEU* 1.3 65.1 + - - +
161N ASP* 3.2 11.8 + - + +
162N VAL* 3.0 55.9 + - + +
163N PHE 3.5 2.9 + - - -
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Residues in contact with LEU 160 (chain N).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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154N ALA 5.3 1.3 - - - +
155N LEU* 5.3 1.8 - - + -
158N ARG 4.6 1.6 - - - +
159N ARG* 1.3 71.6 - - - +
161N ASP* 1.3 63.5 + - - +
162N VAL 3.4 0.2 - - - -
163N PHE* 3.3 38.2 - - + +
164N GLU* 2.9 29.3 + - - +
193N PHE* 3.6 33.2 - - + -
196N LYS* 3.8 20.6 - - + +
197N VAL* 3.9 31.0 - - + -
200N VAL* 3.9 18.4 - - + +
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Residues in contact with ASP 161 (chain N).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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159N ARG* 3.2 9.6 - - + +
160N LEU* 1.3 76.7 + - - +
162N VAL* 1.3 66.2 + - + +
164N GLU* 3.8 5.8 - - - +
165N LYS* 3.0 27.0 + - - +
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Residues in contact with VAL 162 (chain N).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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135N ASN* 5.0 1.1 - - - +
138N PHE* 3.3 46.0 - - + -
153N ILE* 5.2 1.8 - - + -
154N ALA* 3.6 23.6 - - + +
157N THR* 4.3 4.9 - - + -
159N ARG* 3.0 59.7 - - + +
161N ASP* 1.3 77.5 - - - +
163N PHE* 1.3 55.9 + - - +
165N LYS* 4.0 1.5 - - - +
166N THR* 2.9 32.6 + - - -
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Residues in contact with PHE 163 (chain N).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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151N ILE* 3.5 34.3 - - + -
154N ALA* 3.6 24.2 - - + +
155N LEU* 5.0 9.6 - - + -
159N ARG 3.5 2.2 + - - +
160N LEU* 3.3 35.9 - - + +
161N ASP 3.2 0.4 - - - -
162N VAL* 1.3 79.9 - - - +
164N GLU* 1.3 62.2 + - - +
166N THR* 3.6 3.3 + - - -
167N ILE* 3.3 35.7 + - + +
180N SER* 3.6 27.8 - - - -
197N VAL* 4.5 14.8 - - + -
200N VAL* 3.9 22.2 - - + -
201N LEU* 5.1 3.4 - - + -
204N ILE* 4.6 14.4 - - + -
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Residues in contact with GLU 164 (chain N).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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160N LEU 2.9 19.3 + - - +
161N ASP* 3.2 7.4 + - - +
163N PHE* 1.3 78.3 - - - +
165N LYS* 1.3 62.0 + - - +
167N ILE* 3.1 18.7 - - - +
168N LEU* 3.3 28.9 - - - +
200N VAL* 3.6 22.7 - - + -
203N LYS* 6.5 0.4 - - + -
204N ILE* 3.3 24.0 - - + +
208N LEU* 5.7 0.2 - - - +
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Residues in contact with LYS 165 (chain N).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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138N PHE* 3.9 7.3 - - - -
139N GLN* 2.9 28.4 + - - +
142N LEU* 3.4 21.9 - - + +
161N ASP 3.0 15.8 + - - +
162N VAL* 4.2 1.9 - - - +
164N GLU* 1.3 79.2 + - - +
166N THR* 1.3 64.2 + - - +
167N ILE 3.2 1.8 - - - -
168N LEU* 3.3 18.4 + - + +
169N GLU* 3.3 31.8 + - - +
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Residues in contact with THR 166 (chain N).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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138N PHE* 3.5 22.9 - - - -
142N LEU* 3.8 10.8 - - - +
147N TYR* 3.7 39.4 - - + +
150N ALA* 3.6 24.4 + - + +
151N ILE* 4.0 12.3 - - + +
162N VAL 2.9 23.5 + - - -
163N PHE* 3.9 8.7 - - - -
164N GLU 3.5 0.2 - - - -
165N LYS* 1.3 76.9 - - - +
167N ILE* 1.3 61.9 + - - +
169N GLU* 3.6 7.1 + - - +
176N MET* 4.2 8.8 - - - +
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Residues in contact with ILE 167 (chain N).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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151N ILE* 4.4 5.6 - - + -
163N PHE* 3.3 32.8 - - + +
164N GLU* 3.1 29.4 - - + +
166N THR* 1.3 76.0 - - - +
168N LEU* 1.3 67.5 + - + +
169N GLU 3.5 0.7 + - - +
172N ASP 3.5 17.8 - - - +
173N VAL* 3.5 15.2 - - + +
176N MET* 3.8 29.6 - - + -
177N LEU* 5.5 2.0 - - + +
180N SER* 5.6 0.7 - - - +
204N ILE* 3.2 51.4 - - + -
208N LEU* 4.6 6.1 - - + -
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Residues in contact with LEU 168 (chain N).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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164N GLU* 3.3 39.7 - - - +
165N LYS* 3.3 15.5 + - + +
167N ILE* 1.3 76.7 - - + +
169N GLU* 1.3 67.2 + - + +
170N SER 2.9 11.8 + - - +
173N VAL* 4.0 7.5 - - + +
208N LEU* 3.3 46.4 - - + -
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Residues in contact with GLU 169 (chain N).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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142N LEU* 4.1 21.0 - - + +
147N TYR* 3.2 38.2 + - + +
165N LYS* 3.3 40.4 - - - +
166N THR 3.9 3.2 - - - +
167N ILE 3.3 4.9 - - - +
168N LEU* 1.3 73.3 - - - +
170N SER* 1.3 77.5 + - - +
172N ASP* 3.6 13.9 + - - +
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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