Contacts of the helix formed by residues 147 - 159 (chain Y) in PDB entry 2X17
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 147 (chain Y).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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148L PRO* 6.3 0.4 - - - -
149L GLN* 3.5 15.8 + - - -
144Y ALA* 4.0 15.9 - - - +
145Y LYS 3.3 3.6 - - - +
146Y ASP* 1.3 78.6 - - - +
148Y PRO* 1.3 60.8 - - - +
149Y GLN* 3.0 21.7 + - - -
150Y ILE* 3.5 27.9 + - - +
151Y LEU* 3.7 16.8 + - - +
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Residues in contact with PRO 148 (chain Y).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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143J PHE* 3.6 39.1 - - + +
150J ILE* 4.0 10.1 - - + +
146Y ASP 3.3 11.0 - - - +
147Y SER* 1.3 82.6 - - - +
149Y GLN* 1.3 80.4 + - - +
150Y ILE 3.4 0.2 - - - -
151Y LEU* 3.8 12.1 - - + +
152Y PHE* 3.2 19.2 + - - +
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Residues in contact with GLN 149 (chain Y).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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147J SER* 3.4 33.0 + - - +
149J GLN* 4.2 21.2 + - + +
150J ILE* 4.0 15.4 - - + +
153J MET* 4.3 7.4 - - + +
149L GLN* 3.9 27.3 + - + -
147Y SER* 3.0 19.6 + - - +
148Y PRO* 1.3 98.8 - - - +
150Y ILE* 1.3 60.9 + - - +
152Y PHE* 3.6 4.3 + - - +
153Y MET* 3.4 28.5 + - + +
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Residues in contact with ILE 150 (chain Y).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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148L PRO* 3.9 32.8 - - + +
149L GLN* 3.9 22.9 - - + +
152L PHE* 4.1 29.4 - - + -
140Y LYS 5.1 0.4 - - - +
143Y PHE* 4.5 10.3 - - + +
144Y ALA* 3.6 28.0 - - + -
147Y SER* 3.5 25.2 + - - +
149Y GLN* 1.3 74.8 - - - +
151Y LEU* 1.3 60.2 + - - +
152Y PHE 3.2 0.9 - - - -
153Y MET* 3.3 7.0 + - + +
154Y LEU* 2.9 38.5 + - + +
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Residues in contact with LEU 151 (chain Y).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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143J PHE* 3.7 27.4 - - + -
36Y LEU* 4.3 13.7 - - + +
39Y PHE* 4.1 12.9 - - + -
83Y PRO* 4.2 25.1 - - + -
141Y LEU* 3.9 28.5 - - + -
144Y ALA* 4.7 7.0 - - + +
147Y SER 3.7 13.3 + - - +
148Y PRO* 3.6 11.2 + - + +
149Y GLN 3.4 0.6 - - - -
150Y ILE* 1.3 77.9 - - - +
152Y PHE* 1.3 55.3 + - - +
154Y LEU* 3.6 6.7 + - - +
155Y ASP* 3.2 25.8 + - - +
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Residues in contact with PHE 152 (chain Y).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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140J LYS* 4.8 21.5 - - + -
143J PHE* 4.3 16.8 - + + -
150J ILE* 4.3 18.8 - - + -
153J MET* 3.7 50.0 - - + -
154J LEU* 4.9 8.1 - - + -
157J GLU* 3.4 34.3 - - - -
36Y LEU* 5.5 1.6 - - + -
148Y PRO 3.2 17.4 + - - +
149Y GLN* 3.7 4.7 - - - +
150Y ILE 3.2 0.2 - - - -
151Y LEU* 1.3 77.2 - - - +
153Y MET* 1.3 63.9 + - + +
155Y ASP* 3.3 20.0 + - + +
156Y LYS* 3.3 17.1 + - + +
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Residues in contact with MET 153 (chain Y).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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11745 AG 3.0 27.8 - - - -
153J MET* 3.7 22.4 - - + +
149L GLN* 3.9 33.4 - - + +
152L PHE* 3.7 26.8 - - + -
153L MET* 3.9 12.3 - - + -
149Y GLN* 3.4 21.0 + - + +
150Y ILE* 3.3 7.4 + - - +
152Y PHE* 1.3 78.3 - - + +
154Y LEU* 1.3 58.7 + - - +
155Y ASP 3.4 0.2 - - - -
156Y LYS* 3.8 6.7 + - - +
157Y GLU* 3.3 28.4 + - - +
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Residues in contact with LEU 154 (chain Y).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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152L PHE* 4.2 10.5 - - + -
39Y PHE* 4.2 10.5 - - + -
137Y ILE* 4.8 9.2 - - + -
140Y LYS* 3.8 55.9 - - + +
141Y LEU* 4.6 16.4 - - + +
144Y ALA* 5.2 1.8 - - + -
150Y ILE* 2.9 27.3 + - + +
151Y LEU* 3.9 7.4 - - - +
153Y MET* 1.3 76.5 - - - +
155Y ASP* 1.3 59.3 + - - +
156Y LYS 3.3 0.4 - - - -
157Y GLU* 3.3 15.6 + - - +
158Y LEU* 3.0 46.9 + - + +
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Residues in contact with ASP 155 (chain Y).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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140J LYS* 5.8 3.8 - - - -
35Y GLY 4.5 2.9 - - - +
36Y LEU* 3.3 27.4 - - + +
37Y GLU* 3.9 5.9 + - - +
38Y GLY* 2.9 51.6 + - - -
39Y PHE* 3.2 22.4 + - + +
151Y LEU 3.2 14.5 + - - +
152Y PHE* 3.3 17.2 + - + +
154Y LEU* 1.3 77.5 - - - +
156Y LYS* 1.3 60.7 + - - +
158Y LEU 3.7 0.2 + - - -
159Y SER* 3.3 6.9 + - - -
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Residues in contact with LYS 156 (chain Y).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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156J LYS* 5.6 8.3 - - - +
157J GLU* 4.0 27.9 + - - +
156L LYS* 5.3 9.8 - - - +
152Y PHE* 3.3 14.0 + - + +
153Y MET* 4.1 9.4 - - - +
154Y LEU 3.3 0.4 - - - -
155Y ASP* 1.3 77.3 + - - +
157Y GLU* 1.3 64.7 + - - +
159Y SER* 2.6 28.9 + - - +
160Y ALA* 4.0 2.6 + - - +
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Residues in contact with GLU 157 (chain Y).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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152L PHE* 3.3 30.7 - - + +
156L LYS* 4.7 23.7 - - + +
140Y LYS* 3.5 23.9 + - - -
153Y MET 3.3 14.8 + - - +
154Y LEU* 3.3 17.5 + - + +
156Y LYS* 1.3 81.4 - - - +
158Y LEU* 1.3 63.3 + - + +
159Y SER 3.5 0.2 + - - -
160Y ALA* 3.7 16.8 + - - +
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Residues in contact with LEU 158 (chain Y).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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38Y GLY 3.6 19.5 - - - +
39Y PHE* 3.6 43.3 - - + +
42Y TRP* 3.6 33.4 - - + +
87Y PHE* 4.7 1.8 - - + -
137Y ILE* 3.8 32.1 - - + -
154Y LEU* 3.0 22.9 + - + +
157Y GLU* 1.3 77.3 - - + +
159Y SER* 1.3 60.6 + - - +
160Y ALA 3.1 6.2 + - - -
161Y ARG* 3.3 22.9 + - - +
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Residues in contact with SER 159 (chain Y).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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38Y GLY* 3.8 17.0 - - - -
41Y ASN* 5.1 9.8 + - - -
155Y ASP 3.3 15.2 + - - -
156Y LYS* 2.6 28.4 + - - +
157Y GLU 3.3 0.2 - - - -
158Y LEU* 1.3 75.1 - - - +
160Y ALA* 1.3 64.4 + - - +
161Y ARG 3.2 8.6 + - - +
162Y ALA* 4.7 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