Contacts of the helix formed by residues 146 - 160 (chain J) in PDB entry 5XTD
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 VAL 146 (chain J).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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142J GLU* 3.1 48.8 + - + +
143J ASP 3.3 2.0 + - - -
145J PHE* 1.3 85.3 - - + +
147J LYS* 1.3 82.0 + - + +
149J PRO* 3.3 3.8 - - - +
150J GLN* 3.2 31.6 + - - +
183J ASN* 4.7 5.2 - - - +
186J VAL* 4.2 22.2 - - + -
187J GLY* 5.1 1.6 - - - -
190J VAL* 4.4 10.5 - - + +
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Residues in contact with LYS 147 (chain J).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
111J ARG* 5.8 2.7 - - - +
140J ASP* 5.3 1.8 + - - -
142J GLU* 4.2 15.8 - - - +
143J ASP* 3.1 36.9 + - - +
146J VAL* 1.3 88.5 - - + +
148J ILE* 1.3 64.4 + - + +
150J GLN* 3.2 9.2 + - - +
151J ALA* 3.0 28.6 + - - +
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Residues in contact with ILE 148 (chain J).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
108J TRP* 5.7 1.8 - - + -
110J ALA* 4.4 32.3 - - + +
111J ARG* 6.2 1.3 - - - +
116J ILE* 5.3 6.7 - - + -
130J ILE* 4.0 24.0 - - + -
143J ASP* 3.2 41.3 + - + +
144J VAL* 4.4 4.5 - - + +
147J LYS* 1.3 79.8 - - + +
149J PRO* 1.4 74.3 - - + +
150J GLN 3.1 0.2 + - - -
151J ALA* 3.1 7.1 + - - +
152J ILE* 2.9 47.2 + - + +
401J NDP 4.9 7.9 - - - +
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Residues in contact with PRO 149 (chain J).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
128J ASN* 4.2 5.4 - - - +
143J ASP 3.6 2.9 - - - +
144J VAL 3.5 17.5 - - - +
145J PHE* 3.6 15.7 - - - +
146J VAL 3.3 20.4 - - - +
148J ILE* 1.4 94.7 - - + +
150J GLN* 1.3 55.9 + - - +
152J ILE* 3.4 13.2 + - + +
153J ALA* 2.9 28.2 + - - +
164J PHE* 4.2 1.9 - - - -
166J HIS* 4.0 16.6 - - + +
187J GLY* 5.2 1.8 - - - +
190J VAL* 6.1 0.4 - - + -
191J VAL* 3.7 26.3 - - + +
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Residues in contact with GLN 150 (chain J).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
146J VAL* 3.2 22.9 + - - +
147J LYS* 3.4 6.8 - - - +
148J ILE 3.1 0.6 - - - -
149J PRO* 1.3 76.8 - - - +
151J ALA* 1.3 66.6 + - - +
153J ALA* 2.9 8.6 + - - +
154J GLN* 2.9 44.5 + - - +
190J VAL* 3.3 32.6 - - + +
191J VAL* 5.3 0.7 - - - -
194J ALA* 4.2 11.5 - - + +
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Residues in contact with ALA 151 (chain J).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
113J LYS* 3.3 32.8 - - + +
116J ILE* 4.7 9.9 - - + -
147J LYS 3.0 17.3 + - - +
148J ILE* 3.8 6.3 - - - +
150J GLN* 1.3 75.6 - - - +
152J ILE* 1.3 62.8 + - - +
154J GLN* 4.6 6.1 - - - +
155J LEU* 3.0 39.2 + - + +
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Residues in contact with ILE 152 (chain J).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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59J PHE* 3.4 41.1 - - + -
108J TRP* 6.2 0.2 - - + -
116J ILE* 4.3 17.5 - - + -
120J VAL* 5.3 2.5 - - + +
126J VAL* 4.2 7.2 - - + -
128J ASN* 3.3 24.7 - - - +
130J ILE* 4.6 1.6 - - + -
148J ILE* 2.9 40.0 + - + +
149J PRO 3.5 6.1 - - - +
151J ALA* 1.3 77.3 - - - +
153J ALA* 1.3 53.6 + - - +
155J LEU* 4.2 0.8 - - - +
156J SER* 2.3 43.2 + - - +
164J PHE* 3.3 21.8 - - + -
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Residues in contact with ALA 153 (chain J).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
149J PRO 2.9 15.2 + - - +
150J GLN* 2.9 9.8 + - - +
152J ILE* 1.3 75.1 - - - +
154J GLN* 1.3 60.6 + - - +
156J SER* 3.2 4.8 + - - -
157J LYS* 2.9 21.8 + - - +
164J PHE* 4.1 16.1 - - + -
191J VAL* 4.6 7.4 - - - -
194J ALA* 3.7 18.2 - - + -
195J PHE* 3.4 28.9 - - + +
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Residues in contact with GLN 154 (chain J).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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113J LYS* 5.1 6.4 + - - +
150J GLN* 2.9 40.5 + - - +
151J ALA* 4.1 7.2 - - - +
153J ALA* 1.3 74.2 - - - +
155J LEU* 1.3 63.0 + - + +
157J LYS* 2.8 24.0 + - - +
158J GLU* 2.9 22.6 + - + +
194J ALA* 3.7 21.2 - - + +
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Residues in contact with LEU 155 (chain J).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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113J LYS* 3.5 35.2 - - + +
116J ILE* 4.0 16.4 - - + -
117J ARG* 3.5 38.4 - - + +
120J VAL* 4.4 16.9 - - + +
151J ALA* 3.0 21.4 + - + +
152J ILE* 4.2 2.7 - - - +
154J GLN* 1.3 78.8 - - + +
156J SER* 1.3 58.3 + - - +
158J GLU* 3.3 29.3 + - - +
159J ALA* 2.8 30.2 + - - +
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Residues in contact with SER 156 (chain J).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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120J VAL* 5.0 4.4 - - - +
126J VAL* 4.2 8.3 - - - +
152J ILE* 2.3 32.5 + - - +
153J ALA 3.4 5.8 - - - -
154J GLN 3.1 0.2 - - - -
155J LEU* 1.3 78.7 - - - +
157J LYS* 1.3 59.2 + - - +
159J ALA* 4.0 1.3 - - - -
160J GLY 3.1 3.3 + - - -
161J VAL* 3.0 48.6 + - - +
164J PHE* 3.2 33.0 - - - -
195J PHE* 3.8 2.6 - - - -
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Residues in contact with LYS 157 (chain J).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
153J ALA 2.9 7.5 + - - +
154J GLN* 2.8 11.9 + - - +
156J SER* 1.3 75.6 - - - +
158J GLU* 1.3 61.0 + - + +
160J GLY* 3.0 18.9 + - - -
194J ALA 4.3 11.9 - - - +
195J PHE* 3.4 26.9 - - + -
196J PRO* 5.2 7.6 - - + +
197J GLU* 3.3 24.1 + - - +
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Residues in contact with GLU 158 (chain J).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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117J ARG* 4.3 15.5 + - - -
154J GLN* 2.9 18.0 + - - +
155J LEU* 3.4 32.9 - - - +
157J LYS* 1.3 72.4 - - + +
159J ALA* 1.3 60.2 - - - +
160J GLY* 3.0 6.5 + - - -
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Residues in contact with ALA 159 (chain J).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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120J VAL* 3.7 25.8 - - + +
121J GLN* 4.4 12.2 - - - +
123J SER 4.8 3.8 - - - +
155J LEU 2.8 18.6 + - - +
156J SER* 3.4 8.3 - - - +
157J LYS 3.1 0.2 - - - -
158J GLU* 1.3 76.0 - - - +
160J GLY* 1.3 63.1 + - - +
161J VAL* 3.6 16.3 - - + -
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Residues in contact with GLY 160 (chain J).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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123J SER 5.2 0.7 - - - +
124J ASN* 5.7 0.2 - - - -
156J SER 3.1 0.2 + - - -
157J LYS* 3.0 17.3 + - - -
158J GLU 3.0 2.1 - - - -
159J ALA* 1.3 80.4 - - - +
161J VAL* 1.3 67.5 + - - +
162J GLU* 3.3 7.8 + - - +
195J PHE* 5.9 0.2 - - - -
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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