Contacts of the helix formed by residues 147 - 161 (chain J) in PDB entry 3IT8
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 LEU 147 (chain J).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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68J PHE* 4.2 21.1 - - + -
72J LEU* 4.3 26.2 - - + +
75J GLU* 5.3 4.3 - - - +
145J ASN* 2.6 18.9 + - - +
146J THR* 1.3 85.1 - - + +
148J TRP* 1.3 53.9 + - - +
149J LYS* 3.1 3.6 - - - -
150J ASP* 2.8 46.9 + - - +
151J VAL* 3.1 11.7 + - - +
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Residues in contact with TRP 148 (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 TYR* 4.1 11.0 - + - -
125J LYS 3.6 19.7 - - - -
126J ARG* 4.0 7.9 - - - -
127J PHE* 3.7 28.9 - + - -
140J MET* 3.3 26.0 - - - -
141J LEU 4.5 2.0 - - - -
142J THR 3.6 17.7 - - - +
143J VAL* 3.5 49.0 - - + +
145J ASN* 3.1 20.7 + - + +
146J THR 3.4 0.6 - - - -
147J LEU* 1.3 77.3 - - - +
149J LYS* 1.3 75.0 + - + +
151J VAL* 2.9 21.2 + - + +
152J LYS* 2.9 59.4 + - + +
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Residues in contact with LYS 149 (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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143J VAL* 4.8 7.4 - - - +
146J THR 5.2 6.5 - - - +
147J LEU 3.1 1.5 + - - -
148J TRP* 1.3 89.8 - - + +
150J ASP* 1.3 63.6 + - - +
152J LYS* 3.5 36.0 + - + +
153J ALA* 3.2 21.7 + - - +
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Residues in contact with ASP 150 (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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68J PHE* 3.5 24.7 - - + -
147J LEU* 2.8 36.4 + - - +
149J LYS* 1.3 74.0 - - - +
151J VAL* 1.3 57.5 + - - +
153J ALA* 3.2 4.7 + - - +
154J TYR* 2.7 58.6 + - + +
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Residues in contact with VAL 151 (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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68J PHE* 4.4 2.0 - - + -
69J TRP* 4.2 21.3 - - + -
72J LEU* 3.7 30.7 - - + -
120J TYR* 5.2 1.8 - - + -
127J PHE* 4.3 11.0 - - + -
140J MET* 4.3 13.5 - - + +
145J ASN* 6.3 0.2 - - - -
147J LEU 3.1 10.0 + - - +
148J TRP* 2.9 39.8 + - + +
150J ASP* 1.3 75.4 - - - +
152J LYS* 1.3 59.9 + - - +
155J LEU* 2.8 45.0 + - + +
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Residues in contact with LYS 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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86I SER 5.3 0.2 - - - +
120J TYR* 3.8 20.8 + - - +
125J LYS* 3.9 30.4 - - + +
143J VAL* 5.4 1.4 - - - +
148J TRP* 2.9 47.0 + - + +
149J LYS* 3.5 36.7 - - + +
151J VAL* 1.3 76.8 - - - +
153J ALA* 1.3 58.1 + - - +
156J GLY* 2.9 28.2 + - - +
157J GLY 3.1 3.6 + - - -
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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
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86I SER 5.7 2.2 - - - -
87I TYR* 5.6 1.0 - - - -
149J LYS 3.2 14.8 + - - +
150J ASP* 3.2 7.2 + - - +
152J LYS* 1.3 81.0 - - - +
154J TYR* 1.3 72.0 + - + +
157J GLY* 3.2 20.9 + - - +
158J PHE 4.2 0.3 + - - -
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Residues in contact with TYR 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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60J PRO* 6.0 1.0 - - - +
62J ASN* 4.9 4.3 + - - -
65J ASN* 3.6 38.6 + - + +
68J PHE* 3.7 43.7 - + + -
69J TRP* 3.7 19.3 - - + +
150J ASP* 2.7 38.3 + - + +
153J ALA* 1.3 82.4 - - + +
155J LEU* 1.3 61.2 + - - +
158J PHE* 3.3 22.0 + - - +
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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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69J TRP* 3.9 16.4 - - + -
93J LEU* 4.3 20.9 - - + -
95J THR* 3.7 32.8 - - + +
108J GLY* 4.1 13.2 - - - +
120J TYR* 3.9 22.7 - - + -
127J PHE* 3.6 32.1 - - + -
151J VAL* 2.8 23.7 + - + +
154J TYR* 1.3 73.7 - - - +
156J GLY* 1.3 66.0 + - - +
158J PHE* 3.4 2.7 + - + +
159J GLU* 3.1 24.5 + - - +
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Residues in contact with GLY 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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86I SER* 4.5 2.5 - - - -
120J TYR* 3.4 31.2 - - - -
122J THR* 4.1 2.5 + - - -
151J VAL 3.4 2.0 + - - -
152J LYS* 2.9 15.8 + - - +
155J LEU* 1.3 78.7 - - - +
157J GLY* 1.3 52.1 + - - +
159J GLU* 3.3 2.1 + - - +
160J TYR* 2.7 38.2 + - - +
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Residues in contact with GLY 157 (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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86I SER 3.0 25.3 + - - +
87I TYR* 3.8 15.6 - - - -
152J LYS 3.1 10.1 + - - -
153J ALA 3.2 14.2 + - - -
156J GLY* 1.3 77.0 - - - +
158J PHE* 1.3 61.9 + - - +
160J TYR* 3.1 1.8 + - - +
161J MET 3.0 19.9 + - - -
162J GLY 3.2 6.1 + - - -
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Residues in contact with PHE 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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87I TYR* 4.7 2.4 - + - -
3J LEU* 4.6 1.8 - - + -
5J TYR* 3.1 50.5 - + - -
58J HIS 4.1 8.7 - - - -
60J PRO* 4.1 23.1 - - + -
95J THR* 3.7 28.5 - - + -
96J GLY* 4.3 3.6 - - - -
153J ALA 4.2 0.6 + - - -
154J TYR 3.3 21.7 + - - +
155J LEU* 3.4 4.2 + - - +
156J GLY 3.3 0.4 - - - -
157J GLY* 1.3 75.5 - - - +
159J GLU* 1.3 61.6 + - - +
161J MET 3.6 0.7 + - - -
162J GLY* 3.3 9.0 + - - +
163J CYS* 2.7 77.4 + - + +
164J SER 4.6 0.2 + - - -
166J ALA* 4.8 2.2 - - + -
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Residues in contact with GLU 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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95J THR* 4.7 2.7 - - - +
96J GLY 5.8 0.2 - - - -
106J SER* 2.6 44.5 + - - +
107J TYR* 3.5 19.3 - - - +
108J GLY* 3.4 28.6 + - - -
120J TYR* 3.1 40.4 - - - +
122J THR* 4.2 14.2 + - - +
155J LEU* 3.1 17.6 + - - +
156J GLY* 3.7 3.8 - - - +
158J PHE* 1.3 78.5 - - - +
160J TYR* 1.3 64.5 + - - +
161J MET* 4.6 0.3 - - - -
163J CYS* 5.1 0.4 - - - -
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Residues in contact with TYR 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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82I ARG* 3.5 27.3 + - - -
84I ALA* 4.5 3.4 - - + -
86I SER* 3.9 22.4 - - - -
87I TYR* 4.7 1.8 - - + -
125I GLN 5.3 1.0 + - - -
126I LEU 5.9 0.2 - - - -
127I GLU* 3.5 43.1 - - + +
122J THR* 3.3 35.0 + - + +
156J GLY 2.7 23.0 + - - +
157J GLY* 3.1 6.7 + - - +
159J GLU* 1.3 76.1 - - - +
161J MET* 1.3 76.3 + - + +
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Residues in contact with MET 161 (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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33G ALA* 4.9 10.5 - - + +
34G ASN* 3.5 24.9 - - - +
82I ARG* 3.0 34.8 - - - +
84I ALA* 5.0 4.3 - - + -
87I TYR* 4.3 14.8 - - + -
91I VAL* 4.2 11.0 - - - -
157J GLY 3.0 3.2 + - - -
158J PHE 3.8 0.2 - - - -
159J GLU 3.4 1.6 - - - -
160J TYR* 1.3 98.4 - - + +
162J GLY* 1.3 72.0 + - - +
163J CYS 3.3 2.5 - - - -
164J SER* 2.7 30.7 + - - +
165J LEU* 3.1 30.0 + - + +
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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