Contacts of the helix formed by residues 145 - 152 (chain J) in PDB entry 3ISE
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 GLY 145 (chain J).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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147E GLU* 4.0 11.3 + - - -
141J ILE 2.8 16.0 + - - -
142J GLN 4.2 2.7 + - - -
143J LYS 3.7 1.0 - - - -
144J VAL* 1.3 80.7 - - - +
146J LEU* 1.3 66.3 + - - -
147J GLU* 3.4 7.2 - - - -
148J ASN 3.1 1.9 + - - -
149J TYR* 2.9 21.8 + - - +
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Residues in contact with LEU 146 (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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83J THR* 5.1 8.1 - - + -
84J GLN* 4.8 15.7 - - + +
141J ILE* 3.7 35.8 + - + +
145J GLY* 1.3 70.6 - - - -
147J GLU* 1.3 82.6 + - - +
148J ASN 3.1 0.2 + - - -
149J TYR* 3.3 2.4 + - + +
150J LEU* 2.9 54.4 + - + +
143Q LYS 5.6 1.6 - - - +
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Residues in contact with GLU 147 (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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145J GLY* 3.4 3.3 - - - -
146J LEU* 1.3 96.0 + - - +
148J ASN* 1.3 58.3 + - - +
150J LEU* 3.4 3.1 + - - +
151J GLN* 3.0 26.5 + - - +
143Q LYS 3.8 11.5 - - - +
144Q VAL* 3.4 36.4 - - - +
145Q GLY* 5.6 1.1 - - - -
148Q ASN* 3.7 8.0 + - - +
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Residues in contact with ASN 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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147E GLU* 3.7 23.8 + - - +
148E ASN* 3.6 18.0 + - - +
151E GLN* 2.9 40.2 + - - +
144J VAL* 3.0 33.5 + - + +
145J GLY* 3.1 1.2 + - - -
146J LEU 3.1 0.6 - - - -
147J GLU* 1.3 77.1 + - - +
149J TYR* 1.3 65.3 + - - +
151J GLN* 3.1 1.7 + - - +
152J SER* 3.0 12.0 + - - -
148Q ASN* 3.2 19.8 + - - +
161V K 3.6 5.5 - - - -
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Residues in contact with TYR 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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154E MET* 4.4 5.4 - - + -
40J LEU* 3.8 25.9 - - + +
83J THR* 4.5 5.2 - - + -
87J LEU* 4.6 1.0 - - + +
137J GLN* 2.6 48.6 + - + +
140J LEU* 3.9 26.5 - - + -
141J ILE* 3.4 35.4 - - + -
144J VAL* 3.8 10.2 - - + +
145J GLY 2.9 15.9 + - - +
146J LEU 3.6 3.6 - - - +
148J ASN* 1.3 74.6 - - - +
150J LEU* 1.3 75.3 - - + +
152J SER* 3.1 9.9 + - - -
153J HIS* 2.8 54.8 + + - -
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Residues in contact with LEU 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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37J LEU* 3.3 32.7 - - + +
40J LEU* 4.4 3.8 - - + -
83J THR* 3.6 38.4 - - + +
146J LEU* 2.9 41.6 + - + +
147J GLU 3.7 4.3 - - - +
149J TYR* 1.3 86.4 - - + +
151J GLN* 1.3 55.2 + - - +
153J HIS* 2.8 21.7 + - - +
154J MET* 3.4 1.9 + - - +
143Q LYS* 3.7 36.1 - - + +
144Q VAL* 3.8 12.1 - - + -
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Residues in contact with GLN 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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151E GLN* 2.6 27.2 + - - +
147J GLU 3.0 13.9 + - - +
148J ASN 3.1 6.9 + - - +
150J LEU* 1.3 73.3 - - - +
152J SER* 1.3 58.0 + - - +
153J HIS 3.0 5.9 + - - -
154J MET* 3.1 25.6 + - - +
155J HIS* 4.7 1.6 + - - -
144Q VAL* 3.8 10.7 - - + +
148Q ASN* 3.1 42.3 + - + +
151Q GLN* 2.9 28.3 + - - +
152Q SER* 3.2 22.3 + - - +
161V K 3.0 12.2 - - - -
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Residues in contact with SER 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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151E GLN* 3.2 34.2 + - - +
154E MET* 3.9 21.1 - - - -
155E HIS* 3.5 23.5 + - - -
39J ARG* 3.6 8.1 + - - -
148J ASN 3.0 4.8 + - - -
149J TYR 3.4 11.0 - - - -
151J GLN* 1.3 75.0 - - - +
153J HIS* 1.3 64.5 + - - +
154J MET 3.6 0.6 + - - -
155J HIS 4.3 2.8 - - - +
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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