Contacts of the helix formed by residues 152 - 162 (chain D) in PDB entry 2I6A
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 152 (chain D).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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147D GLU 4.3 16.4 - - - +
148D LYS* 3.9 17.9 - - - +
149D HIS* 2.9 16.2 + - + +
151D ASP* 1.3 76.1 - - - +
153D GLU* 1.3 57.3 + - - +
154D LYS* 3.4 23.6 - - + +
155D ASN* 2.9 22.4 + - - +
156D TRP 2.8 29.9 + - - -
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Residues in contact with GLU 153 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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151D ASP 3.3 5.7 + - - -
152D LEU* 1.3 68.9 - - - +
154D LYS* 1.3 65.2 + - - +
156D TRP* 4.4 4.9 - - - +
157D MET* 2.8 53.7 + - + +
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Residues in contact with LYS 154 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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92B ILE 5.9 1.2 + - - -
152D LEU* 4.3 21.6 - - + +
153D GLU* 1.3 78.0 + - - +
155D ASN* 1.3 88.8 + - - +
157D MET* 3.1 25.4 - - - +
158D LEU* 3.6 13.3 + - - +
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Residues in contact with ASN 155 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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87D PHE* 3.4 36.8 - - + -
111D HIS* 4.7 16.4 + - - +
149D HIS* 2.9 52.4 + - + +
150D LEU 4.6 0.2 - - - +
152D LEU* 2.9 18.9 + - - +
154D LYS* 1.3 95.9 - - - +
156D TRP* 1.3 65.3 + - - +
157D MET 3.1 2.8 + - - -
158D LEU* 3.2 12.8 + - - +
159D VAL 3.5 3.6 + - - -
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Residues in contact with TRP 156 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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150D LEU* 3.2 41.2 + - + +
151D ASP 4.5 4.9 - - - +
152D LEU 2.8 18.5 + - - +
153D GLU* 4.2 4.3 - - - +
155D ASN* 1.3 73.5 - - - +
157D MET* 1.3 61.6 + - - +
159D VAL* 3.2 32.7 + - + +
160D GLU* 3.2 38.4 + - + +
181D LYS* 3.1 50.6 - - + +
182D VAL* 4.1 5.8 - - + -
185D HIS* 3.5 43.5 - + + -
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Residues in contact with MET 157 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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153D GLU* 2.8 58.7 + - + +
154D LYS* 3.1 16.2 - - - +
156D TRP* 1.3 76.7 - - - +
158D LEU* 1.3 59.7 + - + +
160D GLU* 3.1 26.8 + - - +
161D LYS* 3.4 15.4 + - + +
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Residues in contact with LEU 158 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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7D ASN* 4.0 20.4 - - - +
10D PHE* 4.8 4.3 - - - -
85D THR* 4.2 15.8 + - + -
87D PHE* 4.3 9.2 - - + -
109D ASP* 4.0 4.5 - - - +
111D HIS* 3.3 43.5 - - + +
154D LYS 3.7 16.2 - - - +
155D ASN* 3.2 7.7 + - - +
157D MET* 1.3 76.2 - - + +
159D VAL* 1.3 65.9 + - - +
161D LYS* 3.2 39.0 + - + +
162D ALA* 3.6 5.7 + - - +
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Residues in contact with VAL 159 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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10D PHE* 3.6 48.0 - - + -
87D PHE* 4.0 0.9 - - + -
150D LEU* 4.0 8.5 - - + -
155D ASN 3.8 12.6 - - - +
156D TRP* 3.2 46.3 + - + +
158D LEU* 1.3 79.8 - - - +
160D GLU* 1.3 61.0 + - - +
161D LYS 3.4 0.7 + - - -
162D ALA* 3.4 17.8 + - - +
165D CYS* 4.7 5.3 - - - -
182D VAL* 4.5 11.4 - - + -
185D HIS* 4.4 11.4 + - + -
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Residues in contact with GLU 160 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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156D TRP* 3.2 42.0 + - + +
157D MET* 3.1 13.5 + - - +
159D VAL* 1.3 75.6 - - - +
161D LYS* 1.3 60.1 + - + +
162D ALA 4.8 0.4 - - - -
185D HIS* 3.0 32.6 + - + +
191D ARG* 3.5 22.3 + - - -
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Residues in contact with LYS 161 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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5D ARG* 5.7 4.1 - - - -
6D GLU* 4.0 21.9 + - - +
7D ASN* 3.0 42.6 + - + +
8D ILE* 4.1 5.7 - - - +
157D MET* 3.6 15.3 - - + +
158D LEU* 3.2 27.8 + - + +
160D GLU* 1.3 78.3 - - - +
162D ALA* 1.3 62.5 + - - +
163D ARG* 3.6 6.4 + - - +
191D ARG* 5.3 1.1 + - - -
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Residues in contact with ALA 162 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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7D ASN 3.2 8.6 + - - +
8D ILE 3.0 13.5 - - - +
10D PHE* 3.5 32.5 - - + -
158D LEU 3.6 1.9 + - - +
159D VAL 3.4 13.9 + - - +
160D GLU 4.4 0.2 - - - +
161D LYS* 1.3 78.7 - - - +
163D ARG* 1.3 61.8 + - - +
164D VAL 3.6 8.7 - - - +
165D CYS* 4.2 6.9 - - - -
185D HIS* 5.8 0.5 + - - -
191D ARG* 3.3 26.5 + - - +
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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