Contacts of the helix formed by residues 153 - 164 (chain D) in PDB entry 2Q41
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 ASP 153 (chain D).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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73D SER* 3.0 20.7 + - - -
75D TYR* 3.2 19.8 - - + +
76D GLN* 2.6 29.3 + - - +
78D VAL* 4.9 1.4 - - - +
92D LEU* 4.9 0.2 - - - +
151D GLU* 2.8 25.9 + - - +
152D ILE* 1.3 73.1 - - + +
154D LYS* 1.3 59.3 + - - +
155D MSE 2.7 45.5 + - - +
156D VAL* 2.9 29.2 + - + +
157D VAL* 3.5 2.1 - - - +
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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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74D ASP* 5.6 3.8 + - - -
75D TYR* 5.0 2.6 - - - -
152D ILE 3.1 8.0 + - - +
153D ASP* 1.3 70.2 + - - +
155D MSE 1.3 61.6 - - - +
157D VAL* 3.5 21.8 - - + +
158D ASP* 3.1 25.2 + - - +
180D ILE* 3.9 25.6 - - + -
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Residues in contact with MSE 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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69D PHE* 4.1 23.1 - - + -
71D GLY* 5.1 0.9 - - - -
72D LYS 3.5 28.3 - - - +
73D SER* 3.3 33.3 - - - +
78D VAL* 3.8 21.3 - - + -
153D ASP* 2.7 21.0 + - - +
154D LYS* 1.3 72.8 - - - +
156D VAL* 1.3 63.1 + - - +
157D VAL 3.0 2.3 + - - -
158D ASP* 3.3 12.3 + - + +
159D VAL* 3.2 24.0 + - + +
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Residues in contact with VAL 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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76D GLN* 4.1 1.6 - - - +
78D VAL* 4.9 4.5 - - + -
90D LEU* 5.0 8.9 - - + +
92D LEU* 3.6 39.0 - - + -
129D GLY* 3.8 17.3 - - - -
130D GLY 3.9 11.2 - - - +
151D GLU* 2.9 23.3 - - - +
153D ASP* 2.9 27.3 + - + +
155D MSE 1.3 77.1 - - - +
157D VAL* 1.3 58.7 + - - +
159D VAL* 4.2 5.3 - - - +
160D SER* 2.9 30.9 + - - +
171D TYR* 5.3 0.2 - - - -
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Residues in contact with VAL 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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151D GLU* 3.3 28.5 - - + -
153D ASP 3.5 4.3 - - - +
154D LYS* 3.5 15.5 - - + +
156D VAL* 1.3 74.9 - - - +
158D ASP* 1.3 69.4 + - - +
160D SER* 3.1 3.1 + - - -
161D LYS* 2.8 38.6 + - + +
171D TYR* 4.1 23.3 - - + +
178D LEU* 4.1 25.1 - - + -
180D ILE* 3.6 18.4 - - + -
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Residues in contact with ASP 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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154D LYS* 3.1 28.9 + - - +
155D MSE 3.3 16.0 + - + +
157D VAL* 1.3 78.0 - - - +
159D VAL* 1.3 56.1 + - + +
161D LYS* 3.1 5.9 + - - +
162D GLN* 2.6 42.3 + - + +
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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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69D PHE* 3.7 34.5 - - + -
78D VAL* 3.8 8.3 - - + -
80D VAL* 3.1 31.9 - - + -
90D LEU* 4.3 17.7 - - + -
155D MSE 3.2 18.1 + - + +
156D VAL* 4.2 4.5 - - - +
158D ASP* 1.3 79.8 - - + +
160D SER* 1.3 58.2 + - - +
163D PHE* 2.7 52.0 + - + +
164D PHE* 3.5 3.3 + - + -
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Residues in contact with SER 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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90D LEU* 4.7 5.5 - - - +
130D GLY 2.3 29.8 + - - -
131D ASP* 3.2 17.3 - - - +
156D VAL* 2.9 18.4 + - - +
157D VAL 3.1 3.9 + - - -
159D VAL* 1.3 78.0 - - - +
161D LYS* 1.3 66.6 + - - +
164D PHE* 3.0 37.7 + - - +
168D ALA* 3.5 4.0 - - - +
171D TYR* 3.9 11.4 - - - -
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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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157D VAL* 2.8 33.2 + - + +
158D ASP* 3.6 5.4 - - - +
160D SER* 1.3 76.6 - - - +
162D GLN* 1.3 63.8 + - - +
165D PRO* 3.8 8.5 - - - +
168D ALA* 3.6 18.8 - - + +
171D TYR* 3.7 49.1 - - + +
172D GLU* 4.9 10.7 - - - +
178D LEU* 4.7 7.4 - - - -
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Residues in contact with GLN 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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158D ASP* 2.6 24.0 + - + +
161D LYS* 1.3 72.5 - - - +
163D PHE* 1.3 110.3 + - + +
165D PRO* 3.1 25.1 - - - +
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Residues in contact with PHE 163 (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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68D LEU* 4.5 27.5 - - + +
69D PHE* 3.3 46.0 - + + -
80D VAL* 3.9 20.4 - - + -
88D LYS* 3.1 26.1 - - + +
159D VAL* 2.7 50.3 + - + +
162D GLN* 1.3 99.1 - - + +
164D PHE* 1.3 56.9 + - + +
165D PRO* 3.0 13.7 - - - +
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Residues in contact with PHE 164 (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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80D VAL* 4.0 13.5 - - + -
88D LYS* 3.4 36.1 - - + -
89D VAL 3.9 13.2 - - - -
90D LEU* 4.4 7.0 - - + -
98D LEU* 3.5 31.4 - - + -
100D GLU* 4.1 9.4 - - + -
103D GLU* 4.7 2.0 - - - -
131D ASP* 3.7 28.9 - - + +
159D VAL* 4.1 12.6 - - + -
160D SER* 3.0 21.6 + - - +
163D PHE* 1.3 82.0 - - + +
165D PRO* 1.3 51.8 - - - +
166D ASP* 2.7 45.2 + - - +
168D ALA* 2.9 16.5 + - - +
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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