Contacts of the helix formed by residues 151 - 158 (chain B) in PDB entry 3QI2
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 SER 151 (chain B).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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76B ASN* 6.0 0.2 - - - -
149B ASN* 3.1 12.6 + - - -
150B ASP* 1.3 78.3 - - - +
152B ALA* 1.3 66.3 + - - +
153B ALA 3.5 1.8 - - - -
154B TYR* 3.3 9.4 + - - +
155B TYR* 3.2 29.7 + - - -
176B ARG* 2.8 30.6 + - - +
178B ARG* 4.2 3.6 - - - -
356B GDP 2.7 37.4 + - - -
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Residues in contact with ALA 152 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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80B SER* 3.5 31.0 - - - +
84B ILE* 5.0 1.1 - - + -
140B PHE* 5.0 4.3 - - + -
148B LEU* 3.9 20.9 - - + -
149B ASN* 3.1 18.8 + - - +
150B ASP 3.4 0.6 - - - -
151B SER* 1.3 78.7 - - - +
153B ALA* 1.3 64.3 + - - +
155B TYR* 4.0 1.4 - - - +
156B LEU* 3.0 36.2 + - + +
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Residues in contact with ALA 153 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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131B TRP* 4.2 14.8 - - + -
140B PHE* 3.8 27.7 - - + -
150B ASP 5.0 2.7 + - - +
152B ALA* 1.3 79.6 - - - +
154B TYR* 1.3 63.1 + - - +
156B LEU* 4.6 0.2 - - - +
157B ASN* 3.0 42.3 + - - +
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Residues in contact with TYR 154 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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150B ASP 5.1 1.0 + - - -
151B SER* 3.3 10.9 + - - +
152B ALA 3.2 0.2 - - - -
153B ALA* 1.3 79.4 - - - +
155B TYR* 1.3 81.5 + + - +
157B ASN* 4.0 2.4 - - - +
158B ASP* 3.6 27.3 + - - +
161B ARG* 4.4 8.9 + - - -
170B THR* 4.1 0.3 + - - -
172B GLN* 3.2 30.7 - - + +
173B ASP* 2.7 30.8 + - - -
176B ARG* 3.4 63.9 - - + +
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Residues in contact with TYR 155 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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73B VAL* 3.5 35.7 - - + -
76B ASN* 4.2 20.2 - - + -
77B THR* 3.3 30.1 - - + +
80B SER* 5.5 0.2 - - - -
149B ASN* 5.7 0.2 - - - -
151B SER* 3.2 29.3 + - - -
152B ALA* 4.2 3.4 - - - +
154B TYR* 1.3 91.6 - + - +
156B LEU* 1.3 61.0 + - - +
157B ASN 2.9 11.1 + - - -
158B ASP* 3.0 22.2 + - - +
159B LEU* 3.4 5.8 + - - +
162B ILE* 4.6 15.5 - - + +
173B ASP* 3.0 16.5 + - + -
176B ARG* 3.1 18.6 - - + -
177B THR* 2.9 35.6 + - + +
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Residues in contact with LEU 156 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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77B THR* 3.6 33.9 - - + +
80B SER* 4.3 13.9 - - - -
81B ILE* 4.2 10.3 - - + +
84B ILE* 4.3 11.0 - - + -
127B ILE* 3.9 20.6 - - + -
131B TRP* 3.3 65.4 - - + -
152B ALA* 3.0 23.6 + - - +
153B ALA 4.2 0.4 - - - +
155B TYR* 1.3 76.2 - - + +
157B ASN* 1.3 59.3 + - - +
159B LEU* 3.6 19.0 - - + +
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Residues in contact with ASN 157 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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131B TRP* 3.0 27.4 + - - +
153B ALA* 3.0 32.0 + - - +
154B TYR* 4.0 2.8 - - - +
155B TYR 3.0 0.8 - - - -
156B LEU* 1.3 75.8 - - - +
158B ASP* 1.3 67.5 + - - +
159B LEU* 2.9 11.8 + - - +
160B ASP 4.8 0.2 + - - -
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Residues in contact with ASP 158 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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154B TYR* 3.6 20.4 + - - +
155B TYR* 3.0 8.0 + - - +
157B ASN* 1.3 82.0 - - - +
159B LEU* 1.3 60.4 + - - +
160B ASP 3.5 2.2 - - - -
161B ARG* 2.8 45.8 + - + +
162B ILE* 3.0 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