Contacts of the helix formed by residues 152 - 162 (chain B) in PDB entry 3QFR
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 ALA 152 (chain B).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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88B GLY* 4.3 2.5 - - - -
117B PRO* 4.4 7.4 - - + -
140B MET* 3.6 29.4 - - + -
148B PRO* 4.3 1.3 - - - -
149B THR* 2.9 29.2 + - - +
151B ASN* 1.3 81.2 + - - +
153B GLN* 1.3 58.6 + - - +
154B ASP 3.3 2.2 - - - -
155B PHE* 3.2 7.6 + - + +
156B TYR* 2.8 29.5 + - - +
187B MET* 4.1 4.7 - - + +
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Residues in contact with GLN 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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147B ASP* 5.3 2.4 - - - +
148B PRO* 3.2 31.0 + - - +
149B THR 3.2 7.0 + - - +
150B ASP* 3.3 19.3 + - - +
151B ASN 3.6 0.2 - - - -
152B ALA* 1.3 77.4 - - - +
154B ASP* 1.3 63.7 + - - +
156B TYR* 3.2 12.5 + - - +
157B ASP* 2.8 64.5 + - - +
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Residues in contact with ASP 154 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
117B PRO 5.8 1.3 - - - +
118B GLU* 4.3 36.3 - - - +
120B TYR 6.0 1.6 - - - +
150B ASP 5.2 0.2 - - - +
151B ASN 5.0 1.7 + - - +
152B ALA 3.3 0.4 - - - -
153B GLN* 1.3 82.9 - - - +
155B PHE* 1.3 57.3 + - - +
157B ASP* 3.8 7.6 - - - +
158B TRP* 3.0 28.2 + - - +
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Residues in contact with PHE 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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117B PRO* 4.5 9.2 - - + -
122B LEU* 3.3 48.9 - - + +
125B LEU* 4.6 4.3 - - + -
138B PHE* 3.5 34.8 - + - -
140B MET* 3.9 19.3 - - + -
151B ASN 5.5 0.4 + - - -
152B ALA* 3.2 12.7 + - - +
153B GLN 3.1 0.2 - - - -
154B ASP* 1.3 76.4 - - - +
156B TYR* 1.3 68.1 + - - +
158B TRP* 3.1 9.8 + + - +
159B LEU* 3.0 51.4 + - + +
187B MET* 4.1 4.3 - - + -
191B VAL* 3.4 28.5 - - + -
195B LEU* 5.1 2.0 - - + -
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Residues in contact with TYR 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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146B GLY 5.1 8.1 + - - -
147B ASP* 5.8 2.0 - - - -
148B PRO* 3.7 27.8 - - + -
152B ALA 2.8 19.1 + - - +
153B GLN* 3.5 21.8 - - - +
155B PHE* 1.3 73.1 - - - +
157B ASP* 1.3 71.4 + - - +
159B LEU* 3.1 17.1 + - - +
160B GLN* 3.1 43.7 + - - +
187B MET* 4.0 20.2 - - + -
190B TYR* 3.4 43.2 - + + -
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Residues in contact with ASP 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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153B GLN* 2.8 53.5 + - - +
154B ASP* 3.8 7.5 - - - +
156B TYR* 1.3 79.6 - - - +
158B TRP* 1.3 62.9 + - - +
160B GLN* 3.0 20.0 + - - +
161B GLU* 2.3 34.1 - - - +
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Residues in contact with TRP 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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121B ASP* 5.3 2.7 - - - -
122B LEU* 3.6 18.4 - - + -
123B ALA* 3.5 42.7 - - + +
125B LEU* 4.2 17.3 - - + -
126B SER 6.1 0.2 - - - -
154B ASP 3.0 15.8 + - - +
155B PHE* 3.4 17.5 - + + +
157B ASP* 1.3 74.8 - - - +
159B LEU* 1.3 90.1 + - + +
161B GLU* 4.3 4.3 - - + -
162B THR* 2.8 63.4 + - + +
164B VAL* 4.4 21.5 - - + +
166B LEU* 4.8 4.9 - - + -
198B LEU* 4.4 8.1 - - + -
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Residues in contact with LEU 159 (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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155B PHE* 3.0 52.8 + - + +
156B TYR* 3.1 10.1 + - - +
158B TRP* 1.3 100.8 - - + +
160B GLN* 1.3 61.2 + - - +
161B GLU 3.6 0.2 + - - -
162B THR* 3.9 5.3 - - - +
190B TYR* 3.8 15.5 - - + -
191B VAL* 3.8 24.9 - - + +
194B ARG* 2.9 47.8 + - + -
195B LEU* 4.3 10.8 - - + -
198B LEU* 4.2 11.0 - - + -
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Residues in contact with GLN 160 (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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156B TYR* 3.1 50.2 + - - +
157B ASP* 3.0 15.3 + - - +
159B LEU* 1.3 76.7 - - - +
161B GLU* 1.3 73.4 + - - +
162B THR 4.4 1.4 - - - +
190B TYR* 3.2 25.9 + - + +
194B ARG* 4.7 5.7 + - - +
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Residues in contact with GLU 161 (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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157B ASP* 2.3 48.9 + - - +
158B TRP* 4.1 3.9 - - + +
160B GLN* 1.3 92.0 - - - +
162B THR* 1.3 71.8 + - - +
163B ASP* 4.6 1.9 - - - +
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Residues in contact with THR 162 (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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158B TRP* 2.8 69.4 + - + +
159B LEU* 3.9 6.0 - - - +
161B GLU* 1.3 87.5 - - - +
163B ASP* 1.3 71.2 + - - +
164B VAL* 3.1 26.2 - - - +
194B ARG* 3.3 16.5 + - - -
198B LEU* 4.7 7.2 - - + -
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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