Contacts of the helix formed by residues 154 - 163 (chain B) in PDB entry 1QAG
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 LYS 154 (chain B).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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155A ILE* 4.6 10.5 - - - +
158A SER* 4.3 23.1 + - - -
147B LEU* 4.5 10.6 - - + +
151B ASN* 3.4 42.4 + - + +
152B SER 3.4 1.0 - - - -
153B GLU* 1.3 77.2 - - - +
155B ILE* 1.3 74.0 + - + +
157B LEU* 2.7 35.9 + - + +
158B SER* 2.8 33.8 + - - -
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Residues in contact with ILE 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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140A MSE 4.3 11.9 - - - -
143A VAL* 4.3 11.4 - - + -
144A MSE 4.4 16.8 - - + -
147A LEU* 3.6 15.9 - - + +
155A ILE* 4.8 8.3 - - + -
144B MSE 4.1 25.6 - - + +
147B LEU* 3.8 35.7 - - + -
148B GLN* 3.9 22.4 - - + +
151B ASN 4.8 1.0 + - - -
152B SER 4.7 1.0 + - - -
153B GLU 3.4 0.2 - - - -
154B LYS* 1.3 90.3 - - + +
156B LEU* 1.3 65.3 + - - +
158B SER* 3.3 8.7 + - - +
159B TRP* 3.3 17.0 + - - +
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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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139A VAL* 5.6 0.7 - - + -
140A MSE 3.3 34.2 - - + +
143A VAL* 4.5 18.8 - - + -
152B SER 4.8 0.4 + - - -
153B GLU* 3.2 10.1 + - - +
154B LYS 3.2 0.8 - - - -
155B ILE* 1.3 82.4 - - - +
157B LEU* 1.3 61.6 + - - +
159B TRP* 3.4 14.6 + - + +
160B VAL* 3.3 19.2 + - - +
175B PHE* 3.6 27.1 - - + -
244B ILE* 4.0 24.0 - - + -
247B LEU* 4.0 20.4 - - + -
248B THR* 4.7 12.1 - - + -
251B PHE* 5.9 2.9 - - + -
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Residues in contact with LEU 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 GLU* 2.7 18.5 + - + +
154B LYS* 2.7 14.9 + - + +
156B LEU* 1.3 74.7 - - - +
158B SER* 1.3 56.0 + - - +
159B TRP 3.0 5.1 + - - -
160B VAL* 3.1 4.9 + - - +
161B ARG* 2.9 43.5 + - - +
172B VAL* 3.5 34.1 - - + +
173B LEU* 3.8 28.7 - - - +
174B ASN* 3.9 3.6 - - - +
175B PHE* 3.6 20.6 - - + -
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Residues in contact with SER 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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147A LEU* 3.2 28.8 - - - +
151A ASN* 4.4 7.2 + - - +
155A ILE* 4.0 12.6 - - - +
154B LYS* 2.8 31.4 + - - -
155B ILE* 3.3 3.5 + - - +
157B LEU* 1.3 78.9 - - - +
159B TRP* 1.3 60.3 + - - +
161B ARG* 3.9 12.0 - - - +
162B GLN* 3.3 22.5 + - - +
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Residues in contact with TRP 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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143A VAL* 3.5 34.1 - - + -
146A ASP* 3.6 25.8 + - + +
147A LEU* 3.3 25.1 - - + -
155B ILE 3.3 2.7 + - - +
156B LEU* 3.5 15.0 - - + +
157B LEU 3.0 0.8 - - - -
158B SER* 1.3 79.0 + - - +
160B VAL* 1.3 94.1 + - + +
162B GLN* 3.3 7.0 + - - +
163B THR* 2.9 52.6 + - + -
188B VAL* 4.2 26.0 - - + -
192B HIS* 5.0 10.5 - + - -
247B LEU* 5.0 6.1 - - + -
251B PHE* 3.4 39.2 - + + -
254B LEU* 4.5 12.6 - - + -
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Residues in contact with VAL 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 LEU 3.3 7.5 + - - +
157B LEU* 3.1 9.0 + - - +
159B TRP* 1.3 101.6 - - + +
161B ARG* 1.3 59.9 + - - +
163B THR* 4.2 2.9 - - - -
164B THR* 2.8 42.2 + - + +
172B VAL* 3.8 20.6 - - + -
175B PHE* 4.6 1.6 - - + -
179B TRP* 3.6 30.7 - - + -
188B VAL* 4.5 2.9 - - + -
247B LEU* 3.7 28.9 - - + -
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Residues in contact with ARG 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 LEU* 2.9 33.6 + - + +
158B SER* 3.9 10.5 - - - +
160B VAL* 1.3 79.9 - - - +
162B GLN* 1.3 57.3 + - - +
164B THR* 3.8 4.1 + - - -
165B ARG* 3.1 28.6 + - - +
171B ASN* 3.2 27.1 + - - -
172B VAL* 2.4 48.0 + - + +
173B LEU* 4.4 9.6 - - - +
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Residues in contact with GLN 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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146A ASP* 4.0 9.3 + - - +
147A LEU* 4.4 12.8 - - - +
150A THR* 2.7 32.1 + - - +
151A ASN* 2.8 42.3 + - - +
158B SER 3.3 16.1 + - - +
159B TRP* 3.3 7.4 + - - +
161B ARG* 1.3 78.6 - - - +
163B THR* 1.3 64.3 + - - +
165B ARG* 3.5 39.3 + - - +
191B ARG* 3.8 12.8 + - - +
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Residues in contact with THR 163 (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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159B TRP* 2.9 50.0 + - + -
160B VAL* 3.8 7.4 - - - -
161B ARG 3.3 0.2 - - - -
162B GLN* 1.3 78.0 - - - +
164B THR* 1.3 67.6 + - + +
165B ARG 3.3 2.0 + - - -
166B PRO* 3.8 1.4 - - - +
188B VAL* 4.2 14.6 - - + +
191B ARG* 3.0 54.5 + - + +
192B HIS* 4.5 11.9 - - + -
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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