Contacts of the helix formed by residues 152 - 163 (chain A) 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 SER 152 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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147A LEU 4.0 1.3 + - - -
148A GLN* 3.7 23.1 - - - +
149A GLN 5.0 1.3 - - - -
150A THR 2.7 14.1 + - - -
151A ASN* 1.3 69.2 - - - +
153A GLU* 1.3 78.3 + - - +
155A ILE* 3.0 17.3 + - - +
156A LEU* 3.0 13.3 + - - +
132B LEU* 5.9 1.0 - - - +
136B VAL* 5.1 5.7 - - - +
137B LYS* 4.9 10.6 - - - +
140B MSE 3.6 29.9 - - - +
144B MSE 5.6 0.7 - - - -
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Residues in contact with GLU 153 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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150A THR 4.6 1.7 + - - +
152A SER* 1.3 82.5 + - - +
154A LYS* 1.3 63.4 + - + +
156A LEU* 3.5 7.1 + - - +
157A LEU* 3.3 16.2 + - + +
175A PHE* 3.5 27.7 + - + -
240A LYS* 2.7 40.9 + - - +
244A ILE* 5.0 8.2 - - + +
140B MSE 4.8 2.0 - - - -
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Residues in contact with LYS 154 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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150A THR 5.2 0.2 + - - -
151A ASN* 2.7 50.3 - - + +
152A SER 3.1 0.6 - - - -
153A GLU* 1.3 78.8 - - + +
155A ILE* 1.3 69.6 + - + +
157A LEU* 3.2 20.1 + - + +
158A SER* 3.3 14.1 + - - -
165B ARG* 5.5 2.0 - - - +
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Residues in contact with ILE 155 (chain A).
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* 4.6 4.9 - - + -
151A ASN* 3.0 40.8 + - + +
152A SER 3.0 5.5 + - - +
154A LYS* 1.3 82.1 - - + +
156A LEU* 1.3 63.0 + - - +
158A SER* 3.5 16.9 + - - -
159A TRP* 3.6 5.9 + - - +
140B MSE 4.5 6.5 - - - -
143B VAL* 4.2 8.0 - - + +
144B MSE 4.2 35.7 - - + -
147B LEU* 3.6 27.9 - - + +
154B LYS* 4.6 10.3 - - - +
155B ILE* 4.8 3.8 - - + -
158B SER* 4.0 20.9 - - - +
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Residues in contact with LEU 156 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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152A SER 3.0 7.2 + - - +
153A GLU* 3.9 5.6 - - - +
155A ILE* 1.3 78.6 - - - +
157A LEU* 1.3 63.4 + - - +
159A TRP* 3.5 15.4 + - + +
160A VAL* 3.4 18.4 + - - +
175A PHE* 3.6 23.1 - - + -
244A ILE* 3.9 24.0 - - + -
247A LEU* 4.1 19.3 - - + -
248A THR* 4.6 11.7 - - + -
251A PHE* 5.9 3.8 - - + -
139B VAL* 5.8 0.2 - - + -
140B MSE 3.5 35.4 - - + -
143B VAL* 4.4 18.8 - - + -
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Residues in contact with LEU 157 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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153A GLU* 3.3 12.5 + - + +
154A LYS* 3.2 15.5 + - + +
156A LEU* 1.3 75.3 - - - +
158A SER* 1.3 58.2 + - - +
159A TRP 3.0 4.9 + - - -
160A VAL* 3.3 3.4 + - - +
161A ARG* 3.0 43.4 + - - +
172A VAL* 3.6 31.4 - - + +
173A LEU* 3.7 28.3 - - - +
174A ASN* 3.9 3.4 - - - +
175A PHE* 3.6 21.3 - - + -
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Residues in contact with SER 158 (chain A).
Click here for Legend to table.
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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154A LYS 3.3 10.2 + - - -
155A ILE* 3.5 11.2 + - - -
156A LEU 3.4 0.2 - - - -
157A LEU* 1.3 79.9 - - - +
159A TRP* 1.3 60.2 + - - +
161A ARG* 4.0 11.7 - - - +
162A GLN* 3.4 22.7 + - - +
147B LEU* 3.6 19.6 - - - +
154B LYS* 4.3 17.2 + - - -
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Residues in contact with TRP 159 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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155A ILE 3.6 3.3 + - - +
156A LEU* 3.5 16.5 + - + +
157A LEU 3.0 0.6 - - - -
158A SER* 1.3 79.8 + - - +
160A VAL* 1.3 93.0 + - + +
162A GLN* 3.2 8.2 + - - +
163A THR* 2.8 51.7 + - + -
188A VAL* 4.3 24.0 - - + -
192A HIS* 4.9 10.1 - + - -
247A LEU* 5.1 5.4 - - + -
251A PHE* 3.3 38.8 - + + -
254A LEU* 4.6 11.9 - - + -
143B VAL* 3.6 38.4 - - + -
146B ASP* 3.7 25.7 + - + +
147B LEU* 3.9 15.0 - - + -
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Residues in contact with VAL 160 (chain A).
Click here for Legend to table.
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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156A LEU 3.4 8.7 + - - +
157A LEU* 3.3 9.5 + - - +
159A TRP* 1.3 102.0 - - + +
161A ARG* 1.3 65.3 + - - +
163A THR* 4.2 3.1 - - - -
164A THR* 2.9 37.3 + - + +
172A VAL* 3.7 22.2 - - + -
175A PHE* 4.6 1.8 - - + -
179A TRP* 3.6 29.4 - - + -
188A VAL* 4.6 2.5 - - + -
247A LEU* 3.6 28.9 - - + -
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Residues in contact with ARG 161 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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157A LEU* 3.0 34.1 + - + +
158A SER* 4.1 11.2 - - - +
159A TRP 3.2 0.2 - - - -
160A VAL* 1.3 77.4 - - - +
162A GLN* 1.3 58.0 + - - +
164A THR* 3.7 4.6 + - - -
165A ARG* 3.0 29.3 + - - +
171A ASN* 3.3 26.7 + - - +
172A VAL* 2.5 47.7 + - + +
173A LEU* 4.4 10.0 - - - +
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Residues in contact with GLN 162 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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158A SER 3.4 15.6 + - - +
159A TRP* 3.2 8.1 + - - +
161A ARG* 1.3 77.0 - - - +
163A THR* 1.3 67.3 + - - +
165A ARG* 3.5 45.5 + - - +
191A ARG* 3.8 12.8 + - - +
146B ASP 4.4 7.7 + - - -
147B LEU* 4.3 20.4 - - - +
150B THR* 3.1 36.7 + - + +
151B ASN* 6.1 0.2 - - - +
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Residues in contact with THR 163 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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159A TRP* 2.8 48.0 + - + -
160A VAL* 3.7 7.9 - - - -
162A GLN* 1.3 79.2 - - - +
164A THR* 1.3 66.7 + - + +
165A ARG 3.3 1.8 + - - -
166A PRO* 3.7 1.7 - - - +
188A VAL* 4.2 15.9 - - + +
191A ARG* 3.0 53.3 + - + +
192A HIS* 4.4 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