Contacts of the helix formed by residues 160 - 173 (chain A) in PDB entry 2AJA
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 GLN 160 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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156A MSE 3.0 44.9 + - - +
157A ALA* 3.8 9.8 - - - +
159A ILE* 1.3 76.3 - - + +
161A ALA* 1.3 65.7 + - - +
162A GLU 3.4 2.6 + - - -
163A ASN* 3.5 9.7 + - - -
164A TYR* 3.4 35.1 + - + -
189A GLU* 5.3 3.1 + - + -
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Residues in contact with ALA 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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128A ASN* 3.5 24.9 - - - +
129A TYR* 3.7 14.1 - - + -
133A ARG* 4.4 6.6 - - - -
157A ALA 2.8 19.6 + - - +
158A MSE 3.4 13.5 - - - +
159A ILE 3.2 2.8 - - - +
160A GLN* 1.3 77.2 - - - +
162A GLU* 1.3 67.9 + - - +
165A HIS* 3.2 19.8 + - - +
166A ALA 4.6 0.3 + - - -
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Residues in contact with GLU 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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128A ASN* 3.0 36.1 + - - +
133A ARG* 4.2 24.0 + - - +
160A GLN 3.4 1.4 + - - -
161A ALA* 1.3 73.7 - - - +
163A ASN* 1.3 71.7 + - - +
165A HIS* 3.4 17.4 - - + +
168A ARG* 3.2 14.7 + - - -
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Residues in contact with ASN 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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160A GLN 3.5 5.6 + - - -
161A ALA 3.4 0.6 - - - -
162A GLU* 1.3 74.4 - - - +
164A TYR* 1.3 70.8 + - - +
168A ARG* 2.7 33.9 + - - +
196A ALA* 4.0 6.0 - - + +
197A GLU* 4.0 30.1 + - - +
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Residues in contact with TYR 164 (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 ILE* 3.3 24.0 - - + -
160A GLN* 3.4 31.2 + - + +
161A ALA 3.5 2.8 + - - -
163A ASN* 1.3 77.8 - - - +
165A HIS* 1.3 64.6 + - - +
166A ALA 3.4 2.2 - - - -
167A PHE* 3.4 4.3 + - - +
168A ARG* 3.2 21.3 + - - +
189A GLU* 2.6 48.0 + - + +
192A ALA* 3.6 19.7 - - + +
193A MSE 3.4 31.9 - - + -
196A ALA* 3.9 24.7 - - + -
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Residues in contact with HIS 165 (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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133A ARG* 3.2 41.5 + - - -
161A ALA 3.2 11.7 + - - +
162A GLU* 3.4 18.2 - - + +
163A ASN 3.0 1.8 + - - -
164A TYR* 1.3 73.0 - - - +
166A ALA* 1.3 68.3 + - - +
168A ARG* 2.9 35.8 + - - +
169A LEU* 2.8 59.3 + - + +
200A TYR* 5.7 3.4 - + - -
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Residues in contact with ALA 166 (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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132A PHE* 3.6 37.0 - - + -
133A ARG* 4.2 11.3 - - + +
136A ALA* 3.4 21.2 - - + +
158A MSE 4.4 5.6 - - - +
159A ILE 4.6 4.5 - - - +
161A ALA 4.6 0.8 + - - -
164A TYR 3.4 0.4 - - - -
165A HIS* 1.3 78.4 - - - +
167A PHE* 1.3 63.9 + - - +
169A LEU* 3.5 2.6 + - - +
170A ALA* 3.0 24.4 + - - +
182A LEU* 4.0 9.2 - - + -
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Residues in contact with PHE 167 (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 ILE* 5.2 0.8 + - + +
164A TYR* 3.4 10.1 + - - +
165A HIS 3.2 0.6 - - - -
166A ALA* 1.3 76.9 - - - +
168A ARG* 1.3 60.2 + - - +
170A ALA* 3.1 5.9 + - - +
171A ALA* 2.8 25.7 + - + -
179A LEU* 3.5 32.2 - - + +
182A LEU* 3.6 19.1 - - + +
183A CYS* 4.0 21.8 - - - -
193A MSE 3.5 59.0 - - + -
194A ILE* 3.9 21.8 - - + -
201A ALA* 3.6 27.4 - - + -
217A PHE* 5.0 2.0 - + - -
218A LEU* 4.0 10.1 - - + -
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Residues in contact with ARG 168 (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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162A GLU 3.2 19.2 + - - -
163A ASN* 2.7 23.1 + - - +
164A TYR 3.2 8.7 + - - +
165A HIS* 2.9 35.6 + - - +
167A PHE* 1.3 77.9 - - + +
169A LEU* 1.3 62.3 + - - +
171A ALA* 3.0 6.9 + - - +
172A GLU* 2.9 24.4 + - - +
193A MSE 4.6 6.7 - - - +
196A ALA* 3.8 19.7 - - + -
197A GLU* 4.0 15.6 + - - +
200A TYR* 3.4 68.0 - - + -
201A ALA* 4.6 4.9 - - - +
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Residues in contact with LEU 169 (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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133A ARG* 3.7 28.9 - - + +
137A GLU* 3.9 40.2 - - + +
165A HIS* 2.8 59.5 + - + +
166A ALA* 3.9 3.4 - - - +
168A ARG* 1.3 73.1 - - - +
170A ALA* 1.3 64.0 + - - +
172A GLU* 3.3 22.8 + - - +
173A ASN* 3.0 30.0 + - - -
200A TYR* 4.9 0.4 - - - +
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Residues in contact with ALA 170 (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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136A ALA 3.7 14.1 + - - +
166A ALA 3.0 14.2 + - - +
167A PHE* 3.2 10.5 - - - +
169A LEU* 1.3 78.4 - - - +
171A ALA* 1.3 62.2 + - - +
173A ASN* 3.3 1.0 + - - -
174A GLY 3.2 3.3 + - - -
175A HIS* 3.0 28.1 + - - +
178A VAL* 3.4 29.6 - - + -
179A LEU* 3.3 17.9 - - + -
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Residues in contact with ALA 171 (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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167A PHE* 2.8 11.8 + - + +
168A ARG 3.5 5.2 - - - +
170A ALA* 1.3 78.4 - - - +
172A GLU* 1.3 63.0 + - - +
174A GLY* 3.0 13.2 + - - -
179A LEU* 3.6 13.2 - - + +
201A ALA* 3.5 35.7 - - + +
205A ALA* 3.5 17.0 - - - +
214A VAL* 3.8 20.9 - - + +
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Residues in contact with GLU 172 (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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137A GLU* 5.2 1.1 - - - +
168A ARG 2.9 11.0 + - - +
169A LEU* 3.3 43.0 - - - +
171A ALA* 1.3 76.9 - - - +
173A ASN* 1.3 65.0 + - - +
174A GLY 3.4 0.2 - - - -
200A TYR* 3.4 30.6 + - + -
201A ALA 4.5 0.8 + - - -
204A TRP* 3.5 44.2 - - + +
205A ALA 4.2 0.4 - - - +
211A HIS* 3.1 18.1 + - - -
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Residues in contact with ASN 173 (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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137A GLU* 3.4 36.8 + - - +
169A LEU* 3.0 19.9 + - - +
170A ALA 3.3 0.8 + - - +
171A ALA 3.1 0.8 - - - -
172A GLU* 1.3 86.6 - - - +
174A GLY* 1.3 61.8 + - - +
175A HIS* 3.4 33.7 + - + +
211A HIS* 3.3 14.6 + - - -
209B ARG* 3.3 22.6 + - + +
210B GLY 4.4 5.0 - - - +
211B HIS* 4.7 4.5 - - - -
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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