Contacts of the helix formed by residues 214 - 227 (chain A) in PDB entry 2AOQ
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 ARG 214 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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92A THR* 4.3 6.7 - - + -
175A ALA 2.8 19.9 + - - -
176A ARG 3.2 16.1 + - - -
177A ILE 3.2 7.7 + - - -
178A GLY 2.9 29.6 + - - -
179A GLU 3.4 17.7 + - - +
180A VAL* 2.8 23.6 + - - +
182A GLN* 3.2 28.5 - - + +
213A LEU* 1.3 76.4 - - - +
215A LYS* 1.3 65.8 + - - +
216A GLU* 3.2 20.9 - - + +
217A PHE* 3.1 17.1 + - - +
218A THR* 3.5 6.1 + - - -
3B A 4.3 3.4 + - - -
4B T 2.9 27.5 + - - -
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Residues in contact with LYS 215 (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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88A TYR* 4.1 17.2 - - + -
89A PRO* 3.3 18.9 + - + +
90A LEU* 3.6 33.0 + - - +
91A GLU* 3.7 23.8 - - - +
92A THR* 4.4 9.7 - - + +
213A LEU 3.8 1.0 + - - -
214A ARG* 1.3 74.1 - - - +
216A GLU* 1.3 67.6 + - - +
218A THR* 3.2 9.8 + - - -
219A ALA* 2.8 31.9 + - - +
2B C 4.6 8.5 - - - +
3B A 2.7 36.5 + - - +
4B T 6.5 0.2 - - - -
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Residues in contact with GLU 216 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
88A TYR* 2.9 25.8 + - - +
179A GLU 5.9 2.5 - - - +
180A VAL* 6.2 2.0 - - + -
214A ARG* 3.2 22.2 - - + +
215A LYS* 1.3 84.2 + - - +
217A PHE* 1.3 62.1 + - - +
219A ALA* 3.4 4.3 + - - +
220A GLN* 3.2 21.7 + - - +
3B A 4.3 13.8 + - - +
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Residues in contact with PHE 217 (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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117A LEU* 5.7 0.2 - - + -
144A TRP* 4.1 13.9 - + - -
150A GLN* 3.9 31.8 + - + -
153A GLN* 4.0 11.4 - - - -
154A LEU* 3.8 29.2 - - + -
180A VAL* 3.5 50.1 - - + +
213A LEU* 4.0 27.4 - - + -
214A ARG* 3.1 12.3 + - - +
216A GLU* 1.3 78.9 - - - +
218A THR* 1.3 63.6 + - - +
220A GLN* 3.1 18.0 + - + +
221A ILE* 3.3 31.5 + - + +
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Residues in contact with THR 218 (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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81A LEU* 4.0 16.4 - - + +
89A PRO* 3.5 14.9 - - - +
91A GLU 4.9 1.6 + - - -
92A THR* 6.0 0.5 - - - -
93A THR* 3.7 21.9 + - - +
122A TRP* 3.9 26.0 - - + -
213A LEU* 4.1 19.5 - - + +
214A ARG 3.5 1.8 + - - +
215A LYS* 3.2 17.7 + - - -
217A PHE* 1.3 80.5 - - + +
219A ALA* 1.3 60.7 + - - +
221A ILE* 3.1 12.6 + - - +
222A LEU* 3.0 24.3 + - - +
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Residues in contact with ALA 219 (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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87A GLY 6.0 0.2 - - - +
88A TYR* 3.5 29.8 - - + -
89A PRO* 3.8 13.0 - - + -
215A LYS 2.8 19.9 + - - +
216A GLU* 3.6 7.0 - - - +
218A THR* 1.3 78.1 + - - +
220A GLN* 1.3 58.3 + - - +
222A LEU* 3.1 7.3 + - - +
223A ASN* 2.8 36.5 + - - +
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Residues in contact with GLN 220 (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 GLN* 4.0 17.3 + - - +
216A GLU 3.2 12.0 + - - +
217A PHE* 3.1 13.5 + - + +
219A ALA* 1.3 74.2 - - - +
221A ILE* 1.3 61.5 + - - +
223A ASN* 4.2 10.5 - - - +
224A ALA* 2.7 46.7 + - - +
227A GLU* 5.0 5.9 + - - -
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Residues in contact with ILE 221 (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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81A LEU* 6.2 1.3 - - + -
122A TRP* 3.8 39.7 - - + +
142A ILE* 4.5 9.6 - - + +
144A TRP* 3.5 57.2 - - + +
150A GLN* 3.9 11.4 - - - +
217A PHE* 3.3 20.6 + - + +
218A THR* 3.1 15.6 + - - +
220A GLN* 1.3 77.6 - - - +
222A LEU* 1.3 65.2 + - + +
224A ALA* 3.6 4.6 + - - +
225A PHE* 3.3 22.2 + - - +
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Residues in contact with LEU 222 (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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81A LEU* 4.0 18.8 - - + -
83A ILE* 3.9 17.7 - - + -
87A GLY 3.4 25.1 - - - +
89A PRO* 3.9 22.9 - - + -
122A TRP* 6.2 0.7 - - + -
124A PRO* 4.1 13.0 - - + -
142A ILE* 3.8 23.3 - - + -
218A THR 3.0 13.1 + - - +
219A ALA* 3.3 7.9 - - - +
221A ILE* 1.3 81.3 - - + +
223A ASN* 1.3 63.4 + - - +
225A PHE* 3.3 7.4 + - - +
226A LEU* 3.1 31.3 + - + +
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Residues in contact with ASN 223 (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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87A GLY 5.7 0.5 - - - +
88A TYR* 6.1 0.5 - - - -
219A ALA* 2.8 22.7 + - - +
220A GLN* 3.7 15.3 - - - +
222A LEU* 1.3 75.6 - - - +
224A ALA* 1.3 57.7 + - - +
225A PHE 2.9 5.4 + - - -
226A LEU* 3.0 15.0 + - - +
227A GLU* 2.9 42.6 + - + +
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Residues in contact with ALA 224 (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 GLN* 5.9 1.6 - - - +
220A GLN* 2.7 35.8 + - - +
221A ILE* 4.1 5.6 - - - +
223A ASN* 1.3 73.2 - - - +
225A PHE* 1.3 58.0 + - - +
227A GLU* 4.0 15.8 + - - +
228A THR* 2.9 19.8 + - - -
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Residues in contact with PHE 225 (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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140A ALA* 5.5 9.4 - - + -
141A PRO 4.0 11.4 - - - -
142A ILE* 3.4 51.8 - - + -
143A PHE 5.5 1.6 - - - -
221A ILE 3.3 13.6 + - - +
222A LEU 3.4 9.2 - - - +
223A ASN 2.9 0.8 - - - -
224A ALA* 1.3 78.2 - - - +
226A LEU* 1.3 81.2 + - + +
228A THR* 2.9 31.4 - - + -
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Residues in contact with LEU 226 (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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87A GLY* 6.6 0.9 - - - -
222A LEU* 3.1 20.6 + - + +
223A ASN* 3.0 15.8 + - - +
225A PHE* 1.3 87.1 - - + +
227A GLU* 1.3 58.6 + - + +
228A THR* 2.8 17.2 + - - -
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Residues in contact with GLU 227 (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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220A GLN* 5.0 6.6 + - - -
223A ASN* 2.9 26.9 + - + +
224A ALA* 4.1 12.4 + - - +
225A PHE 3.2 0.6 - - - -
226A LEU* 1.3 74.4 - - + +
228A THR* 1.3 59.9 + - - +
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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