Contacts of the helix formed by residues 212 - 230 (chain A) in PDB entry 2HXO
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 ASP 212 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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210A GLY 3.3 6.7 + - - +
211A HIS* 1.3 77.0 + - - +
213A ASP* 1.3 67.3 + - - +
214A ARG* 3.2 15.3 + - - +
215A GLU* 3.0 39.6 + - + +
216A GLN* 3.1 21.1 + - - +
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Residues in contact with ASP 213 (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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98A TRP* 3.7 24.9 - - + -
163A ASN* 4.6 6.7 - - - +
166A ASN* 5.6 9.5 + - - +
183A LEU* 4.8 13.1 - - - +
211A HIS* 3.9 21.1 + - - +
212A ASP* 1.3 75.7 + - - +
214A ARG* 1.3 52.7 + - - +
216A GLN* 3.0 9.3 + - - +
217A PHE* 2.8 34.7 + - - +
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Residues in contact with ARG 214 (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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95A LEU* 4.0 35.9 - - + +
98A TRP* 3.7 28.3 - - + +
99A ASP* 3.1 38.4 + - - -
102A GLU* 5.5 3.3 + - - -
212A ASP* 3.2 14.8 + - - +
213A ASP* 1.3 77.6 - - - +
215A GLU* 1.3 72.6 + - - +
217A PHE* 3.2 5.0 - - - +
218A LEU* 3.1 27.4 + - + +
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Residues in contact with GLU 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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212A ASP* 3.0 35.0 + - + +
213A ASP 3.3 0.4 - - - -
214A ARG* 1.3 83.8 + - - +
216A GLN* 1.3 66.8 + - - +
218A LEU* 3.3 22.9 + - - +
219A ALA* 2.9 24.5 + - - +
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Residues in contact with GLN 216 (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 TYR* 3.7 1.6 + - - -
211A HIS* 3.3 37.3 + - + +
212A ASP 3.1 5.7 + - - +
213A ASP 3.0 9.8 + - - +
215A GLU* 1.3 76.5 - - - +
217A PHE* 1.3 65.4 + - - +
219A ALA* 3.1 4.9 + - - +
220A GLY* 2.8 22.0 + - - +
146B PHE* 4.1 2.1 - - - -
147B THR* 3.2 49.3 + - - +
150B SER* 3.7 16.3 - - - -
151B ALA* 3.9 10.7 - - - +
154B HIS* 4.0 25.5 + - + +
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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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94A ALA* 3.2 49.4 - - + -
95A LEU* 3.9 15.5 - - + -
98A TRP* 3.4 41.3 - + + -
155A TYR* 3.0 33.5 + + - -
156A ILE* 4.1 25.6 - - + -
159A ALA* 3.4 32.1 - - + -
160A ALA* 4.2 0.7 - - + -
213A ASP 2.8 12.6 + - - +
214A ARG* 3.2 9.9 - - - +
216A GLN* 1.3 76.5 - - - +
218A LEU* 1.3 64.4 + - + +
221A ILE* 3.1 13.1 + - + +
154B HIS* 5.9 0.2 - - - -
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Residues in contact with LEU 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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91A ARG* 4.3 26.9 - - + +
94A ALA* 5.6 0.2 - - + -
95A LEU* 3.3 52.0 - - + -
214A ARG* 3.1 12.9 + - - +
215A GLU* 3.9 29.4 - - - +
217A PHE* 1.3 79.9 - - + +
219A ALA* 1.3 56.2 + - - +
221A ILE* 3.0 16.7 - - + +
222A THR* 2.8 28.8 + - - +
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Residues in contact with ALA 219 (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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215A GLU 2.9 18.3 + - - +
216A GLN* 3.5 5.4 - - - +
218A LEU* 1.3 74.3 - - - +
220A GLY* 1.3 61.4 - - - +
222A THR* 3.2 8.2 + - - +
223A LEU* 2.9 32.9 + - - +
147B THR* 3.7 26.0 - - + -
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Residues in contact with GLY 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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155A TYR* 3.2 26.5 - - - -
216A GLN* 2.8 13.3 + - - +
219A ALA* 1.3 74.5 - - - +
221A ILE* 1.3 64.5 + - - +
223A LEU* 3.1 6.4 + - - +
224A VAL* 3.0 25.1 + - - +
151B ALA* 4.1 19.3 - - - +
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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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90A VAL* 4.3 12.3 - - + +
91A ARG* 3.9 24.2 - - + -
94A ALA* 4.3 14.6 - - + -
152A LEU* 3.6 29.8 - - + +
155A TYR* 3.6 27.2 - - + -
156A ILE* 3.9 22.4 - - + -
217A PHE* 3.1 11.7 + - + +
218A LEU* 3.0 28.0 - - + +
220A GLY* 1.3 75.4 - - - +
222A THR* 1.3 62.8 + - - +
224A VAL* 3.1 5.5 + - + +
225A LEU* 2.8 33.3 + - + +
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Residues in contact with THR 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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91A ARG* 3.0 35.7 + - - +
218A LEU* 2.8 20.2 + - - +
219A ALA* 3.5 7.9 - - - -
220A GLY 3.2 0.2 - - - -
221A ILE* 1.3 79.9 - - - +
223A LEU* 1.3 57.5 + - + +
225A LEU* 3.3 9.5 + - + +
226A THR* 2.9 39.4 + - - +
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Residues in contact with LEU 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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219A ALA 2.9 13.9 + - - +
220A GLY* 3.1 11.2 + - - +
222A THR* 1.3 78.3 - - + +
224A VAL* 1.3 63.4 + - + +
226A THR* 3.3 4.7 + - - +
227A GLY* 3.2 15.8 + - - -
147B THR* 4.6 9.9 - - + +
148B ALA* 4.3 12.6 - - + -
151B ALA* 3.9 25.8 - - + -
223B LEU 4.2 1.4 - - - +
224B VAL* 4.6 7.2 - - + +
227B GLY* 3.4 36.2 + - - +
228B ILE* 4.0 24.2 - - + +
231B LEU* 3.9 24.2 - - + -
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Residues in contact with VAL 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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151A ALA* 4.5 15.9 - - + -
152A LEU* 3.8 25.6 - - + +
155A TYR* 4.2 25.8 - - + -
220A GLY 3.0 15.6 + - - +
221A ILE* 3.5 6.5 - - - +
223A LEU* 1.3 76.2 - - + +
225A LEU* 1.3 58.5 + - - +
227A GLY* 3.0 4.0 + - - -
228A ILE* 2.9 38.2 + - + +
151B ALA* 6.5 0.2 - - + -
155B TYR* 5.6 0.9 - - + -
223B LEU* 4.6 13.7 - - + +
224B VAL* 4.0 24.2 - - + +
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Residues in contact with LEU 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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87A GLN* 3.7 40.8 - - + +
90A VAL* 3.8 35.4 - - + -
91A ARG* 4.3 13.2 - - + +
138A MSE 3.5 21.0 - - + +
152A LEU* 4.0 17.3 - - + -
221A ILE* 2.8 26.4 + - + +
222A THR* 3.6 9.6 - - - +
224A VAL* 1.3 76.0 - - - +
226A THR* 1.3 51.5 + - - +
228A ILE* 3.2 5.3 + - + -
229A THR* 2.7 40.2 + - - +
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Residues in contact with THR 226 (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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222A THR* 2.9 27.5 + - - +
223A LEU* 3.6 9.0 - - - +
224A VAL 3.2 0.2 - - - -
225A LEU* 1.3 75.8 - - - +
227A GLY* 1.3 62.9 + - - +
229A THR* 2.9 26.0 + - - +
230A ALA* 3.4 9.2 + - - +
226B THR* 4.8 1.9 - - + +
227B GLY* 4.0 9.4 - - - +
230B ALA* 3.9 28.0 - - + -
231B LEU* 6.6 0.2 - - + -
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Residues in contact with GLY 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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223A LEU 3.2 4.9 + - - -
224A VAL 3.0 4.9 + - - -
226A THR* 1.3 80.2 - - - +
228A ILE* 1.3 62.6 - - - +
230A ALA* 3.2 17.0 + - - +
231A LEU* 3.8 3.6 + - - +
223B LEU* 3.4 37.8 - - - +
226B THR* 3.9 17.6 - - - +
227B GLY* 4.1 1.1 - - - -
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Residues in contact with ILE 228 (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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135A VAL* 4.8 3.1 - - + -
138A MSE 3.7 16.6 - - + -
140A VAL* 3.6 26.7 - - + +
148A ALA* 3.6 29.8 - - + +
152A LEU* 3.6 38.6 - - + -
224A VAL* 2.9 25.3 + - + +
225A LEU* 3.6 9.6 - - + +
227A GLY* 1.3 77.6 - - - +
229A THR* 1.3 57.6 + - - +
231A LEU* 2.9 28.2 + - + +
232A HIS 4.2 0.2 + - - -
223B LEU* 3.9 20.0 - - + -
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Residues in contact with THR 229 (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 GLN* 3.3 20.9 - - + +
138A MSE 3.0 28.9 - - + +
225A LEU 2.7 32.5 + - - +
226A THR* 2.9 19.8 + - - +
228A ILE* 1.3 75.6 - - - +
230A ALA* 1.3 59.9 + - - +
231A LEU 3.1 1.5 + - - -
232A HIS* 3.4 19.6 + - - +
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Residues in contact with ALA 230 (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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226A THR 3.4 7.3 + - - +
227A GLY 3.2 12.3 + - - +
228A ILE 3.1 1.4 - - - -
229A THR* 1.3 77.6 + - - +
231A LEU* 1.3 60.9 + - - +
232A HIS 3.2 6.7 + - - +
233A ARG* 3.7 17.2 + - - -
226B THR* 4.0 18.4 - - + -
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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