Contacts of the helix formed by residues 222 - 238 (chain A) in PDB entry 2NUN
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 TYR 222 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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171A ASN* 5.0 2.7 - - - -
173A ILE* 3.7 32.0 - - + +
174A PRO* 3.8 43.6 - - + +
218A THR* 4.4 2.2 - - + -
219A ASN* 3.1 35.6 + - + +
220A ALA 2.9 1.4 + - - -
221A SER* 1.3 86.4 - - - +
223A LEU* 1.3 63.0 + - - +
224A PRO* 3.4 2.9 - - - -
225A ILE* 3.5 18.4 - - + +
226A ILE* 3.1 38.8 + - + +
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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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116A GLU* 4.1 8.5 - - + +
117A ARG* 3.5 34.1 - - + +
218A THR* 5.4 0.9 - - + -
219A ASN 5.0 2.0 - - - +
220A ALA* 2.9 30.3 + - + +
222A TYR* 1.3 77.3 - - - +
224A PRO* 1.3 57.1 - - + +
226A ILE* 3.0 6.0 + - + +
227A LYS* 2.6 53.7 + - + +
261A ALA* 4.0 32.8 - - + +
263A PRO* 3.8 32.5 - - + +
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Residues in contact with PRO 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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220A ALA 3.9 3.6 - - - +
221A SER* 3.8 12.8 - - - +
222A TYR 3.5 3.1 - - - -
223A LEU* 1.3 94.7 - - + +
225A ILE* 1.3 61.4 + - + +
227A LYS* 3.3 14.2 + - + +
228A ASP* 2.9 37.6 + - - +
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Residues in contact with ILE 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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168A LEU* 3.8 29.0 - - + +
169A HIS* 5.9 2.8 - - + +
171A ASN* 4.6 15.7 - - - +
173A ILE* 4.7 6.3 - - + -
222A TYR* 3.5 31.8 + - + +
224A PRO* 1.3 79.5 - - + +
226A ILE* 1.3 62.9 + - + +
228A ASP* 3.7 11.7 - - - +
229A HIS* 2.9 28.4 + - - +
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Residues in contact with ILE 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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168A LEU* 5.3 0.9 - - + -
173A ILE* 4.5 5.2 - - + -
175A LEU* 4.3 14.8 - - + -
218A THR* 4.2 13.9 - - + -
222A TYR* 3.1 33.5 + - + +
223A LEU* 3.0 8.6 + - + +
225A ILE* 1.3 80.5 - - + +
227A LYS* 1.3 61.1 + - + +
229A HIS* 3.1 7.5 + - - +
230A LEU* 2.8 40.4 + - + +
257A TRP* 4.2 29.4 - - + +
261A ALA* 3.6 34.5 - - + -
263A PRO* 6.0 0.4 - - + -
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Residues in contact with LYS 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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88A PHE* 5.3 4.0 - - + -
89A GLU* 6.1 9.4 - - + -
92A TRP* 6.4 1.8 - - + -
116A GLU* 2.6 44.3 + - - +
223A LEU* 2.6 35.8 + - + +
224A PRO* 3.8 11.9 - - + +
226A ILE* 1.3 73.4 - - + +
228A ASP* 1.3 65.2 + - - +
230A LEU* 3.2 13.5 + - + +
231A ASN* 3.0 28.7 + - - +
263A PRO* 5.1 13.9 - - + -
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Residues in contact with ASP 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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224A PRO* 2.9 27.7 + - - +
225A ILE* 3.7 9.7 - - - +
227A LYS* 1.3 77.8 - - - +
229A HIS* 1.3 63.8 + - - +
231A ASN* 3.1 14.6 + - - +
232A ASP* 3.0 27.4 + - - +
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Residues in contact with HIS 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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168A LEU* 3.4 28.7 - - + +
169A HIS* 4.6 9.6 - + + +
225A ILE 2.9 18.4 + - - +
226A ILE* 3.1 8.7 + - - +
228A ASP* 1.3 78.3 - - - +
230A LEU* 1.3 61.2 + - - +
232A ASP* 3.0 19.2 + - + +
233A LEU* 3.0 49.1 + - + +
236A GLN* 5.8 0.8 + - - -
257A TRP* 3.5 45.6 - + + -
305A GLU* 5.1 2.0 - - - -
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Residues in contact with LEU 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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88A PHE* 3.7 39.0 - - + +
226A ILE* 2.8 32.8 + - + +
227A LYS* 3.2 13.7 + - + +
229A HIS* 1.3 72.5 - - + +
231A ASN* 1.3 57.8 + - - +
233A LEU* 3.3 7.9 + - + +
234A TYR* 3.0 27.4 + - - +
254A THR* 3.5 45.2 + - + +
257A TRP* 3.8 16.4 - - + -
258A ALA* 3.9 20.0 - - + +
263A PRO* 5.2 7.9 - - + -
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Residues in contact with ASN 231 (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 SER* 3.8 10.9 - - - +
88A PHE* 2.8 42.7 - - - +
89A GLU* 3.3 19.9 - - - +
227A LYS* 3.0 17.0 + - - +
228A ASP* 3.1 16.3 + - - +
230A LEU* 1.3 76.9 - - - +
232A ASP* 1.3 59.9 + - - +
234A TYR* 3.3 3.9 + - - +
235A ARG* 3.0 28.6 + - - +
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Residues in contact with ASP 232 (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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169A HIS* 5.0 9.5 + - - -
228A ASP* 3.0 21.4 + - - +
229A HIS* 3.0 24.1 + - + +
231A ASN* 1.3 78.3 - - - +
233A LEU* 1.3 61.4 + - - +
235A ARG* 3.5 7.5 + - - +
236A GLN* 3.2 33.7 + - - +
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Residues in contact with LEU 233 (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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229A HIS* 3.0 49.5 + - + +
230A LEU* 3.3 11.2 + - + +
231A ASN 3.3 0.2 - - - -
232A ASP* 1.3 74.1 - - - +
234A TYR* 1.3 56.5 + - - +
236A GLN* 3.3 22.1 + - - +
237A ALA* 2.7 36.7 + - - +
250A LEU* 4.1 18.9 - - + +
253A ARG* 4.2 13.2 - - + -
254A THR* 3.7 31.6 + - - +
257A TRP* 3.8 19.7 - - + +
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Residues in contact with TYR 234 (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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80A ILE* 3.5 20.5 - - + +
85A ILE* 3.0 29.9 + - + +
86A THR 3.5 24.9 - - - -
87A SER* 3.6 20.2 - - - -
88A PHE* 3.8 21.3 - - + -
91A LEU* 4.1 20.9 - - + -
230A LEU 3.0 13.7 + - - +
231A ASN 3.5 9.0 - - - +
232A ASP 3.3 0.2 - - - -
233A LEU* 1.3 73.6 - - - +
235A ARG* 1.3 72.9 + - - +
237A ALA* 3.1 5.7 + - - -
238A ILE* 3.0 52.6 + - + +
254A THR* 4.9 1.0 + - - -
279A ILE* 4.2 22.2 - - + -
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Residues in contact with ARG 235 (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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25A SER 5.4 6.1 + - - -
26A PHE* 6.1 1.8 - - - +
27A ARG* 5.2 19.6 - - - +
86A THR 5.2 8.2 + - - -
231A ASN 3.0 14.0 + - - +
232A ASP* 3.6 11.4 - - - +
233A LEU 3.3 0.2 - - - -
234A TYR* 1.3 80.1 - - - +
236A GLN* 1.3 63.5 + - + +
238A ILE* 3.3 32.7 - - - +
239A SER* 4.2 5.8 + - - +
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Residues in contact with GLN 236 (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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229A HIS* 5.8 1.0 + - - -
232A ASP* 3.2 23.6 + - - +
233A LEU* 3.5 24.7 - - - +
234A TYR 3.1 0.6 - - - -
235A ARG* 1.3 78.6 - - + +
237A ALA* 1.3 61.9 + - - +
239A SER* 3.1 27.4 + - - -
242A LEU* 3.4 7.3 - - + +
250A LEU* 3.9 25.3 - - + +
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Residues in contact with ALA 237 (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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233A LEU 2.7 22.1 + - - +
234A TYR* 3.1 8.7 + - - +
236A GLN* 1.3 73.5 - - - +
238A ILE* 1.3 50.5 + - + +
239A SER 3.2 1.3 + - - -
242A LEU* 3.9 5.1 - - - +
247A LEU* 4.0 3.2 - - + +
250A LEU* 3.8 24.9 - - + +
254A THR* 5.2 2.7 - - - +
279A ILE* 3.8 26.2 - - + +
283A HIS* 2.6 35.3 + - - -
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Residues in contact with ILE 238 (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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26A PHE* 6.2 4.0 - - + -
27A ARG* 4.8 10.6 + - - +
29A LEU* 3.9 18.2 - - + +
80A ILE* 3.8 19.1 - - + +
85A ILE 5.8 1.1 - - - +
86A THR* 5.3 3.4 - - - +
234A TYR* 3.0 51.8 + - + +
235A ARG* 3.3 42.0 - - - +
236A GLN 3.2 0.2 + - - -
237A ALA* 1.3 78.3 - - + +
239A SER* 1.3 63.1 + - - +
240A SER 3.7 1.2 + - - -
279A ILE* 5.4 3.8 - - + -
283A HIS* 4.1 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