Contacts of the helix formed by residues 221 - 238 (chain A) in PDB entry 3ZHP
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 ASN 221 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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173A GLU* 4.1 6.1 + - - +
174A LEU 5.5 4.8 + - - -
177A PHE* 5.2 5.5 - - - -
180A ALA* 6.4 0.2 - - - +
219A SER* 3.1 13.2 + - - +
220A GLU* 1.3 77.3 - - - +
222A TYR* 1.4 59.5 + - - +
223A VAL* 3.1 14.4 + - - +
224A THR* 2.9 36.6 + - - +
225A LYS* 2.9 29.9 + - - +
90D LEU* 3.4 26.6 - - - +
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Residues in contact with TYR 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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220A GLU 3.5 5.3 + - - +
221A ASN* 1.4 69.7 + - - +
223A VAL* 1.3 60.7 + - + +
225A LYS* 3.4 8.9 + - - +
226A ARG* 2.8 55.1 + - + +
266A SER* 3.4 25.8 - - - -
268A ASN* 3.0 30.4 + - + +
269A ILE* 3.8 21.8 - - + -
57D LEU* 3.6 41.5 + - + -
58D GLU* 3.9 4.5 + - - -
64D ILE* 4.7 4.0 - - + -
90D LEU* 4.6 1.4 - - + +
92D ASP* 3.3 26.7 + - - +
93D THR* 4.0 19.1 - - - -
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Residues in contact with VAL 223 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
177A PHE* 3.7 21.3 - - + -
181A SER* 5.4 0.2 - - - +
221A ASN* 3.1 6.8 + - - +
222A TYR* 1.3 75.8 - - + +
224A THR* 1.4 58.5 + - - +
226A ARG* 3.2 3.7 + - - +
227A GLN* 2.9 55.1 + - + +
57D LEU* 3.8 25.4 - - + -
64D ILE* 4.2 12.6 - - + -
68D GLN* 4.0 18.8 - - - +
90D LEU* 3.7 20.6 - - + -
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Residues in contact with THR 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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172A VAL* 3.7 19.2 + - + +
173A GLU* 3.4 28.4 + - + +
184A PHE* 5.9 4.0 - - + -
216A LEU* 3.9 20.2 - - + +
219A SER* 3.4 20.2 - - - +
221A ASN* 2.9 21.6 + - - +
223A VAL* 1.4 73.9 - - - +
225A LYS* 1.3 58.9 + - - +
227A GLN* 5.1 2.0 - - - -
228A SER* 2.6 37.5 + - - +
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Residues in contact with LYS 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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216A LEU 3.6 8.9 + - - +
217A LEU* 3.4 30.9 - - - +
218A GLN* 4.9 2.7 - - - +
219A SER* 3.3 23.7 + - - +
220A GLU* 5.4 3.8 + - - +
221A ASN 2.9 18.4 + - - +
222A TYR* 3.7 7.9 - - - +
224A THR* 1.3 76.3 - - - +
226A ARG* 1.3 58.3 + - - +
228A SER* 4.3 0.7 - - - -
229A LEU* 3.2 29.0 + - + +
261A LEU* 4.2 8.7 - - + -
264A ASP* 3.1 26.3 + - - -
269A ILE* 3.8 30.6 - - + +
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Residues in contact with ARG 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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222A TYR* 2.8 47.1 + - + +
223A VAL* 3.8 4.9 - - - +
225A LYS* 1.3 71.0 - - - +
227A GLN* 1.3 78.4 + - - +
229A LEU* 3.4 4.9 + - - +
230A LYS* 3.0 49.2 + - - +
268A ASN* 4.2 23.6 - - - +
269A ILE* 3.5 17.9 - - + +
272A GLU* 3.2 30.4 + - + +
61D GLU* 4.6 2.6 - - - +
62D ASP* 3.1 43.6 + - - +
64D ILE* 3.6 18.6 - - + +
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Residues in contact with GLN 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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184A PHE* 3.4 33.0 - - + -
223A VAL* 2.9 37.4 + - + +
224A THR* 4.6 1.3 - - - +
226A ARG* 1.3 99.7 + - + +
228A SER* 1.4 57.6 + - - +
230A LYS* 3.5 11.2 + - - +
231A LEU* 2.9 30.3 + - - +
64D ILE* 4.2 14.2 - - - +
65D GLU* 4.7 9.3 - - - +
68D GLN* 3.8 23.6 - - - +
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Residues in contact with SER 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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184A PHE* 3.7 12.3 - - - -
213A TYR* 2.6 34.5 + - - -
216A LEU* 3.4 40.6 - - - +
217A LEU* 4.0 6.7 - - - -
224A THR* 2.6 26.6 + - - +
225A LYS 4.3 0.7 - - - -
227A GLN* 1.4 73.4 - - - +
229A LEU* 1.3 59.2 + - - +
231A LEU 3.5 0.2 + - - -
232A LEU* 2.9 17.7 + - - +
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Residues in contact with LEU 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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217A LEU* 3.8 20.5 - - + +
225A LYS* 3.2 20.4 + - + +
226A ARG 3.6 4.5 - - - +
228A SER* 1.3 77.1 - - - +
230A LYS* 1.3 62.7 + - - +
232A LEU* 3.6 3.8 + - + +
233A GLY* 3.2 17.0 + - - -
258A MET* 3.8 32.1 - - + -
261A LEU* 3.9 13.7 - - + -
269A ILE* 3.3 37.2 - - + +
272A GLU* 3.8 17.6 - - + +
273A ALA* 3.5 14.4 - - + +
276A VAL* 3.7 13.1 - - + +
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Residues in contact with LYS 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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188A LYS* 6.3 1.1 - - - +
226A ARG* 3.0 45.5 + - - +
227A GLN* 3.7 15.3 - - - +
229A LEU* 1.3 73.3 - - - +
231A LEU* 1.4 59.0 + - - +
233A GLY* 3.3 3.3 + - - -
234A GLU* 2.9 55.3 + - + +
272A GLU* 3.5 26.4 + - + +
62D ASP* 4.2 14.6 + - - +
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Residues in contact with LEU 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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184A PHE* 3.7 23.6 - - + -
187A PHE* 4.0 17.3 - - + -
188A LYS* 3.8 27.6 - - + +
191A LEU* 4.5 7.9 - - + -
192A THR* 3.8 29.6 - - + -
213A TYR* 3.4 14.8 - - - +
227A GLN 2.9 18.3 + - - +
230A LYS* 1.4 71.5 - - - +
232A LEU* 1.4 54.2 + - - +
234A GLU* 3.1 18.1 + - + +
235A LEU* 2.8 45.6 + - + +
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Residues in contact with LEU 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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210A PHE* 3.8 26.5 - - + -
213A TYR* 3.3 19.4 + - + -
217A LEU* 3.9 20.2 - - + -
228A SER 2.9 18.6 + - - +
229A LEU* 3.6 4.0 - - + +
231A LEU* 1.4 74.1 - - - +
233A GLY* 1.3 62.2 + - - +
235A LEU* 3.3 11.2 + - + +
236A ILE* 3.1 48.4 + - + +
248A TYR* 3.4 30.1 - - + +
258A MET* 4.0 5.4 - - + -
276A VAL* 3.8 19.1 - - + -
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Residues in contact with GLY 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 LEU 3.2 11.9 + - - -
230A LYS 3.6 3.8 - - - -
232A LEU* 1.3 80.1 - - - +
234A GLU* 1.4 60.3 + - - +
236A ILE* 4.1 5.9 - - - +
237A LEU* 3.3 37.9 + - - +
275A HIS* 5.3 4.9 - - - -
276A VAL* 4.0 19.5 - - - +
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Residues in contact with GLU 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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188A LYS* 4.0 23.4 + - - -
192A THR* 5.7 3.6 - - + -
230A LYS* 2.9 47.5 + - + +
231A LEU* 3.3 26.1 + - + +
233A GLY* 1.4 76.1 - - - +
235A LEU* 1.4 63.1 + - - +
237A LEU* 3.6 5.9 + - - +
238A ASP* 3.5 18.7 + - - +
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Residues in contact with LEU 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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191A LEU* 3.4 43.1 - - + +
192A THR* 4.9 4.0 - - + -
198A VAL* 4.6 0.2 - - + -
202A LEU* 4.1 27.6 - - + -
210A PHE* 5.7 7.2 - - + -
213A TYR* 4.5 9.6 - - + +
231A LEU* 2.8 44.2 + - + +
232A LEU* 3.6 13.9 - - + +
234A GLU* 1.4 71.4 - - - +
236A ILE* 1.3 62.3 + - + +
238A ASP* 3.2 8.4 + - - -
241A ASN* 2.7 37.7 + - - +
244A ILE* 6.1 3.4 - - + -
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Residues in contact with ILE 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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210A PHE* 5.5 2.0 - - + -
232A LEU* 3.1 37.3 + - + +
233A GLY* 4.1 7.2 - - - +
235A LEU* 1.3 79.8 - - + +
237A LEU* 1.3 61.3 + - - +
238A ASP 3.5 6.1 + - - +
241A ASN* 4.4 2.6 - - - +
244A ILE* 5.0 5.8 - - + +
245A MET* 3.3 48.4 - - + +
248A TYR* 3.6 35.2 - - + -
249A ILE* 5.4 2.0 - - + -
276A VAL* 4.5 7.9 - - + -
279A VAL* 3.8 40.2 - - + -
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Residues in contact with LEU 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 GLY* 3.3 24.9 + - - +
234A GLU* 4.1 5.4 - - - +
235A LEU 3.3 0.4 - - - -
236A ILE* 1.3 73.7 - - - +
238A ASP* 1.4 61.9 + - - +
239A ARG* 3.7 1.7 + - - -
275A HIS* 4.8 9.0 - - + +
278A LYS* 4.6 24.9 - - - +
279A VAL* 4.3 20.6 - - + -
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Residues in contact with ASP 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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195A LYS* 3.4 31.3 + - - +
234A GLU 3.5 10.5 + - - +
235A LEU* 3.2 4.8 + - - +
236A ILE 3.8 7.4 - - - +
237A LEU* 1.4 77.6 - - - +
239A ARG* 1.3 66.8 + - - +
240A HIS* 2.7 45.0 + - - +
241A ASN* 3.2 34.5 + - - +
242A PHE* 4.1 1.0 + - - -
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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