Contacts of the helix formed by residues 225 - 248 (chain A) in PDB entry 2Z43
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 225 (chain A).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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219A GLU 5.3 0.4 + - - -
220A TYR* 3.7 29.4 - - + +
221A PRO* 3.4 21.5 + - - +
222A GLY 3.0 3.0 + - - -
224A GLU* 1.3 101.1 + - - +
226A LEU* 1.3 64.7 + - - +
227A ALA 3.4 2.2 - - - -
228A VAL* 3.3 21.3 + - + +
229A ARG* 2.9 23.9 + - - +
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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
----------------------------------------------------------
222A GLY 3.1 3.8 + - - -
223A ARG* 3.3 51.1 - - + +
224A GLU 3.3 2.2 - - - -
225A ASN* 1.3 78.0 - - - +
227A ALA* 1.3 60.1 + - - +
229A ARG* 3.1 35.8 + - - +
230A GLN* 2.9 62.9 + - + +
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Residues in contact with ALA 227 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
223A ARG* 4.8 2.6 + - - +
224A GLU 4.9 3.5 + - - +
225A ASN 3.4 0.6 - - - -
226A LEU* 1.3 79.6 - - - +
228A VAL* 1.3 65.8 + - + +
230A GLN* 3.3 11.3 + - - +
231A GLN* 3.1 21.1 + - - +
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Residues in contact with VAL 228 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
220A TYR* 4.1 22.2 - - + -
224A GLU 5.1 2.7 - - - +
225A ASN* 3.3 26.8 + - - +
227A ALA* 1.3 78.7 - - + +
229A ARG* 1.3 63.6 + - - +
231A GLN* 3.1 18.9 + - + +
232A LYS* 3.2 22.0 + - + +
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Residues in contact with ARG 229 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
216A PHE* 4.7 13.4 - - + +
217A ARG* 4.1 35.8 + - - +
220A TYR* 3.9 37.9 + - + -
221A PRO* 5.2 0.2 - - - +
222A GLY 3.2 32.5 + - - +
223A ARG* 4.2 2.2 - - - +
225A ASN 2.9 11.5 + - - +
226A LEU* 3.2 40.6 - - - +
228A VAL* 1.3 78.5 - - - +
230A GLN* 1.3 67.2 + - + +
231A GLN 3.2 0.2 + - - -
232A LYS* 3.4 2.0 + - - +
233A LEU* 3.1 31.8 + - + +
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Residues in contact with GLN 230 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
226A LEU* 2.9 56.3 + - + +
227A ALA* 3.5 9.4 - - - +
229A ARG* 1.3 81.6 - - + +
231A GLN* 1.3 61.9 + - - +
233A LEU* 4.0 9.8 - - - +
234A ASN* 3.1 27.7 + - - +
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Residues in contact with GLN 231 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
227A ALA 3.1 12.5 + - - +
228A VAL* 3.2 16.9 - - + +
229A ARG 3.1 0.2 - - - -
230A GLN* 1.3 77.2 - - - +
232A LYS* 1.3 81.3 + - - +
234A ASN* 2.7 36.3 + - - +
235A LYS* 3.2 10.3 + - - +
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Residues in contact with LYS 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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188A ILE* 4.8 6.7 - - + -
216A PHE* 3.7 21.7 - - + -
220A TYR* 3.7 29.3 + - + +
228A VAL* 3.2 17.0 + - + +
229A ARG 4.1 2.5 - - - +
231A GLN* 1.3 92.7 + - - +
233A LEU* 1.3 58.5 + - - +
235A LYS* 3.0 41.2 + - - +
236A HIS* 2.9 27.7 + - - +
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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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212A VAL* 4.5 6.1 - - + -
213A THR* 3.6 34.5 - - + -
216A PHE* 3.7 36.7 - - + -
229A ARG* 3.1 21.5 + - + +
230A GLN* 4.0 10.1 - - - +
232A LYS* 1.3 78.3 - - - +
234A ASN* 1.3 52.6 + - - +
236A HIS* 3.2 2.1 + - - +
237A LEU* 2.8 66.0 + - + +
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Residues in contact with ASN 234 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
230A GLN 3.1 18.2 + - - +
231A GLN* 2.7 32.9 + - - +
233A LEU* 1.3 77.5 - - - +
235A LYS* 1.3 73.1 + - - +
237A LEU* 3.5 6.3 + - - +
238A HIS* 3.0 25.3 + - - +
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Residues in contact with LYS 235 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
188A ILE* 4.1 24.0 - - - +
231A GLN* 3.7 14.8 - - - +
232A LYS* 3.0 48.0 + - + +
234A ASN* 1.3 88.8 - - - +
236A HIS* 1.3 62.9 + - - +
238A HIS* 3.0 18.9 + - + +
239A GLN* 3.1 12.3 + - - +
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Residues in contact with HIS 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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187A GLN* 2.8 42.6 + - + +
188A ILE* 3.9 25.6 - - + -
191A VAL* 3.1 36.6 - - + +
209A VAL* 4.9 3.6 - - + -
212A VAL* 4.1 15.0 - - + +
216A PHE* 3.7 19.7 - + + -
232A LYS 2.9 11.8 + - - +
233A LEU 3.5 7.8 + - - +
235A LYS* 1.3 79.5 - - - +
237A LEU* 1.3 63.2 + - - +
239A GLN* 3.0 19.6 + - + +
240A LEU* 3.1 19.3 + - + +
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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
----------------------------------------------------------
109A MET* 3.4 33.4 - - + +
212A VAL* 4.2 10.3 - - + -
213A THR* 5.6 0.9 - - + -
233A LEU* 2.8 51.4 + - + +
234A ASN* 3.9 7.0 - - - +
236A HIS* 1.3 73.7 - - - +
238A HIS* 1.3 59.2 + - - +
240A LEU* 3.4 19.7 + - + +
241A THR* 2.9 29.9 + - - +
253A ILE* 3.5 24.2 - - + -
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Residues in contact with HIS 238 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
234A ASN* 3.0 16.2 + - - +
235A LYS* 3.0 14.6 + - + +
237A LEU* 1.3 75.6 - - - +
239A GLN* 1.3 69.3 + - - +
241A THR* 2.6 32.4 + - - +
242A ARG* 2.8 34.8 + - + +
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Residues in contact with GLN 239 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
191A VAL* 3.8 25.0 + - + +
192A ASP* 4.4 24.8 + - - +
195A GLN* 4.5 15.7 - - - +
235A LYS 3.1 6.9 + - - +
236A HIS* 3.0 14.2 + - + +
238A HIS* 1.3 83.7 - - - +
240A LEU* 1.3 55.8 + - - +
242A ARG* 3.3 11.5 + - - +
243A LEU* 2.9 29.4 + - + +
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Residues in contact with LEU 240 (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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109A MET* 4.0 10.5 - - - -
191A VAL* 4.3 17.7 - - + -
194A LEU* 5.4 0.4 - - + -
207A ILE* 4.7 7.6 - - + -
209A VAL* 4.0 19.1 - - + -
212A VAL* 4.8 1.3 - - + -
236A HIS* 3.1 30.3 + - + +
237A LEU* 3.5 33.9 - - + +
238A HIS 3.1 0.4 - - - -
239A GLN* 1.3 78.1 - - - +
241A THR* 1.3 56.8 + - - +
243A LEU* 3.2 11.7 + - + +
244A ALA* 2.9 27.8 + - - +
251A VAL* 3.6 32.5 - - + +
253A ILE* 4.1 11.4 - - + -
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Residues in contact with THR 241 (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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109A MET* 4.2 26.2 - - + +
237A LEU 2.9 19.9 + - - +
238A HIS* 2.6 32.3 + - - +
240A LEU* 1.3 71.4 - - - +
242A ARG* 1.3 73.4 + - - +
244A ALA* 3.1 7.7 + - - +
245A GLU* 2.9 41.2 + - - +
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Residues in contact with ARG 242 (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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238A HIS* 2.8 38.8 + - + +
239A GLN* 3.6 15.5 - - - +
241A THR* 1.3 81.6 + - - +
243A LEU* 1.3 64.1 + - - +
245A GLU* 3.4 17.5 + - - +
246A VAL* 3.0 59.4 + - + +
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Residues in contact with LEU 243 (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 VAL* 5.5 4.5 - - + +
194A LEU* 3.9 29.8 - - + -
195A GLN* 4.6 12.3 - - + +
198A VAL* 4.2 8.5 - - + -
207A ILE* 3.3 32.8 - - + -
239A GLN* 2.9 14.4 + - + +
240A LEU* 3.3 14.4 - - + +
241A THR 3.1 0.2 - - - -
242A ARG* 1.3 76.9 - - - +
244A ALA* 1.3 63.6 + - - +
247A TYR* 3.1 59.2 + - + +
249A ILE* 4.1 9.0 - - + -
251A VAL* 4.9 3.1 - - + -
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Residues in contact with ALA 244 (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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107A ARG* 3.4 7.0 - - - +
108A THR* 4.0 21.5 - - - +
109A MET* 4.7 0.4 - - - +
240A LEU 2.9 12.9 + - - +
241A THR* 3.6 9.9 - - - +
243A LEU* 1.3 75.3 - - - +
245A GLU* 1.3 58.9 + - - +
248A ASP* 2.9 25.6 + - - -
249A ILE* 3.0 33.7 + - - +
251A VAL* 3.8 14.8 - - + +
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Residues in contact with GLU 245 (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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107A ARG* 3.4 46.4 + - + +
108A THR* 5.9 0.2 - - - -
241A THR* 2.9 34.9 + - - +
242A ARG* 4.0 25.7 + - - +
244A ALA* 1.3 75.1 - - + +
246A VAL* 1.3 62.9 + - + +
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Residues in contact with VAL 246 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
107A ARG* 5.1 2.2 + - - -
242A ARG* 3.0 58.2 + - - +
245A GLU* 1.3 74.8 - - + +
247A TYR* 1.3 81.7 + - + +
248A ASP 3.5 0.2 - - - -
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Residues in contact with TYR 247 (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 GLN* 3.5 48.4 + - + +
198A VAL* 3.5 25.8 - - + -
199A SER* 4.7 14.4 + - - -
205A LYS* 4.2 3.8 + - - -
243A LEU* 3.1 33.4 + - + +
246A VAL* 1.3 97.5 - - + +
248A ASP* 1.3 73.7 + - - +
249A ILE* 3.4 20.0 - - + +
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Residues in contact with ASP 248 (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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83A ARG 4.7 0.7 - - - +
85A ASN 5.5 0.2 - - - +
87A LYS* 3.4 21.3 + - - +
106A THR* 2.9 26.0 + - - -
107A ARG* 3.1 48.8 + - - +
205A LYS* 2.8 40.9 + - - +
244A ALA 2.9 10.3 + - - -
246A VAL 3.5 2.8 - - - -
247A TYR* 1.3 80.0 - - - +
249A ILE* 1.3 59.8 + - - +
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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
------------------------------------------------------------
Atomic class I II III IV V VI VII VIII
------------------------------------------------------------
I (Hydrophilic) + + + - + + + +
II (Acceptor) + - + - + + + -
III (Donor) + + - - + + - +
IV (Hydrophobic) - - - + + + + +
V (Aromatic) + + + + + + + +
VI (Neutral) + + + + + + + +
VII (Neutral-donor) + + - + + + - +
VIII (Neutral-acceptor) + - + + + + + -
------------------------------------------------------------
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