Contacts of the helix formed by residues 232 - 248 (chain A) in PDB entry 4MZ7
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 THR 232 (chain A).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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218A ASP* 4.0 7.2 - - - -
231A TRP* 1.3 90.5 - - - +
233A HIS* 1.3 65.2 + - - +
234A GLU* 3.4 18.5 + - - +
235A GLN* 3.2 38.4 + - - +
236A GLY 3.1 15.6 + - - -
273A VAL* 5.4 0.3 - - - +
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Residues in contact with HIS 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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206A HIS 4.8 4.0 - - - -
207A ASP* 3.8 11.0 + - - -
209A GLY* 3.4 26.2 - - - +
210A HIS* 3.3 46.6 + + - +
218A ASP* 2.7 34.8 + - + +
231A TRP* 4.6 2.9 - - - +
232A THR* 1.3 73.8 - - - +
234A GLU* 1.3 91.6 + - + +
236A GLY* 3.1 3.2 + - - +
237A SER* 2.7 36.9 + - - -
702A DGT 5.5 6.3 - - - -
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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
----------------------------------------------------------
206A HIS 5.0 2.2 - - - +
232A THR* 3.4 19.5 - - - +
233A HIS* 1.3 109.9 + - + +
235A GLN* 1.3 61.9 + - - +
237A SER* 3.1 18.7 + - - -
238A VAL* 3.2 17.5 + - - +
272A ILE* 4.0 18.7 - - + +
273A VAL* 3.9 18.1 - - + +
304A LYS* 5.1 8.8 + - - +
702A DGT 5.3 4.5 + - - -
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Residues in contact with GLN 235 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
230A LYS* 2.9 46.1 + - - +
231A TRP* 3.9 9.9 - - + +
232A THR* 3.2 34.9 + - - +
234A GLU* 1.3 77.3 - - - +
236A GLY* 1.3 63.1 + - - +
238A VAL* 3.2 8.3 + - - +
239A MET* 3.1 31.2 + - + +
273A VAL* 4.4 14.1 - - + -
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Residues in contact with GLY 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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209A GLY* 3.4 9.1 - - - -
231A TRP* 3.3 32.6 - - - -
232A THR 3.1 4.6 + - - -
233A HIS 3.1 8.1 + - - -
235A GLN* 1.3 79.7 - - - +
237A SER* 1.3 56.0 + - - +
239A MET* 3.7 4.6 - - - +
240A MET* 2.8 32.9 + - - +
416A MET* 4.4 2.0 - - - +
419A TYR* 5.4 0.7 - - - -
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Residues in contact with SER 237 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
205A CYS 3.8 10.9 - - - +
206A HIS 2.7 28.1 + - - -
207A ASP* 3.6 1.4 - - - -
208A LEU* 3.3 5.5 + - - +
209A GLY 2.9 22.9 + - - +
233A HIS* 2.7 18.5 + - - -
234A GLU 3.1 9.8 + - - -
236A GLY* 1.3 73.2 - - - +
238A VAL* 1.3 57.5 + - - +
240A MET* 3.9 0.7 - - - +
241A PHE* 2.8 32.7 + - - +
272A ILE* 3.8 10.8 - - - -
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Residues in contact with VAL 238 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
234A GLU 3.2 11.8 + - - +
235A GLN* 3.2 9.0 + - - +
237A SER* 1.3 77.2 - - - +
239A MET* 1.3 61.2 + - + +
241A PHE* 3.4 6.1 + - - +
242A GLU* 3.0 28.5 + - + +
269A LYS* 3.9 43.3 - - + +
272A ILE* 4.3 8.1 - - + -
273A VAL* 3.8 30.1 - - + -
276A LEU* 5.3 5.8 - - + -
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Residues in contact with MET 239 (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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231A TRP* 4.0 24.9 - - - -
235A GLN* 3.1 17.5 + - - +
236A GLY 3.8 5.2 - - - +
237A SER 3.3 0.2 - - - -
238A VAL* 1.3 78.9 - - + +
240A MET* 1.3 58.1 + - - +
242A GLU* 3.5 7.0 + - - +
243A HIS* 3.0 26.9 + - - +
413A ILE 4.0 16.4 - - - +
414A ASP* 4.9 9.0 - - - +
416A MET* 3.6 23.0 - - + +
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Residues in contact with MET 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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140A GLN* 3.6 41.1 - - + +
143A ARG* 4.5 6.5 - - - -
208A LEU* 3.8 33.4 - - + +
209A GLY* 4.9 0.7 - - - -
236A GLY 2.8 21.8 + - - +
239A MET* 1.3 70.6 - - - +
241A PHE* 1.3 55.9 + - - +
243A HIS* 3.2 10.2 + - - +
244A LEU* 2.7 33.1 + - - +
416A MET* 3.6 18.5 - - - +
419A TYR* 3.6 30.1 - - + -
420A THR* 3.8 23.1 - - - +
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Residues in contact with PHE 241 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
135A ILE* 5.1 3.1 - - + -
201A ILE* 3.8 19.5 - - + -
205A CYS* 3.8 25.8 - - + -
208A LEU* 3.9 11.6 - - + +
237A SER 2.8 19.5 + - - +
238A VAL* 3.6 4.3 - - - +
240A MET* 1.3 74.7 - - - +
242A GLU* 1.3 66.7 + - - +
244A LEU* 3.2 6.2 + - + +
245A ILE* 3.0 56.3 + - + +
254A MET* 4.3 4.0 - - + -
265A ILE* 4.0 20.9 - - + -
268A ILE* 3.6 43.7 - - + -
269A LYS* 4.1 19.7 - - + -
272A ILE* 5.1 3.8 - - + -
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Residues in contact with GLU 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 VAL* 3.0 17.4 + - + +
239A MET* 3.6 7.9 - - - +
240A MET 3.3 0.2 - - - -
241A PHE* 1.3 75.7 - - - +
243A HIS* 1.3 63.5 + - - +
245A ILE* 3.3 7.1 + - - +
246A ASN* 2.8 58.9 + - - +
251A LYS* 5.5 4.4 + - - -
265A ILE* 4.5 6.6 - - - +
269A LYS* 2.7 35.2 + - - +
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Residues in contact with HIS 243 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
140A GLN* 3.7 32.9 + - + -
239A MET 3.0 14.8 + - - +
240A MET* 3.5 8.5 - - - +
242A GLU* 1.3 76.9 - - - +
244A LEU* 1.3 57.0 + - - +
246A ASN* 4.8 3.7 - - - +
247A SER* 2.8 58.5 + - - -
416A MET* 3.5 33.9 - - + +
417A GLU* 3.7 38.0 + - + +
420A THR* 3.8 1.5 + - - -
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Residues in contact with LEU 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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135A ILE* 3.8 31.4 - - + +
138A THR* 3.5 35.7 - - + +
140A GLN* 4.0 18.6 - - + +
141A PHE* 4.2 7.9 - - + -
205A CYS* 4.9 1.3 - - - -
208A LEU* 4.2 18.6 - - + -
240A MET 2.7 20.6 + - - +
241A PHE* 3.5 7.6 - - + +
243A HIS* 1.3 73.9 - - - +
245A ILE* 1.3 68.5 + - + +
248A ASN* 2.9 34.1 + - - +
250A ILE* 3.9 18.6 - - + -
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Residues in contact with ILE 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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135A ILE* 5.1 1.3 - - + -
241A PHE* 3.0 57.1 + - + +
242A GLU* 3.7 8.7 - - - +
244A LEU* 1.3 79.7 - - + +
246A ASN* 1.3 72.4 + - - +
249A GLY* 3.2 20.3 + - - -
250A ILE* 3.3 41.6 + - + -
251A LYS* 3.7 35.0 - - + -
254A MET* 4.1 8.7 - - + -
265A ILE* 3.9 10.3 - - + -
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Residues in contact with ASN 246 (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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242A GLU* 2.8 48.3 + - - +
243A HIS* 4.2 3.5 - - - +
245A ILE* 1.3 88.6 - - - +
247A SER* 1.3 62.6 + - - +
248A ASN 3.4 0.3 + - - -
249A GLY* 4.0 5.5 + - - -
251A LYS* 4.2 12.6 + - - -
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Residues in contact with SER 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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140A GLN* 4.5 9.2 - - - -
243A HIS* 2.8 48.3 + - - -
246A ASN* 1.3 75.9 - - - +
248A ASN* 1.3 70.8 + - - +
249A GLY 3.7 0.2 - - - -
450B TYR* 5.5 1.7 + - - -
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Residues in contact with ASN 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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134A ARG* 5.4 5.0 + - - +
138A THR* 3.5 21.4 - - + +
139A PRO* 4.1 1.9 - - - +
140A GLN* 2.8 28.9 + - - +
244A LEU 2.9 26.2 + - - +
247A SER* 1.3 85.7 - - - +
249A GLY* 1.3 66.0 + - - +
250A ILE* 3.3 20.4 + - + +
450B TYR* 3.4 30.1 + - - -
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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