Contacts of the helix formed by residues 231 - 248 (chain A) in PDB entry 2ZH2
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 SER 231 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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168A ARG* 3.1 39.1 + - - +
229A ASN 3.4 3.2 + - - -
230A LEU* 1.3 75.2 - - - +
232A LEU* 1.3 58.7 + - - +
233A ASP* 3.5 6.8 + - - +
234A ASN* 3.0 28.4 + - - +
235A LEU* 2.9 28.6 + - - +
237A ARG* 4.8 0.5 + - - -
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Residues in contact with LEU 232 (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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197A ARG* 4.0 48.9 - - + +
230A LEU 3.7 1.0 + - - -
231A SER* 1.3 73.4 - - - +
233A ASP* 1.3 67.2 - - - +
235A LEU* 3.3 13.7 + - + +
236A ALA* 3.0 28.1 + - + +
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Residues in contact with ASP 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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231A SER* 3.2 5.6 + - - +
232A LEU* 1.3 87.4 - - - +
234A ASN* 1.3 60.7 + - - +
236A ALA* 3.4 9.3 + - - +
237A ARG* 2.9 59.9 + - - +
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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
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159A GLY 5.0 0.4 + - - -
160A ILE* 3.2 34.4 - - + +
167A VAL 2.7 28.1 - - - +
168A ARG* 3.0 15.4 - - - +
170A PHE* 4.5 0.7 - - - -
230A LEU* 4.0 9.9 - - + -
231A SER* 3.0 22.3 + - - +
233A ASP* 1.3 74.5 - - - +
235A LEU* 1.3 65.4 + - - +
237A ARG* 2.8 26.5 - - - +
238A PHE* 3.0 24.3 + - - +
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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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170A PHE* 5.0 2.0 - - + -
195A TRP* 4.1 15.3 - - + -
196A THR 4.2 12.1 - - - +
197A ARG* 4.2 11.4 - - + +
214A PHE* 3.9 50.0 - - + -
230A LEU* 3.9 26.2 - - + +
231A SER 2.9 12.8 + - - +
232A LEU* 3.4 18.8 - - + +
234A ASN* 1.3 78.0 - - - +
236A ALA* 1.3 62.4 + - - +
238A PHE* 3.2 6.6 + - - +
239A VAL* 3.0 35.6 + - + +
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Residues in contact with ALA 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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232A LEU* 3.0 18.2 + - + +
233A ASP* 3.5 15.0 - - - +
235A LEU* 1.3 75.7 - - - +
237A ARG* 1.3 65.4 + - + +
239A VAL* 3.4 6.5 + - - +
240A HIS* 3.0 25.2 + - - +
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Residues in contact with ARG 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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160A ILE* 5.2 9.2 - - + -
231A SER* 4.8 0.6 + - - -
233A ASP* 2.9 59.1 + - + +
234A ASN* 2.8 42.4 - - - +
235A LEU 3.3 0.2 - - - -
236A ALA* 1.3 75.5 - - + +
238A PHE* 1.3 58.1 + - - +
240A HIS* 3.2 7.3 + - - +
241A LEU* 2.8 38.9 + - + +
317A ARG* 5.2 9.9 - - - +
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Residues in contact with PHE 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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151A LEU* 4.2 17.0 - - + -
154A PHE* 4.1 21.3 - + - -
155A LEU* 3.5 31.2 - - + -
160A ILE* 4.1 9.5 - - + +
170A PHE* 3.5 27.8 - + + -
178A LEU* 5.7 0.4 - - + -
188A THR* 4.9 6.3 - - + -
189A VAL* 5.3 2.5 - - + -
192A ALA* 3.7 14.8 - - + -
195A TRP* 3.7 33.0 - + - -
234A ASN 3.0 14.4 + - - +
235A LEU* 3.4 8.3 - - + +
237A ARG* 1.3 75.4 - - - +
239A VAL* 1.3 65.4 + - - +
241A LEU* 2.9 17.4 + - + +
242A CYS* 2.9 32.0 + - - -
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Residues in contact with VAL 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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192A ALA 3.6 25.4 - - - +
193A ARG* 4.0 2.1 - - - +
195A TRP* 3.9 28.9 - - + +
235A LEU* 3.0 27.9 + - + +
236A ALA* 3.7 6.7 - - - +
238A PHE* 1.3 80.9 - - + +
240A HIS* 1.3 64.6 + - - +
242A CYS* 3.1 15.9 + - - +
243A ARG* 3.2 46.0 + - - +
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Residues in contact with HIS 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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236A ALA 3.0 16.8 + - - +
237A ARG* 3.5 7.2 + - - +
239A VAL* 1.3 77.2 - - - +
241A LEU* 1.3 63.5 + - - +
243A ARG* 3.2 24.5 + - + +
244A GLU* 3.1 58.4 + - + +
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Residues in contact with LEU 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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154A PHE* 4.1 14.9 - - + -
158A ASN* 3.4 46.9 - - + +
160A ILE* 4.5 7.6 - - + -
237A ARG* 2.8 21.9 + - + +
238A PHE* 2.9 15.5 + - + +
240A HIS* 1.3 78.4 - - + +
242A CYS* 1.3 58.5 + - - +
244A GLU* 3.5 19.5 + - - +
245A PHE* 2.9 29.8 + - - +
253A PHE* 3.9 18.8 - - + -
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Residues in contact with CYS 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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154A PHE* 4.6 3.6 - - - -
189A VAL* 3.5 40.4 - - + +
192A ALA* 3.7 14.6 - - - -
193A ARG* 3.6 9.6 - - + +
238A PHE* 2.9 46.2 + - - -
239A VAL 3.1 7.6 + - - +
241A LEU* 1.3 74.8 - - - +
243A ARG* 1.3 68.5 + - - +
245A PHE* 4.5 1.1 - - - +
246A MET* 3.1 29.1 + - - +
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Residues in contact with ARG 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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193A ARG* 3.0 48.9 + - + +
194A ARG* 5.1 1.0 - - - +
195A TRP 4.8 5.3 + - - -
239A VAL* 3.2 28.9 + - - +
240A HIS* 3.2 22.8 + - + +
242A CYS* 1.3 78.4 - - - +
244A GLU* 1.3 57.6 - - + +
246A MET* 3.4 2.3 + - - +
247A GLU* 2.9 34.1 + - - +
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Residues in contact with GLU 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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240A HIS* 3.1 44.9 + - + +
241A LEU* 3.7 23.9 - - - +
243A ARG* 1.3 75.3 - - + +
245A PHE* 1.3 67.5 + - - +
247A GLU* 3.1 11.1 + - - +
248A ALA* 2.9 25.8 + - - +
253A PHE* 4.1 13.8 - - + -
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Residues in contact with PHE 245 (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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3A VAL* 3.8 14.1 - - + -
6A ILE* 4.5 4.7 - - + -
7A LEU* 3.9 22.0 - - + -
154A PHE* 4.1 10.1 - + + -
185A PHE* 4.2 13.2 - + - -
189A VAL* 4.3 5.6 - - + -
241A LEU 2.9 18.7 + - - +
242A CYS* 4.0 3.8 - - - +
244A GLU* 1.3 76.0 - - - +
246A MET* 1.3 93.6 + - + +
248A ALA 4.4 0.2 - - - -
249A PRO* 2.8 48.3 - - + +
250A SER 3.8 17.5 - - - -
253A PHE* 3.6 37.6 - + + -
254A PHE* 3.8 21.1 - + - -
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Residues in contact with MET 246 (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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3A VAL* 4.4 10.5 - - + +
186A LEU* 3.2 35.7 - - + -
189A VAL* 3.5 15.9 - - + -
190A LYS* 4.1 15.0 - - + -
193A ARG* 3.3 37.9 - - - +
242A CYS 3.1 21.2 + - - +
243A ARG 3.8 2.2 - - - +
245A PHE* 1.3 113.4 - - + +
247A GLU* 1.3 60.9 + - - +
249A PRO* 4.0 8.7 - - - +
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Residues in contact with GLU 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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243A ARG* 2.9 20.3 + - - +
244A GLU* 3.1 12.8 + - - +
246A MET* 1.3 78.6 - - - +
248A ALA* 1.3 63.6 + - + +
249A PRO* 4.0 1.4 - - - +
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Residues in contact with ALA 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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244A GLU 2.9 10.2 + - - +
245A PHE 3.2 3.3 - - - +
247A GLU* 1.3 83.0 - - + +
249A PRO* 1.3 71.4 - - - +
250A SER* 3.5 4.0 + - - -
253A PHE* 3.8 13.9 - - - -
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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