Contacts of the helix formed by residues 241 - 252 (chain A) in PDB entry 2VZ6
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 241 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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109A GLU* 2.6 35.5 + - - +
239A THR 5.2 1.1 - - - +
240A VAL* 1.3 78.7 - - - +
242A PRO* 1.3 72.0 - - + +
243A GLU* 3.2 14.7 + - - +
244A ALA 3.3 18.5 + - - -
245A LYS* 3.3 10.2 + - - +
270A TRP* 3.6 6.6 + - - -
277A VAL 3.7 16.8 - - - +
279A SER* 4.0 15.0 - - - +
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Residues in contact with PRO 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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240A VAL 3.6 3.6 - - - +
241A THR* 1.3 89.5 - - + +
243A GLU* 1.3 69.7 + - - +
245A LYS* 3.3 14.8 + - + +
246A ASP* 2.9 28.1 + - - +
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Residues in contact with GLU 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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241A THR* 3.1 19.8 - - - +
242A PRO* 1.3 89.1 - - + +
244A ALA* 1.3 60.6 + - - +
245A LYS 3.3 0.2 - - - -
246A ASP* 4.0 6.3 - - - -
247A LEU* 3.0 22.7 + - - +
268A HIS* 3.2 20.1 - - + -
269A PRO* 5.2 7.0 - - + -
270A TRP* 3.9 10.4 - - + +
277A VAL* 3.7 32.9 - - + +
148B LYS* 3.7 30.7 + - + +
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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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109A GLU* 4.1 1.6 - - - +
203A LEU* 4.6 1.1 - - + +
207A LEU* 3.7 22.4 - - + -
240A VAL* 3.7 6.7 - - + -
241A THR* 3.3 16.5 + - - +
243A GLU* 1.3 76.4 - - - +
245A LYS* 1.3 62.7 + - - +
247A LEU* 3.5 3.8 + - - +
248A ILE* 3.1 29.9 + - - +
270A TRP* 3.6 37.0 - - + +
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Residues in contact with LYS 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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232A PHE* 3.7 36.7 + - + +
237A TRP* 3.1 51.8 + - + +
238A ASP* 4.8 3.6 + - - +
240A VAL* 4.0 18.9 + - + -
241A THR 3.3 11.9 + - - +
242A PRO* 3.6 13.2 - - + +
243A GLU 3.3 0.4 - - - -
244A ALA* 1.3 74.2 - - - +
246A ASP* 1.3 60.5 + - - +
248A ILE* 3.3 4.4 + - - +
249A ASN* 2.8 38.6 + - - +
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Residues in contact with ASP 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 PRO 2.9 17.1 + - - +
243A GLU* 3.5 9.6 - - - +
245A LYS* 1.3 73.8 - - - +
247A LEU* 1.3 63.9 + - - +
249A ASN* 3.2 12.0 + - - +
250A LYS* 3.1 51.3 + - - +
268A HIS* 2.5 28.6 + - - -
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Residues in contact with LEU 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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116A ILE* 5.0 0.4 - - + -
203A LEU* 3.8 23.1 - - + -
243A GLU 3.0 14.6 + - - +
244A ALA* 3.8 5.8 - - - +
245A LYS 3.3 0.4 - - - -
246A ASP* 1.3 79.1 + - - +
248A ILE* 1.3 63.0 + - - +
250A LYS* 3.0 3.3 + - - -
251A MET* 3.0 37.6 + - + +
260A ILE* 3.8 22.2 - - + -
265A ALA* 4.2 10.1 - - + -
268A HIS* 3.8 31.2 - - + +
270A TRP* 3.8 11.2 - - + -
271A ILE* 3.7 30.1 - - + -
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Residues in contact with ILE 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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200A GLY* 4.5 4.5 - - - +
203A LEU* 3.7 21.8 - - + -
204A TYR* 4.0 18.6 - - + +
207A LEU* 3.7 26.2 - - + -
230A TYR* 4.4 3.6 - - + -
232A PHE* 3.9 17.9 - - + -
237A TRP* 3.7 22.9 - - + -
244A ALA 3.1 17.6 + - - +
245A LYS 3.6 6.3 - - - +
247A LEU* 1.3 73.2 - - - +
249A ASN* 1.3 64.9 + - - +
250A LYS 3.1 0.3 + - - -
251A MET* 3.2 6.3 + - - +
252A LEU* 2.9 46.8 + - + +
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Residues in contact with ASN 249 (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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230A TYR* 2.6 29.0 + - - +
232A PHE* 3.4 22.6 - - - -
245A LYS* 2.8 29.2 + - - +
246A ASP* 3.2 11.0 + - - +
248A ILE* 1.3 73.3 - - - +
250A LYS* 1.3 60.3 + - + +
252A LEU 3.6 10.6 - - - +
253A THR* 2.9 17.2 + - - -
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Residues in contact with LYS 250 (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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246A ASP* 3.1 43.9 + - - +
247A LEU 3.0 9.2 + - - +
249A ASN* 1.3 76.3 - - + +
251A MET* 1.3 61.8 + - - +
253A THR* 3.5 13.2 + - - -
258A LYS 4.8 0.8 - - - +
259A ARG* 3.5 2.9 - - - +
260A ILE* 3.0 55.4 + - + +
268A HIS* 4.4 9.2 - - + -
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Residues in contact with MET 251 (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 ILE* 4.5 8.3 - - + -
120A LEU* 4.0 26.0 - - + -
196A LEU* 3.6 17.0 - - + +
197A TRP* 3.6 7.3 - - - -
199A CYS* 3.8 22.9 - - + +
200A GLY* 3.6 28.9 - - - -
203A LEU* 4.2 14.1 - - - -
247A LEU* 3.0 25.9 + - + +
248A ILE 3.8 1.6 - - - +
250A LYS* 1.3 74.4 - - - +
252A LEU* 1.3 58.9 + - - +
253A THR 3.0 10.3 + - - -
259A ARG* 3.2 25.4 + - - -
260A ILE* 3.6 17.3 - - + -
265A ALA* 4.2 14.4 - - + -
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Residues in contact with LEU 252 (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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197A TRP* 3.4 58.5 - - + +
200A GLY* 3.8 19.3 - - - +
201A VAL* 3.8 4.3 - - + +
204A TYR* 4.9 0.7 - - + -
212A PRO* 4.3 19.5 - - + -
213A PHE* 4.4 3.6 - - + -
228A GLY* 5.5 0.9 - - - -
230A TYR* 3.7 43.8 + - + -
248A ILE* 2.9 35.6 + - + +
249A ASN 3.6 9.5 - - - +
251A MET* 1.3 73.0 - - - +
253A THR* 1.3 56.8 + - - +
254A ILE* 3.9 3.1 + - - +
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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