Contacts of the helix formed by residues 242 - 253 (chain A) in PDB entry 2VKZ
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 242 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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233A ILE* 3.8 8.3 - - + +
240A GLY 3.0 11.7 + - - -
241A PHE* 1.3 76.1 - - - +
243A ILE* 1.3 66.4 + - + +
244A THR* 3.0 19.5 - - - +
245A VAL* 3.7 12.3 + - - +
246A ALA* 3.0 26.5 + - - +
1135C GLU* 3.5 49.6 + - + +
1136C ALA* 6.1 0.2 - - - -
1162C GLU* 4.1 7.0 - - - +
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Residues in contact with ILE 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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226A SER 5.9 0.2 - - - +
229A LEU* 4.3 19.5 - - + +
230A SER* 3.9 17.9 - - - +
233A ILE* 3.4 27.8 - - + +
242A THR* 1.3 76.4 - - + +
244A THR* 1.3 62.8 + - - +
246A ALA* 4.0 2.6 - - + +
247A ARG* 3.1 49.6 + - - +
265A LEU* 3.8 30.1 - - + -
1160C THR* 6.5 0.2 - - - -
1162C GLU* 3.2 36.8 - - - +
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Residues in contact with THR 244 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
242A THR* 3.7 8.0 - - - +
243A ILE* 1.3 80.6 - - - +
245A VAL* 1.3 68.2 + - + +
247A ARG* 3.3 13.1 + - - +
248A LYS* 3.2 42.0 + - - +
1135C GLU* 2.4 34.0 + - - +
1160C THR* 3.5 25.5 - - + +
1162C GLU* 4.6 2.1 + - - -
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Residues in contact with VAL 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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240A GLY 4.5 6.1 - - - +
241A PHE* 3.7 37.9 - - + -
242A THR* 3.5 21.4 + - - +
244A THR* 1.3 80.2 - - + +
246A ALA* 1.3 59.1 + - - +
248A LYS* 3.3 22.4 + - - +
249A TYR* 3.1 27.6 + - + +
284A LYS* 6.4 0.2 - - - -
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Residues in contact with ALA 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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233A ILE* 4.1 15.5 - - + -
237A MET* 5.0 0.2 - - + -
241A PHE* 3.4 25.4 - - + -
242A THR 3.0 19.3 + - - +
243A ILE* 4.2 4.3 - - - +
244A THR 3.3 0.4 - - - -
245A VAL* 1.3 76.8 - - - +
247A ARG* 1.3 58.8 + - - +
249A TYR* 4.0 1.1 - - - -
250A LEU* 3.2 30.6 + - - +
265A LEU* 5.1 6.7 - - + -
287A LEU* 3.8 18.5 - - + +
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Residues in contact with ARG 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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221A LEU* 4.0 13.9 - - - +
229A LEU* 5.3 0.8 - - - +
243A ILE* 3.1 36.1 + - - +
244A THR* 3.3 5.9 + - - +
245A VAL 3.2 0.4 - - - -
246A ALA* 1.3 77.0 - - - +
248A LYS* 1.3 56.1 + - + +
249A TYR 3.1 4.7 - - - -
250A LEU* 3.3 4.0 + - - -
251A GLN* 2.9 32.6 + - - +
258A SER 4.2 0.2 + - - -
261A GLN* 3.3 45.7 - - + +
262A ASP* 2.5 31.7 + - - +
265A LEU* 3.8 32.7 - - + +
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Residues in contact with LYS 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 THR* 3.2 44.9 + - - +
245A VAL* 3.3 21.0 + - - +
247A ARG* 1.3 77.4 - - - +
249A TYR* 1.3 57.5 + - - +
251A GLN* 4.0 12.6 - - - +
252A THR* 3.1 30.7 + - - +
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Residues in contact with TYR 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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241A PHE* 4.8 4.3 - - + -
245A VAL* 3.1 16.5 + - + +
246A ALA* 4.1 5.4 - - - +
248A LYS* 1.3 76.0 - - - +
250A LEU* 1.3 67.7 + - + +
251A GLN 3.0 4.3 - - - -
252A THR* 4.5 3.6 - - + +
253A ARG* 3.0 57.7 + - + +
254A TRP* 3.8 2.8 + + - -
284A LYS* 3.4 63.9 + - + +
287A LEU* 4.1 23.1 - - + -
288A ASP* 2.8 37.3 + - - -
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Residues in contact with LEU 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 ALA 3.2 20.5 + - - +
247A ARG* 3.3 8.9 + - + +
249A TYR* 1.3 81.5 - - + +
251A GLN* 1.3 57.1 + - - +
254A TRP* 3.3 23.7 - - + +
256A LEU* 3.2 25.8 + - + +
261A GLN* 3.8 22.2 - - + -
264A VAL* 3.5 41.5 - - + -
265A LEU* 4.0 17.3 - - + -
287A LEU* 3.9 27.8 - - + +
291A ALA* 4.2 9.0 - - + -
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Residues in contact with GLN 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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247A ARG 2.9 17.2 + - - +
248A LYS* 4.5 11.7 - - - +
250A LEU* 1.3 79.6 - - - +
252A THR* 1.3 60.6 + - - +
255A GLY* 3.1 22.5 + - - -
256A LEU 3.2 28.5 + - - +
257A PRO* 4.3 11.7 - - - +
258A SER 5.2 0.6 - - - +
261A GLN* 4.3 6.9 + - - +
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Residues in contact with THR 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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248A LYS* 3.1 21.9 + - - +
249A TYR* 4.1 4.5 - - + -
251A GLN* 1.3 81.5 - - - +
253A ARG* 1.3 71.4 + - + +
254A TRP 3.8 0.3 + - - -
255A GLY* 4.4 1.4 + - - -
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Residues in contact with ARG 253 (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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249A TYR* 3.0 42.6 + - + +
252A THR* 1.3 85.0 - - + +
254A TRP* 1.3 104.8 + - + +
255A GLY 3.8 0.2 - - - -
288A ASP* 3.8 15.2 + - - -
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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