Contacts of the helix formed by residues 238 - 249 (chain A) in PDB entry 2POZ
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 ASP 238 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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175A ARG* 5.9 2.2 - - - +
234A CYS* 3.4 12.8 - - - -
235A ASP* 2.8 17.1 + - + +
236A PRO 4.6 0.2 - - - -
237A PHE* 1.3 77.0 - - + +
239A ASN* 1.3 62.5 + - - +
240A GLY 2.9 6.6 + - - -
241A ALA* 2.8 28.0 + - + +
242A LEU* 3.4 12.8 + - - +
272B GLN* 4.7 0.5 - - - +
299B ALA 3.5 9.9 - - - +
300B TYR 3.5 17.7 - - - -
301B ASN* 3.5 11.6 + - + +
266F ARG* 3.0 29.4 + - - +
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Residues in contact with ASN 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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236A PRO* 3.9 15.8 + - - +
237A PHE 3.7 2.6 + - - -
238A ASP* 1.3 71.2 - - - +
240A GLY* 1.3 64.6 + - - +
241A ALA 3.3 0.2 - - - -
242A LEU* 3.4 12.7 + - - +
243A LYS* 3.2 19.4 + - - +
267A LYS* 3.9 26.3 + - - +
268A ILE* 3.5 20.8 - - - +
271A LEU* 3.5 33.6 - - + +
266F ARG* 5.7 0.4 - - - -
267F LYS* 4.0 22.0 - - - +
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Residues in contact with GLY 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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238A ASP* 2.9 3.8 + - - -
239A ASN* 1.3 75.2 - - - +
241A ALA* 1.3 66.3 + - - +
243A LYS* 3.3 6.2 + - - +
244A VAL* 3.1 26.2 + - - +
271A LEU* 5.8 0.2 - - - -
272B GLN* 3.1 27.5 + - - -
266F ARG* 3.9 7.9 - - - +
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Residues in contact with ALA 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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212A THR* 3.6 23.8 - - - +
234A CYS* 3.9 13.2 - - + -
238A ASP* 2.8 31.1 + - - +
240A GLY* 1.3 76.4 - - - +
242A LEU* 1.3 56.0 + - - +
244A VAL* 3.3 6.5 + - - +
245A ILE* 2.8 36.4 + - + +
272B GLN* 3.6 4.9 + - - +
300B TYR 5.4 0.7 - - - +
301B ASN* 3.9 8.5 - - + +
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Residues in contact with LEU 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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233A PRO* 4.0 15.0 - - + -
234A CYS* 3.4 15.6 - - - -
238A ASP 3.4 7.4 + - - +
239A ASN* 3.5 19.1 - - - +
240A GLY 3.2 0.2 - - - -
241A ALA* 1.3 79.9 - - - +
243A LYS* 1.3 62.2 + - - +
245A ILE* 3.8 2.4 - - - +
246A SER* 3.0 21.5 + - - -
253A ILE* 3.9 30.5 - - + -
255A VAL* 4.1 12.3 - - + -
268A ILE* 4.1 10.3 - - + -
271A LEU* 3.8 21.5 - - + -
273A ALA* 4.4 4.3 - - + -
274A CYS* 3.8 22.2 - - - -
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Residues in contact with LYS 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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239A ASN 3.2 11.2 + - - +
240A GLY* 3.3 7.4 + - - +
241A ALA 3.3 0.2 - - - -
242A LEU* 1.3 76.2 - - - +
244A VAL* 1.3 66.1 + - + +
246A SER* 2.6 25.6 + - - +
247A GLU* 3.1 41.3 + - - +
271A LEU* 3.2 39.8 + - + +
272A GLN* 4.0 10.3 + - - +
273A ALA* 3.9 7.6 - - + +
244D VAL* 5.5 4.2 - - - +
247D GLU* 5.9 1.2 + - - -
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Residues in contact with VAL 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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212A THR* 4.2 18.6 - - + -
216A ILE* 4.6 2.0 - - + -
240A GLY 3.1 15.9 + - - +
241A ALA* 3.7 9.0 - - - +
243A LYS* 1.3 76.6 - - + +
245A ILE* 1.3 64.2 + - - +
247A GLU* 3.2 16.0 + - - +
248A GLN* 3.2 34.1 + - + +
243B LYS* 4.8 7.4 - - - +
272B GLN* 4.0 37.9 - - + +
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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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212A THR* 3.9 23.3 - - + +
215A THR* 4.2 13.0 - - + -
216A ILE* 4.2 14.1 - - + -
233A PRO* 4.0 26.5 - - + +
234A CYS* 3.6 30.3 - - + -
241A ALA* 2.8 26.8 + - + +
242A LEU* 3.8 4.3 - - - +
244A VAL* 1.3 75.9 - - - +
246A SER* 1.3 64.1 + - - +
248A GLN 2.9 10.9 + - - -
249A ILE* 3.1 42.0 + - + +
253A ILE* 4.0 3.8 - - + -
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Residues in contact with SER 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 LEU 3.0 13.5 + - - -
243A LYS* 2.6 22.5 + - - +
245A ILE* 1.3 76.8 - - - +
247A GLU* 1.3 62.8 + - - +
248A GLN 3.5 0.3 + - - -
249A ILE* 3.8 14.4 - - - +
251A LEU 5.6 0.9 - - - +
253A ILE* 3.5 14.8 - - - +
273A ALA* 3.2 42.8 - - - +
248D GLN* 4.5 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 LYS* 3.1 46.0 + - + +
244A VAL* 3.6 16.6 - - - +
245A ILE 3.1 0.8 - - - -
246A SER* 1.3 79.0 - - - +
248A GLN* 1.3 71.9 + - + +
249A ILE 3.7 0.9 - - - -
243B LYS* 5.8 1.7 + - - -
247B GLU* 5.1 7.3 - - - +
247D GLU* 5.4 3.8 - - - +
248D GLN* 4.2 22.3 + - - +
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Residues in contact with GLN 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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216A ILE* 3.7 28.6 - - + +
220A ARG* 2.7 60.5 + - - +
244A VAL* 3.3 24.0 - - + +
245A ILE 2.9 3.5 + - - +
247A GLU* 1.3 91.9 + - + +
249A ILE* 1.3 61.4 + - - +
250A PRO* 4.5 0.2 - - - +
246B SER 4.3 8.6 + - - +
247B GLU* 3.9 33.9 + - - +
249B ILE 4.7 5.2 - - - +
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Residues in contact with ILE 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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216A ILE* 3.9 24.0 - - + +
219A CYS* 3.7 29.6 - - + -
220A ARG* 4.9 0.2 - - + -
230A VAL* 4.0 22.7 - - + -
245A ILE* 3.1 38.2 + - + +
246A SER* 3.8 13.6 - - - +
247A GLU 5.0 0.5 - - - -
248A GLN* 1.3 83.6 - - - +
250A PRO* 1.3 70.0 - - + +
251A LEU* 3.5 25.5 + - + +
253A ILE* 4.0 5.4 - - + -
220D ARG* 5.0 1.0 + - - -
248D GLN* 4.7 7.6 - - - +
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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