Contacts of the helix formed by residues 230 - 242 (chain A) in PDB entry 2P6U
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 LYS 230 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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211A LEU* 4.9 0.9 - - - -
214A GLY* 5.4 7.2 - - - -
229A VAL* 1.3 80.2 - - - +
231A PHE* 1.3 57.4 + - - +
232A GLU* 3.3 5.8 - - + +
233A GLU* 2.6 43.7 + - + +
234A LEU* 3.0 11.8 + - - +
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Residues in contact with PHE 231 (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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211A LEU* 4.4 9.2 - - + +
229A VAL 4.4 0.2 + - - -
230A LYS* 1.3 69.0 - - - +
232A GLU* 1.3 67.3 + - - +
233A GLU 2.8 2.3 + - - -
234A LEU* 2.8 22.5 + - - +
235A VAL* 3.1 28.9 + - + -
247A VAL* 4.3 19.1 - - + -
258A THR* 4.6 10.8 - - + -
261A LYS* 5.2 3.8 - - - -
262A LEU* 4.9 5.8 - - + -
344A ILE* 4.1 23.8 - - + -
346A ARG* 3.1 58.8 - - + +
384A ILE* 4.0 18.2 - - + -
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Residues in contact with GLU 232 (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 LYS* 3.3 5.5 - - + +
231A PHE* 1.3 81.6 - - + +
233A GLU* 1.3 58.5 + - - +
235A VAL* 3.7 9.3 - - - +
236A GLU* 3.3 22.5 + - - +
261A LYS* 4.7 20.0 - - - +
262A LEU* 5.3 5.9 - - + +
265A ILE* 3.4 27.9 - - + +
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Residues in contact with GLU 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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229A VAL* 4.8 7.5 - - + +
230A LYS* 2.6 40.8 + - + +
232A GLU* 1.3 70.7 - - - +
234A LEU* 1.3 54.3 + - - +
235A VAL 3.0 2.0 + - - -
236A GLU* 3.1 11.6 + - + +
237A GLU* 2.6 54.7 + - + +
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Residues in contact with LEU 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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211A LEU* 3.1 35.4 - - + -
216A LEU* 4.2 19.7 - - + -
227A ARG* 4.2 6.3 - - - +
229A VAL* 4.7 9.6 - - + -
230A LYS 3.0 7.9 + - - +
231A PHE* 2.8 15.0 + - - +
233A GLU* 1.3 72.6 - - - +
235A VAL* 1.3 64.3 + - - +
237A GLU* 3.5 8.8 + - - +
238A CYS* 3.5 13.3 + - - +
245A VAL* 5.6 0.2 - - - -
342A ARG* 2.8 53.1 + - - +
344A ILE* 3.8 26.9 - - + -
382A ILE* 4.5 10.5 - - + -
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Residues in contact with VAL 235 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
231A PHE* 3.2 44.4 - - + +
232A GLU* 3.7 6.7 - - - +
233A GLU 3.0 0.2 - - - -
234A LEU* 1.3 78.6 - - + +
236A GLU* 1.3 61.6 + - - +
238A CYS 3.4 0.2 + - - -
239A VAL* 2.8 45.1 + - + +
245A VAL* 3.4 21.5 - - + +
247A VAL* 5.1 0.2 - - + -
262A LEU* 3.5 33.2 - - + -
265A ILE* 5.0 3.8 - - + -
266A THR* 5.8 0.2 - - + -
325A VAL* 3.8 14.4 - - + -
344A ILE* 5.1 0.9 - - + -
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Residues in contact with GLU 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 GLU* 3.3 16.0 + - - +
233A GLU* 3.1 13.6 + - + +
235A VAL* 1.3 79.9 - - - +
237A GLU* 1.3 55.1 + - - +
239A VAL* 3.7 7.0 - - - -
240A ALA* 2.4 41.3 + - + +
265A ILE* 3.4 24.8 - - + +
268A LYS* 3.3 27.0 + - - -
269A TYR* 3.0 30.2 + - + +
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Residues in contact with GLU 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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227A ARG* 3.6 14.6 + - - -
229A VAL* 3.8 25.5 - - - +
233A GLU* 2.6 39.4 + - + +
234A LEU* 3.5 9.3 - - - +
236A GLU* 1.3 74.8 - - - +
238A CYS* 1.3 61.6 + - - +
240A ALA* 3.2 15.5 - - - +
241A GLU* 3.2 17.4 + - - +
342A ARG* 3.0 31.6 + - - +
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Residues in contact with CYS 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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234A LEU 3.5 0.8 + - - -
235A VAL 3.4 2.0 + - - -
236A GLU 3.3 0.2 - - - -
237A GLU* 1.3 76.8 - - - +
239A VAL* 1.3 54.6 - - - +
241A GLU* 2.8 13.5 + - - -
242A ASN 2.6 31.9 + - - -
243A GLY* 3.1 19.0 + - - -
244A GLY 3.2 43.3 - - - -
245A VAL* 3.4 14.1 - - + -
341A ARG* 3.6 17.3 - - - -
342A ARG* 3.7 22.0 - - - +
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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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235A VAL* 2.8 32.6 + - + +
236A GLU* 3.4 9.0 - - - +
238A CYS* 1.3 75.2 - - - +
240A ALA* 1.3 56.3 + - - +
242A ASN* 2.8 20.6 + - - +
243A GLY 5.1 0.2 - - - +
244A GLY 5.3 1.1 - - - +
245A VAL* 4.0 5.4 - - + -
265A ILE* 4.8 2.9 - - + -
266A THR* 4.3 8.7 - - + -
269A TYR* 4.4 21.3 - - + -
324A LYS* 2.8 50.8 + - + +
325A VAL* 3.4 31.9 - - + -
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Residues in contact with ALA 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 GLU* 2.4 33.8 + - + +
237A GLU* 3.2 9.6 - - - +
239A VAL* 1.3 72.0 - - - +
241A GLU* 1.3 61.4 + - + +
242A ASN* 4.7 1.4 - - - +
269A TYR* 3.5 32.8 - - + +
324A LYS* 4.8 1.0 + - - -
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Residues in contact with GLU 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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237A GLU* 3.3 17.4 - - - +
238A CYS* 2.8 13.4 + - - +
240A ALA* 1.3 77.2 - - + +
242A ASN* 1.3 69.9 + - - +
243A GLY* 3.6 0.5 + - - -
341A ARG* 2.7 40.5 + - - +
342A ARG* 4.7 7.1 + - - -
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Residues in contact with ASN 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 CYS 2.6 11.5 + - - -
239A VAL* 2.8 12.9 + - - +
240A ALA 4.7 1.3 - - - +
241A GLU* 1.3 77.8 + - - +
243A GLY* 1.3 58.4 + - - +
244A GLY 3.3 3.4 - - - +
320A ARG 5.5 1.2 + - - -
321A GLY* 3.9 18.3 - - - -
324A LYS* 3.2 35.5 - - - +
372A ARG* 3.0 18.1 + - - +
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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