Contacts of the helix formed by residues 250 - 263 (chain A) in PDB entry 4B92
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 250 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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222A GLU* 3.5 33.9 + - - +
225A GLU* 3.2 11.9 + - - -
248A VAL* 3.7 1.7 - - - +
249A SER* 1.3 82.8 - - - +
251A ILE* 1.3 63.8 + - - +
252A SER* 3.5 2.3 + - - -
253A ALA* 3.0 27.5 + - - +
254A GLY* 2.9 22.2 + - - -
301A ARG* 3.9 2.5 - - - -
306A THR* 4.0 4.9 - - - -
310A LEU* 3.9 11.8 - - - +
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Residues in contact with ILE 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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222A GLU* 3.7 10.1 + - - +
250A SER* 1.3 72.7 - - - +
252A SER* 1.3 57.7 + - - +
254A GLY* 3.3 2.4 + - - -
255A ASP* 2.9 39.8 + - - +
303A ASP* 4.0 20.4 - - + +
305A ASN* 4.4 11.7 - - + +
306A THR* 3.8 35.4 - - + +
309A TYR* 3.6 38.8 - - + -
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Residues in contact with SER 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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222A GLU* 2.3 36.0 + - - +
223A GLU* 5.0 1.3 + - - -
226A ALA* 3.4 22.9 - - - -
250A SER* 3.2 3.3 - - - -
251A ILE* 1.3 77.5 - - - +
253A ALA* 1.3 63.8 + - - +
255A ASP* 3.2 10.7 + - - +
256A VAL* 3.1 23.7 + - - +
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Residues in contact with ALA 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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225A GLU* 3.3 35.0 - - + +
226A ALA* 4.0 11.4 - - - +
229A THR* 4.1 9.8 - - + +
248A VAL* 4.3 5.2 - - + -
250A SER* 3.0 17.6 + - - +
252A SER* 1.3 79.3 - - - +
254A GLY* 1.3 64.4 + - - +
256A VAL* 3.0 17.4 + - - +
257A ILE* 3.0 18.5 + - + +
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Residues in contact with GLY 254 (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 VAL* 4.2 6.2 - - - +
250A SER 2.9 15.0 + - - -
251A ILE 3.5 4.3 - - - -
253A ALA* 1.3 76.4 - - - +
255A ASP* 1.3 57.6 + - - +
257A ILE* 3.4 13.1 + - - +
258A ALA* 2.9 26.0 + - - +
313A LEU* 3.9 21.0 - - - +
318A THR* 3.8 7.4 - - - +
319A LEU* 5.5 0.9 - - - -
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Residues in contact with ASP 255 (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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251A ILE* 2.9 27.5 + - - +
252A SER* 3.2 10.5 + - - +
254A GLY* 1.3 72.7 - - - +
256A VAL* 1.3 67.6 + - + +
258A ALA* 3.1 8.4 + - - +
259A ALA* 2.8 26.7 + - - +
309A TYR* 2.5 30.8 + - - -
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Residues in contact with VAL 256 (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 ALA* 3.7 22.4 - - + +
229A THR* 3.7 11.2 - - + -
230A HIS* 3.5 42.0 - - + +
233A ILE* 4.0 7.0 - - + -
252A SER 3.1 16.2 + - - +
253A ALA 3.0 8.0 + - - +
255A ASP* 1.3 74.8 - - - +
257A ILE* 1.3 66.0 + - - +
259A ALA* 3.3 5.6 + - - +
260A ALA* 2.9 23.2 + - + +
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Residues in contact with ILE 257 (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 THR* 3.9 9.0 - - + +
233A ILE* 4.4 7.0 - - + -
245A LEU* 3.5 26.7 - - + -
248A VAL* 3.6 39.0 - - + -
253A ALA* 3.0 16.8 + - + +
254A GLY* 3.6 7.6 - - - +
256A VAL* 1.3 75.8 - - - +
258A ALA* 1.3 63.6 + - - +
260A ALA* 3.3 2.6 + - - +
261A LYS* 3.0 28.8 + - + +
267A VAL* 4.1 17.3 - - + -
269A ALA* 4.2 8.1 - - + -
318A THR* 3.8 24.9 - - + +
319A LEU* 4.4 2.2 - - + -
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Residues in contact with ALA 258 (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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254A GLY 2.9 15.7 + - - +
255A ASP* 3.3 15.0 - - - +
257A ILE* 1.3 77.2 - - - +
259A ALA* 1.3 63.9 - - - +
261A LYS* 3.2 6.5 + - - +
262A MET* 3.1 27.6 + - + +
309A TYR* 5.9 0.9 - - - +
313A LEU* 6.0 1.6 - - + -
318A THR* 3.9 19.3 - - + +
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Residues in contact with ALA 259 (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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255A ASP 2.8 16.2 + - - +
256A VAL* 3.6 6.3 - - - +
258A ALA* 1.3 76.2 - - - +
260A ALA* 1.3 62.4 + - - +
262A MET* 3.0 25.9 + - + +
263A GLN* 3.1 25.6 + - - +
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Residues in contact with ALA 260 (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* 3.8 37.2 - - + -
256A VAL* 2.9 17.9 + - + +
257A ILE 3.6 4.3 - - - +
259A ALA* 1.3 74.8 - - - +
261A LYS* 1.3 62.7 + - - +
263A GLN* 3.2 20.6 + - - +
264A GLY 3.3 0.2 + - - -
265A LYS* 3.1 27.2 + - + +
267A VAL* 4.1 7.4 - - + -
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Residues in contact with LYS 261 (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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257A ILE* 3.0 19.9 + - + +
258A ALA* 3.3 11.0 - - - +
259A ALA 3.2 0.2 - - - -
260A ALA* 1.3 76.9 - - - +
262A MET* 1.3 58.8 + - + +
264A GLY* 2.8 22.2 + - - -
265A LYS 4.1 8.5 + - - +
267A VAL* 3.1 34.4 + - + +
268A LEU* 5.1 1.3 - - - -
269A ALA* 4.5 2.0 - - - +
317A ASP* 3.1 19.6 + - - +
318A THR* 2.6 35.7 + - + +
320A ASN* 3.1 20.0 + - - +
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Residues in contact with MET 262 (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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258A ALA* 3.2 17.9 - - + +
259A ALA* 3.0 14.7 + - + +
261A LYS* 1.3 78.2 - - + +
263A GLN* 1.3 61.9 + - + +
264A GLY* 3.1 1.4 + - - -
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Residues in contact with GLN 263 (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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259A ALA* 3.1 19.4 + - - +
260A ALA* 3.4 14.4 - - - +
261A LYS 3.2 0.4 - - - -
262A MET* 1.3 75.9 - - + +
264A GLY* 1.3 59.4 + - - +
265A LYS* 3.0 34.6 + - - +
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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