Contacts of the helix formed by residues 272 - 281 (chain K) in PDB entry 2I2X
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 GLU 272 (chain K).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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218K THR* 4.0 0.9 - - - +
219K ASP* 3.1 19.1 + - - +
247K ARG* 2.9 38.0 + - + +
250K SER* 3.4 35.7 - - - +
251K ALA* 4.0 12.8 - - + -
254K SER* 2.9 27.5 + - - +
270K GLY* 3.4 12.6 - - - -
271K TYR* 1.3 72.3 + - - +
273K ASN* 1.3 55.7 + - - +
274K ILE 3.0 2.9 - - - -
275K ILE* 2.7 32.0 + - + +
276K VAL* 3.1 10.6 + - + +
370K LEU* 4.6 7.0 - - - -
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Residues in contact with ASN 273 (chain K).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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217K ASP 4.6 7.6 - - - +
254K SER* 5.3 2.8 - - - -
258K TYR* 4.7 2.6 + - - -
266K GLY* 3.5 15.6 - - - -
267K LYS 2.9 26.5 + - - -
270K GLY* 2.8 23.4 + - - +
272K GLU* 1.3 79.6 - - - +
274K ILE* 1.3 56.1 + - - +
276K VAL* 3.6 13.3 - - - +
277K LYS* 2.7 32.6 + - - +
284K MET* 3.6 23.9 - - + +
285K THR 3.0 15.0 + - - -
286K MET* 3.6 13.2 - - - -
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Residues in contact with ILE 274 (chain K).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
17K MET* 4.0 7.4 - - + +
271K TYR 3.4 18.8 + - - +
272K GLU 3.0 0.4 + - - +
273K ASN* 1.3 78.7 - - - +
275K ILE* 1.3 64.6 + - - +
277K LYS* 3.4 4.3 + - + +
278K ALA* 3.1 21.3 + - - +
286K MET* 4.1 13.8 - - + +
305K GLN* 3.5 27.4 - - + +
306K CYS* 3.8 34.8 - - + +
370K LEU* 3.6 31.9 - - + +
372K TYR* 3.9 7.0 - - + -
375K ALA* 3.6 19.4 - - + +
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Residues in contact with ILE 275 (chain K).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
248K ALA* 4.7 3.1 - - - -
251K ALA* 3.8 29.8 - - + -
272K GLU* 2.7 19.1 + - + +
274K ILE* 1.3 72.5 - - + +
276K VAL* 1.3 63.9 + - - +
278K ALA* 3.1 12.5 + - - +
279K ILE* 3.3 15.4 + - + +
369K MET* 3.9 30.1 - - + -
370K LEU* 4.2 9.6 - - + -
375K ALA* 3.8 38.8 - - + +
378K VAL* 4.1 10.3 - - + -
379K GLY* 3.9 9.6 - - - +
382K ILE* 3.8 18.2 - - + -
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Residues in contact with VAL 276 (chain K).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
251K ALA* 4.1 21.8 - - + +
254K SER* 4.4 11.7 - - - -
255K LEU* 4.2 12.8 - - + +
258K TYR* 3.5 35.2 - - + -
272K GLU* 3.1 15.5 + - + +
273K ASN* 3.2 15.5 + - - +
275K ILE* 1.3 76.6 - - - +
277K LYS* 1.3 57.3 + - - +
279K ILE* 3.1 8.1 + - - -
280K THR* 2.8 43.6 + - + +
284K MET* 3.9 9.6 - - + -
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Residues in contact with LYS 277 (chain K).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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11K TYR* 3.4 27.2 - - + +
17K MET* 4.2 8.3 - - + -
18K THR 3.3 11.2 + - - +
21K VAL 2.9 21.9 + - - -
22K SER* 3.6 5.8 - - - -
273K ASN 2.7 20.9 + - - +
274K ILE* 3.7 7.0 - - + +
276K VAL* 1.3 73.4 - - - +
278K ALA* 1.3 58.8 + - - +
280K THR* 3.9 5.6 - - - -
281K GLY* 2.8 28.6 + - - -
282K MET 3.3 16.8 - - - +
284K MET* 3.9 9.8 - - + +
306K CYS* 2.9 33.9 + - + +
307K CYS 4.5 0.6 + - - -
308K ASP* 2.8 30.5 + - - +
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Residues in contact with ALA 278 (chain K).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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9K MET* 3.5 25.0 - - + +
10K ALA 3.6 11.8 + - - -
11K TYR* 3.7 14.1 + - - +
17K MET* 3.6 30.9 - - + +
274K ILE 3.1 9.4 + - - +
275K ILE* 3.1 11.2 + - - +
277K LYS* 1.3 75.7 - - - +
279K ILE* 1.3 59.7 + - - +
375K ALA 4.9 0.4 - - - +
376K TYR* 3.9 19.3 - - + +
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Residues in contact with ILE 279 (chain K).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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6K TYR* 3.8 30.7 - - + -
8K SER 3.9 5.3 - - - +
9K MET* 3.8 26.2 - - + -
10K ALA* 3.0 24.6 + - - +
251K ALA* 6.0 0.7 - - + -
255K LEU* 3.8 20.0 - - + -
275K ILE* 3.5 16.8 - - + +
276K VAL* 3.1 5.8 + - + +
277K LYS 3.1 0.6 - - - -
278K ALA* 1.3 78.8 - - - +
280K THR* 1.3 59.7 + - - +
379K GLY* 3.8 20.6 - - - +
382K ILE* 4.0 26.9 - - + -
383K VAL* 3.8 17.3 - - + -
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Residues in contact with THR 280 (chain K).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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6K TYR* 3.7 32.9 + - + +
10K ALA* 3.6 3.6 - - - +
24K TYR* 3.4 20.3 - - - -
255K LEU* 3.5 28.5 - - + -
258K TYR* 4.0 9.2 - - + -
276K VAL* 2.8 37.0 + - + +
277K LYS* 3.9 1.4 - - - -
279K ILE* 1.3 74.9 - - - +
281K GLY* 1.3 58.5 + - - +
282K MET* 3.0 32.6 + - - +
284K MET* 4.0 2.9 - - - +
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Residues in contact with GLY 281 (chain K).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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10K ALA* 3.4 16.0 - - - +
11K TYR* 3.7 13.2 - - - -
22K SER* 3.4 5.2 - - - -
23K LYS* 3.0 31.3 + - - -
24K TYR* 3.0 12.2 + - - -
277K LYS* 2.8 16.4 + - - -
280K THR* 1.3 77.0 - - - +
282K MET* 1.3 59.4 + - - +
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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