Contacts of the helix formed by residues 272 - 283 (chain B) in PDB entry 3IOT
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 ASN 272 (chain B).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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3B GLU* 3.8 0.2 - - - +
4B GLU* 3.3 22.6 - - - +
5B GLY* 2.9 24.1 + - - -
6B LYS 2.9 27.7 + - - +
7B LEU* 4.6 2.7 - - + +
58B ASP* 2.9 24.1 + - - +
270B SER* 3.2 6.0 - - - -
271B PRO* 1.3 82.7 - - - +
273B LYS* 1.3 61.8 + - - +
274B GLU* 3.3 2.7 - - - +
275B LEU* 3.3 23.3 + - + +
276B ALA* 3.1 22.7 + - - +
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Residues in contact with LYS 273 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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77B ALA* 4.0 18.4 - - + -
266B ILE* 4.2 21.9 - - + +
267B ASN 3.1 5.5 + - - -
268B ALA* 2.7 37.7 + - - +
269B ALA 3.9 0.4 - - - -
270B SER 2.7 26.8 + - - +
271B PRO* 3.3 6.1 + - + +
272B ASN* 1.3 75.7 - - - +
274B GLU* 1.3 64.7 + - + +
276B ALA* 3.2 7.6 + - - +
277B LYS* 3.0 24.9 + - - +
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Residues in contact with GLU 274 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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271B PRO 5.0 0.8 + - - +
272B ASN* 3.3 0.6 - - - -
273B LYS* 1.3 80.2 - - + +
275B LEU* 1.3 59.5 + - + +
277B LYS* 3.6 23.0 + - - +
278B GLU* 3.0 30.9 + - - +
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Residues in contact with LEU 275 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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5B GLY* 4.8 3.8 - - - -
6B LYS 4.5 5.6 - - - +
7B LEU* 3.9 14.2 - - + +
27B PHE* 4.2 11.0 - - + -
31B THR* 4.9 7.6 - - + -
33B ILE* 4.3 38.1 - - + -
272B ASN* 3.3 32.4 + - + +
273B LYS 3.3 0.4 - - - -
274B GLU* 1.3 77.9 - - + +
276B ALA* 1.3 53.5 + - - +
278B GLU* 3.0 9.8 + - + +
279B PHE* 2.7 35.3 + - - +
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Residues in contact with ALA 276 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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7B LEU* 4.0 14.1 - - + +
58B ASP* 5.2 1.1 - - + +
59B ILE* 3.7 28.3 - - + -
266B ILE* 3.8 17.0 - - + -
272B ASN 3.1 13.8 + - - +
273B LYS 3.2 8.9 + - - +
275B LEU* 1.3 73.6 - - - +
277B LYS* 1.3 58.8 + - - +
279B PHE* 3.0 5.4 + - - +
280B LEU* 2.8 37.1 + - - +
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Residues in contact with LYS 277 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
79B ILE* 6.1 0.4 - - - -
80B THR* 2.5 49.5 + - - +
82B ASP 5.3 0.2 - - - +
106B TYR* 3.8 17.9 - - - +
266B ILE* 4.2 8.6 - - + +
273B LYS 3.0 13.9 + - - +
274B GLU* 3.7 25.1 - - - +
276B ALA* 1.3 78.7 - - - +
278B GLU* 1.3 61.4 + - - +
281B GLU* 3.0 56.2 + - + +
282B ASN* 4.5 0.3 + - - -
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Residues in contact with GLU 278 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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27B PHE* 4.2 16.2 - - + -
31B THR* 5.8 4.3 - - + -
274B GLU* 3.0 20.5 + - - +
275B LEU* 3.0 16.8 + - + +
277B LYS* 1.3 75.8 - - - +
279B PHE* 1.3 66.1 + - - +
282B ASN* 2.7 50.8 + - - +
283B TYR* 3.7 13.3 - - + -
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Residues in contact with PHE 279 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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7B LEU* 4.1 12.8 - - + -
9B ILE* 3.7 27.6 - - + -
20B LEU* 4.1 15.5 - - + -
23B VAL* 4.1 30.1 - - + -
24B GLY* 4.1 1.3 - - - -
27B PHE* 3.6 30.5 - + + -
35B VAL* 3.9 25.1 - - + -
59B ILE* 5.1 0.9 - - + -
275B LEU 2.7 15.3 + - - +
276B ALA* 3.4 9.0 - - - +
278B GLU* 1.3 73.5 - - - +
280B LEU* 1.3 77.4 + - + +
283B TYR* 3.0 12.6 + - + +
284B LEU* 3.0 44.4 + - + -
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Residues in contact with LEU 280 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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59B ILE* 3.6 43.3 - - + -
61B PHE* 3.8 5.2 - - + -
106B TYR* 3.6 31.6 - - + -
108B ILE* 5.7 0.2 - - + -
264B ALA* 4.1 11.9 - - + +
266B ILE* 4.5 5.6 - - + -
276B ALA* 2.8 25.7 + - + +
279B PHE* 1.3 96.8 - - + +
281B GLU* 1.3 61.0 + - - +
284B LEU* 3.6 26.0 - - + -
285B LEU* 3.1 36.5 + - + +
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Residues in contact with GLU 281 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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81B PRO* 3.3 22.7 - - - +
82B ASP* 4.8 4.0 + - - +
85B PHE* 3.5 54.8 - - + +
106B TYR* 3.0 27.4 + - + +
277B LYS* 3.0 42.5 + - - +
280B LEU* 1.3 80.5 - - - +
282B ASN* 1.3 72.0 + - - +
285B LEU* 4.4 7.8 - - - +
286B THR* 4.8 1.4 - - - +
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Residues in contact with ASN 282 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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277B LYS 4.5 0.2 + - - -
278B GLU* 2.7 45.3 + - - +
281B GLU* 1.3 91.2 + - - +
283B TYR* 1.3 71.9 + - + +
286B THR* 3.6 19.5 + - - +
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Residues in contact with TYR 283 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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23B VAL* 3.8 17.3 - - + +
26B LYS* 4.1 28.9 - - + +
27B PHE* 3.5 49.8 - + + -
30B ASP* 3.2 36.9 + - + +
31B THR* 4.8 2.2 + - - +
278B GLU* 3.7 20.4 - - + -
279B PHE* 3.0 16.5 + - + +
281B GLU 3.7 0.6 - - - -
282B ASN* 1.3 91.4 - - + +
284B LEU* 1.3 58.9 + - - +
286B THR* 2.8 19.4 + - - -
289B GLY* 3.6 9.0 - - - -
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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