Contacts of the helix formed by residues 273 - 284 (chain B) in PDB entry 2POD
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 ALA 273 (chain B).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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74B PHE 4.9 2.5 - - - +
75B ARG* 5.2 3.9 + - - +
76B SER* 3.7 37.8 - - - +
77B ALA 4.1 0.2 - - - +
81B MSE 3.8 14.1 - - + -
271B THR 3.9 0.6 + - - -
272B LEU* 1.3 76.9 - - - +
274B THR* 1.3 79.2 + - + +
277B GLY* 3.2 13.9 + - - -
278B PHE* 4.5 0.7 - - - -
296B TRP 3.7 15.0 - - - +
297B CYS* 3.8 4.7 - - - +
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Residues in contact with THR 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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74B PHE* 4.2 9.8 + - + +
81B MSE 3.9 27.1 - - + -
273B ALA* 1.3 82.9 + - - +
275B ARG* 1.3 65.5 + - - +
276B TRP* 3.4 29.0 + - + +
277B GLY 3.6 2.3 + - - -
278B PHE* 3.1 21.0 + - - -
297B CYS* 2.7 25.9 + - - +
298B GLY* 4.8 0.2 - - - -
302B GLU* 3.6 20.2 - - + +
306B ILE* 3.7 12.6 - - - +
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Residues in contact with ARG 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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274B THR* 1.3 72.2 - - - +
276B TRP* 1.3 86.1 + - + +
278B PHE* 3.2 2.3 + - - +
279B ARG* 2.6 37.6 + - - +
302B GLU* 2.9 42.9 + - - +
305B LYS* 3.6 52.3 - - + +
306B ILE* 4.0 14.1 - - + +
309B MSE 4.2 22.9 - - - +
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Residues in contact with TRP 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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75A ARG* 5.5 0.2 - - - -
188A TYR* 6.1 0.9 - - - -
248A ARG* 5.6 9.9 - - - -
250A ASP* 3.2 54.5 + - + -
251A SER* 2.9 32.9 + - - +
66B LYS* 6.1 5.2 - - + -
74B PHE 6.0 0.7 - - - +
75B ARG* 6.4 0.2 - - + -
274B THR* 3.2 20.8 - - + +
275B ARG* 1.3 117.8 - - + +
277B GLY* 1.3 62.8 + - - +
279B ARG* 4.4 9.7 - - + +
280B ASP* 3.3 17.4 + - - -
302B GLU* 3.9 9.6 - - - -
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Residues in contact with GLY 277 (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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75A ARG* 4.2 20.6 - - - -
75B ARG 6.4 0.2 - - - -
252B LEU* 4.1 0.2 - - - +
272B LEU* 4.1 17.1 - - - +
273B ALA 3.2 22.8 + - - -
274B THR* 3.6 0.2 + - - -
276B TRP* 1.3 77.0 - - - +
278B PHE* 1.3 60.7 - - - +
280B ASP* 3.5 5.1 - - - +
281B LEU* 3.3 22.5 + - - +
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Residues in contact with PHE 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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269B SER 3.5 15.7 - - - -
272B LEU* 3.4 28.0 - - + -
273B ALA 4.4 1.6 - - - -
274B THR 3.1 26.6 + - - +
275B ARG* 3.9 2.5 - - - +
277B GLY* 1.3 77.0 - - - +
279B ARG* 1.3 59.0 + - - +
280B ASP 3.2 0.9 - - - -
281B LEU* 3.4 25.2 + - + +
282B LEU* 2.9 41.2 + - + +
290B VAL* 3.7 25.4 - - + -
291B MSE 3.2 28.5 - - - -
292B LEU* 3.7 19.7 - - + -
297B CYS* 4.7 0.2 - - + -
306B ILE* 3.5 26.2 - - + -
309B MSE 5.4 2.5 - - - -
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Residues in contact with ARG 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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250A ASP* 5.6 0.6 + - - -
251A SER* 3.3 34.3 + - - +
253A SER* 3.7 17.0 - - - -
254A SER* 2.5 33.5 + - - +
275B ARG 2.6 22.0 + - - +
276B TRP* 3.9 11.9 - - - +
278B PHE* 1.3 71.6 - - - +
280B ASP* 1.3 59.6 - - - +
282B LEU* 3.2 2.5 + - - +
283B GLU* 2.9 57.7 + - - +
309B MSE 4.0 22.2 - - + +
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Residues in contact with ASP 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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75A ARG* 2.9 30.2 + - - +
250A ASP 3.7 14.2 - - - +
251A SER* 2.7 27.9 + - - -
252A LEU 4.5 3.0 + - - -
253A SER* 5.3 1.9 + - - -
75B ARG* 4.2 4.0 + - - -
252B LEU* 3.8 10.7 - - + +
276B TRP 3.3 12.2 + - - +
277B GLY 3.5 10.1 - - - +
278B PHE 3.2 0.6 - - - -
279B ARG* 1.3 78.8 - - - +
281B LEU* 1.3 61.7 + - - +
283B GLU* 3.7 18.2 + - - +
284B THR* 3.4 18.0 + - - +
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Residues in contact with LEU 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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249B MSE 5.0 0.7 - - - -
252B LEU* 3.8 11.6 - - + +
255B LEU* 3.6 30.5 - - + -
268B ALA* 3.5 37.2 - - + +
272B LEU* 4.1 13.0 - - + -
277B GLY 3.3 11.1 + - - +
278B PHE* 3.7 28.3 - - + +
279B ARG 3.3 0.2 - - - -
280B ASP* 1.3 77.6 - - - +
282B LEU* 1.3 62.5 + - + +
284B THR* 2.7 26.5 + - - +
285B ASN 4.2 0.9 + - - -
286B ALA 4.8 0.9 + - - -
287B ALA* 3.9 24.4 + - + +
290B VAL* 4.6 7.6 - - + -
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Residues in contact with LEU 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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278B PHE* 2.9 22.1 + - + +
279B ARG* 3.2 5.4 + - - +
281B LEU* 1.3 78.5 - - + +
283B GLU* 1.3 61.5 + - - +
285B ASN* 3.4 17.0 + - - +
287B ALA* 5.7 1.6 - - + -
290B VAL* 4.1 15.3 - - + -
306B ILE* 5.5 0.7 - - + +
309B MSE 3.7 30.3 - - + -
310B ALA* 4.2 17.3 - - + +
313B TRP* 3.6 56.7 + - + -
315B LEU* 3.7 29.4 - - + -
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Residues in contact with GLU 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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253A SER* 3.1 27.1 + - - -
279B ARG* 2.9 52.8 + - + +
280B ASP* 3.7 16.6 - - - +
281B LEU 3.3 0.2 - - - -
282B LEU* 1.3 74.1 - - - +
284B THR* 1.3 62.1 + - - +
285B ASN* 3.2 12.7 + - - +
313B TRP* 5.4 6.3 - - + +
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Residues in contact with THR 284 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
252B LEU* 3.4 37.9 - - + +
253B SER* 4.4 4.5 - - - +
255B LEU* 4.4 7.0 - - + +
256B LYS* 3.2 23.5 - - - +
280B ASP 3.4 17.0 - - - +
281B LEU* 2.7 18.3 + - - +
283B GLU* 1.3 77.2 - - + +
285B ASN* 1.3 66.1 + - - +
286B ALA* 3.2 22.3 + - - +
287B ALA 4.3 1.4 + - - -
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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