Contacts of the helix formed by residues 269 - 283 (chain B) in PDB entry 2R5S
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 269 (chain B).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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161B THR 5.2 1.0 + - - -
163B GLN* 4.1 36.7 - - - +
232B ASP* 6.0 0.4 - - - +
265B LEU* 3.3 46.4 + - - +
266B GLY 3.7 6.0 + - - +
267B GLN 3.5 0.8 - - - -
268B GLY* 1.3 73.9 - - - +
270B ALA* 1.3 62.4 + - - +
271B ILE* 2.9 21.6 + - - +
272B ALA* 3.2 14.6 + - + +
273B SER* 2.9 32.7 + - - -
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Residues in contact with ALA 270 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
163B GLN* 5.1 2.4 + - - -
166B LEU* 6.0 6.1 - - + -
268B GLY 3.6 4.2 + - - +
269B ASN* 1.3 74.6 + - - +
271B ILE* 1.3 62.0 + - + +
273B SER* 3.4 7.1 + - - -
274B LYS* 3.0 26.5 + - - +
277B ARG* 4.8 2.9 + - - -
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Residues in contact with ILE 271 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
232B ASP* 4.7 4.5 - - + -
233B GLU* 3.4 47.6 - - + +
236B LEU* 3.9 20.2 - - + -
265B LEU* 5.2 1.6 - - + -
269B ASN* 2.9 14.5 + - - +
270B ALA* 1.3 71.5 - - + +
272B ALA* 1.3 67.3 + - - +
274B LYS* 2.9 29.4 + - + +
275B TYR* 2.9 20.4 + - + -
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Residues in contact with ALA 272 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
236B LEU* 4.6 0.6 - - - +
262B LEU* 3.3 20.3 - - + +
265B LEU* 3.7 32.5 - - + +
269B ASN* 3.2 13.9 + - + +
271B ILE* 1.3 78.7 - - - +
273B SER* 1.3 57.8 + - - +
275B TYR 3.2 1.4 + - - -
276B ARG* 2.8 53.5 + - - +
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Residues in contact with SER 273 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
267B GLN* 3.7 12.8 + - - -
268B GLY 5.0 0.2 - - - -
269B ASN 2.9 20.1 + - - -
270B ALA* 3.7 8.5 - - - -
271B ILE 3.1 0.2 - - - -
272B ALA* 1.3 73.7 - - - +
274B LYS* 1.3 63.6 + - - +
276B ARG* 3.5 17.7 + - - +
277B ARG* 3.2 41.9 + - - +
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Residues in contact with LYS 274 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
233B GLU* 5.3 8.5 + - - +
237B GLU* 5.3 2.0 + - - -
270B ALA 3.0 13.4 + - - +
271B ILE* 2.9 19.5 + - + +
273B SER* 1.3 75.8 - - - +
275B TYR* 1.3 89.3 + - + +
277B ARG* 3.5 24.1 + - - +
278B GLN* 2.9 51.3 + - + +
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Residues in contact with TYR 275 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
233B GLU* 3.8 14.9 + - + +
236B LEU* 3.6 39.9 - - + -
237B GLU* 3.0 37.4 + - - +
240B TRP* 3.9 5.4 - - + -
258B PHE* 3.7 26.6 - + + -
262B LEU* 3.7 16.6 - - + -
271B ILE* 2.9 35.5 + - + +
274B LYS* 1.3 103.1 + - + +
276B ARG* 1.3 59.3 + - - +
278B GLN* 3.2 28.4 + - + +
279B LEU* 2.9 30.5 + - - +
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Residues in contact with ARG 276 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
2B MES 4.1 21.4 - - - +
262B LEU* 2.9 55.3 + - + +
263B SER* 4.7 2.2 - - - +
266B GLY* 2.8 35.4 + - - +
267B GLN* 3.5 29.6 + - - +
272B ALA* 2.8 28.6 + - - +
273B SER* 3.5 29.7 + - - +
275B TYR* 1.3 68.8 - - - +
277B ARG* 1.3 61.3 + - + +
279B LEU* 3.9 3.8 - - - +
280B TYR* 2.9 30.7 + - - +
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Residues in contact with ARG 277 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
2B MES 4.4 22.0 - - + -
270B ALA 4.8 2.6 + - - -
273B SER* 3.2 27.3 + - - +
274B LYS* 3.6 32.0 + - - +
276B ARG* 1.3 77.7 - - + +
278B GLN* 1.3 63.5 + - + +
280B TYR* 3.3 6.5 + - - +
281B SER* 3.1 23.7 + - - -
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Residues in contact with GLN 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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237B GLU* 5.1 1.2 + - - -
240B TRP* 3.2 61.2 - - + +
274B LYS* 2.9 47.5 + - + +
275B TYR* 3.2 24.1 + - - +
277B ARG* 1.3 72.6 - - + +
279B LEU* 1.3 65.0 + - - +
281B SER* 2.8 22.9 + - - +
282B ILE* 3.7 1.6 - - - +
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Residues in contact with LEU 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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240B TRP* 3.7 8.4 - - + -
243B LEU* 4.5 10.5 - - + -
247B LEU* 4.2 18.6 - - + -
255B LYS* 4.4 13.9 - - + -
258B PHE* 3.6 25.1 - - + -
259B MSE 3.5 34.1 - - + -
262B LEU* 4.7 3.6 - - + -
275B TYR 2.9 18.6 + - - +
276B ARG* 3.9 4.0 - - - +
278B GLN* 1.3 74.2 - - - +
280B TYR* 1.3 66.8 + - - +
281B SER 3.1 0.5 + - - -
282B ILE* 3.2 14.5 + - + +
283B LEU* 3.2 40.6 + - + +
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Residues in contact with TYR 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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2B MES 3.6 66.7 + - + -
276B ARG 2.9 18.5 + - - +
277B ARG 3.6 4.3 - - - +
278B GLN 3.2 0.2 - - - -
279B LEU* 1.3 80.1 - - - +
281B SER* 1.4 65.3 + - - +
282B ILE 3.1 1.2 + - - -
283B LEU* 3.3 33.0 + - + +
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Residues in contact with SER 281 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
240B TRP* 4.9 0.5 - - - -
277B ARG 3.1 12.3 + - - -
278B GLN* 2.8 23.2 + - - +
280B TYR* 1.4 80.3 - - - +
282B ILE* 1.3 64.8 + - - +
283B LEU 4.4 3.1 - - - +
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Residues in contact with ILE 282 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
240B TRP* 3.4 35.9 - - + -
243B LEU 4.0 0.9 - - - +
244B LYS* 4.0 21.5 - - + +
247B LEU* 3.8 41.8 - - + +
278B GLN 3.7 4.7 - - - +
279B LEU* 3.4 13.0 - - - +
281B SER* 1.3 91.8 - - - +
283B LEU* 1.3 67.4 + - - +
284B TYR* 3.6 1.9 + - - -
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Residues in contact with LEU 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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247B LEU* 4.5 8.5 - - + -
255B LYS* 3.9 22.9 - - - +
259B MSE 6.4 0.2 - - - -
279B LEU* 3.2 49.2 + - + +
280B TYR* 3.3 35.0 + - + +
281B SER 4.4 2.9 - - - +
282B ILE* 1.3 84.2 + - - +
284B TYR* 1.3 67.9 + - - +
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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