Contacts of the helix formed by residues 262 - 276 (chain B) in PDB entry 1XDS
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 262 (chain B).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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261B TRP* 1.3 76.4 - - - +
263B ASP* 1.3 60.8 + - - +
264B GLU* 3.8 6.3 + - - +
265B ASP* 3.2 26.6 + - - +
266B ALA* 2.8 27.9 + - - +
313B GLY 3.8 16.4 + - - -
314B GLY* 4.9 0.2 - - - -
315B ARG* 5.1 3.8 - - - +
317B ARG* 3.9 2.7 - - - +
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Residues in contact with ASP 263 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
64A GLN* 3.4 26.8 + - - +
262B SER* 1.3 74.8 - - - +
264B GLU* 1.3 57.5 + - - +
266B ALA* 3.7 1.8 - - - +
267B LEU* 2.8 32.3 + - - +
315B ARG* 3.5 16.4 + - - -
317B ARG* 3.1 24.6 + - - +
325B LEU* 4.0 18.3 - - + +
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Residues in contact with GLU 264 (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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262B SER* 3.4 6.3 + - - +
263B ASP* 1.3 78.4 - - - +
265B ASP* 1.3 66.8 + - - +
267B LEU* 3.4 11.3 + - + +
268B THR* 2.9 35.3 + - + +
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Residues in contact with ASP 265 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
242B PHE* 3.7 23.3 - - + -
261B TRP* 3.7 32.1 - - + -
262B SER* 3.2 18.6 + - - +
264B GLU* 1.3 84.9 - - - +
266B ALA* 1.3 63.0 + - - +
268B THR* 3.4 7.2 + - - +
269B ILE* 3.2 28.6 + - - +
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Residues in contact with ALA 266 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
258B LEU* 3.9 17.1 - - + +
261B TRP* 4.0 2.4 - - + +
262B SER 2.8 16.9 + - - +
263B ASP 3.8 0.4 - - - +
265B ASP* 1.3 74.1 - - - +
267B LEU* 1.3 61.0 + - - +
269B ILE* 3.5 12.9 + - - +
270B LEU* 3.0 33.3 + - - +
317B ARG* 3.9 18.4 - - - +
325B LEU* 3.7 22.4 - - + -
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Residues in contact with LEU 267 (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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263B ASP 2.8 18.7 + - - +
264B GLU* 3.4 10.8 - - - +
266B ALA* 1.3 78.4 - - - +
268B THR* 1.3 59.0 + - + +
270B LEU* 3.5 3.8 + - + +
271B ARG* 3.0 64.4 + - - +
325B LEU* 3.6 38.7 - - + +
328B SER* 3.9 18.2 - - - -
329B ALA* 4.1 11.9 - - + +
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Residues in contact with THR 268 (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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241B PHE 4.7 3.0 - - - +
242B PHE* 3.6 30.1 + - + +
264B GLU* 2.9 28.2 + - + +
265B ASP* 3.4 7.4 + - - +
266B ALA 3.3 0.2 - - - -
267B LEU* 1.3 75.1 - - + +
269B ILE* 1.3 65.7 + - - +
271B ARG* 3.8 11.7 - - - +
272B GLY* 3.1 18.7 + - - -
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Residues in contact with ILE 269 (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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189B VAL* 5.0 0.4 - - + -
241B PHE* 3.7 50.0 - - + +
242B PHE* 4.0 9.4 - - + -
245B LEU* 5.2 0.7 - - - +
254B LEU* 3.7 33.0 - - + -
257B VAL* 4.5 5.2 - - + -
258B LEU* 4.5 5.4 - - + -
261B TRP* 3.5 34.3 - - + -
265B ASP 3.2 17.7 + - - +
266B ALA* 3.8 9.4 - - - +
267B LEU 3.4 0.2 - - - -
268B THR* 1.3 71.4 - - - +
270B LEU* 1.3 66.9 + - - +
272B GLY* 3.2 3.3 + - - -
273B CYS* 2.9 23.8 + - - -
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Residues in contact with LEU 270 (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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254B LEU* 4.0 12.1 - - + -
258B LEU* 4.3 19.7 - - + -
266B ALA 3.0 21.2 + - - +
267B LEU* 3.6 4.9 - - - +
269B ILE* 1.3 77.1 - - - +
271B ARG* 1.3 56.9 + - - +
273B CYS* 2.9 22.1 + - - +
274B VAL* 2.9 18.8 + - - +
283B LEU* 3.5 31.0 - - + -
285B VAL* 5.0 2.7 - - + -
322B VAL* 5.3 1.6 - - + +
325B LEU* 4.0 40.2 - - + +
326B ALA* 4.1 13.7 - - + +
329B ALA* 3.9 9.0 - - + -
331B LEU* 3.9 7.9 - - + -
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Residues in contact with ARG 271 (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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267B LEU* 3.0 50.3 + - - +
268B THR* 3.8 11.0 - - - +
269B ILE 3.3 0.4 - - - -
270B LEU* 1.3 75.8 - - - +
272B GLY* 1.3 61.6 + - - +
274B VAL* 3.5 8.9 + - - +
275B ARG* 3.3 20.3 + - - +
328B SER* 3.3 28.7 + - - -
329B ALA* 3.9 17.3 - - + +
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Residues in contact with GLY 272 (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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241B PHE 5.4 4.0 - - - -
243B LYS 5.8 0.4 - - - -
244B PRO* 5.7 5.4 - - - -
245B LEU* 3.4 25.0 + - - +
268B THR 3.1 15.3 + - - -
269B ILE* 3.2 4.2 + - - -
271B ARG* 1.3 76.8 - - - +
273B CYS* 1.3 61.2 + - - +
275B ARG* 3.4 9.1 + - - +
276B ALA* 3.3 16.3 + - - +
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Residues in contact with CYS 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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189B VAL* 4.3 3.8 - - - -
245B LEU* 3.8 16.2 - - - -
252B VAL* 3.9 22.2 - - + +
254B LEU* 3.8 33.0 - - - -
269B ILE* 2.9 18.2 + - - -
270B LEU* 2.9 12.2 + - - +
272B GLY* 1.3 74.5 - - - +
274B VAL* 1.3 65.6 + - - +
276B ALA* 3.2 12.2 + - - +
277B LEU* 3.3 19.1 + - - +
283B LEU* 4.2 20.4 - - + -
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Residues in contact with VAL 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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270B LEU 2.9 14.5 + - - +
271B ARG* 3.7 8.1 - - - +
272B GLY 3.4 0.2 - - - -
273B CYS* 1.3 73.4 - - - +
275B ARG* 1.3 67.8 + - - +
277B LEU* 3.1 26.8 + - - +
283B LEU* 6.0 0.2 - - - +
329B ALA 3.4 26.9 - - - +
330B GLY* 4.9 6.3 - - - +
331B LEU* 3.4 36.1 - - + -
355B ALA* 5.1 12.1 - - + -
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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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244B PRO* 3.8 34.6 - - + +
245B LEU 6.2 1.6 - - - +
248B THR* 4.9 5.4 - - - +
271B ARG 3.3 10.5 + - - +
272B GLY* 3.7 11.0 - - - +
273B CYS 3.3 0.4 - - - -
274B VAL* 1.3 80.3 - - - +
276B ALA* 1.3 58.8 + - + +
277B LEU 3.2 9.0 + - - +
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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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187B LEU* 4.5 7.9 - - + -
245B LEU* 3.9 21.3 - - + +
247B VAL 3.5 21.5 - - - +
248B THR* 3.1 31.2 - - - +
249B ALA 3.1 8.1 + - - +
252B VAL* 4.7 4.3 - - + +
272B GLY 3.3 9.7 + - - +
273B CYS 3.2 9.8 + - - +
274B VAL 3.2 1.0 - - - -
275B ARG* 1.3 78.1 - - + +
277B LEU* 1.3 58.0 + - - +
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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