Contacts of the helix formed by residues 255 - 274 (chain B) in PDB entry 1XAI
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 PRO 255 (chain B).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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170B LYS* 3.9 31.0 - - + +
171B GLN* 5.1 5.4 - - - +
174B SER* 3.4 11.4 - - - +
254B ILE* 1.3 96.2 - - + +
256B HIS* 1.3 66.9 + - - +
257B GLY 3.3 0.2 - - - -
258B HIS* 3.3 39.2 - - + +
259B ALA* 3.1 19.1 + - - +
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Residues in contact with HIS 256 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
127B LEU* 3.6 29.6 - - + -
145B LYS* 4.1 8.9 - - - +
174B SER* 3.8 1.6 + - - -
178B GLU* 3.2 11.0 + - - -
242B HIS* 3.6 6.5 + + - -
245B GLY 6.0 1.3 - - - -
246B HIS* 3.7 29.8 - + - -
249B GLU* 3.1 33.2 + - - +
254B ILE 3.6 0.2 + - - -
255B PRO* 1.3 73.6 - - - +
257B GLY* 1.3 63.1 + - - +
259B ALA* 3.4 2.6 + - - +
260B VAL* 3.1 33.8 + - + +
501B CRB 3.2 4.1 + - - -
601B ZN 2.3 36.1 - - - -
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Residues in contact with GLY 257 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
127B LEU* 4.0 3.0 - - - +
174B SER* 3.0 36.6 + - - -
177B ALA* 3.1 19.3 - - - +
178B GLU* 5.3 0.9 - - - -
256B HIS* 1.3 75.0 - - - +
258B HIS* 1.3 66.1 + - - +
260B VAL* 3.1 3.9 + - - -
261B MET* 2.9 22.7 + - - +
293B TYR* 4.7 0.9 - - - -
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Residues in contact with HIS 258 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
170B LYS* 2.9 39.4 + - + +
173B LEU* 3.7 14.8 - - + +
174B SER* 3.5 17.3 + - - -
254B ILE* 3.9 14.4 - - + -
255B PRO* 3.3 33.9 + - + +
257B GLY* 1.3 74.9 - - - +
259B ALA* 1.3 62.3 + - - +
261B MET* 3.5 3.8 + - - +
262B VAL* 3.3 25.1 + - - +
293B TYR* 4.3 14.0 - + + -
294B PRO* 3.7 36.0 - - + +
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Residues in contact with ALA 259 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
245B GLY* 3.3 30.0 - - - +
248B VAL* 4.4 4.5 - - + +
249B GLU* 3.9 15.3 - - + +
254B ILE* 3.5 17.4 - - + +
255B PRO 3.1 16.5 + - - +
256B HIS* 3.7 4.0 - - - +
258B HIS* 1.3 73.4 - - - +
260B VAL* 1.3 55.5 + - + +
262B VAL* 3.0 8.3 + - - +
263B GLY* 2.7 32.2 + - - -
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Residues in contact with VAL 260 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
177B ALA* 4.0 22.2 - - + +
178B GLU* 3.9 11.4 - - - +
181B LYS* 4.9 2.7 - - + -
240B LEU 4.3 1.3 - - - +
241B GLY 3.8 8.2 - - - +
242B HIS* 3.8 39.9 - - + +
245B GLY* 4.7 2.2 - - - -
256B HIS* 3.1 28.0 + - + +
257B GLY 3.4 8.5 - - - +
259B ALA* 1.3 76.7 - - + +
261B MET* 1.3 52.9 + - - +
263B GLY* 2.8 2.3 + - - -
264B ILE* 2.6 57.5 + - + +
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Residues in contact with MET 261 (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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176B TYR* 5.3 1.8 - - - -
177B ALA* 3.3 34.8 - - + +
180B TYR* 3.5 33.2 - - + -
257B GLY 2.9 11.5 + - - +
258B HIS 3.6 8.7 - - - +
259B ALA 3.3 0.2 - - - -
260B VAL* 1.3 74.3 - - + +
262B VAL* 1.3 62.2 + - + +
264B ILE* 3.1 16.0 + - + +
265B ILE* 3.1 29.4 + - - +
288B LEU* 3.2 35.6 - - + +
291B LEU* 5.5 1.1 - - - -
293B TYR* 3.4 38.6 - - + -
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Residues in contact with VAL 262 (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 PHE* 4.3 11.9 - - + -
248B VAL* 5.0 9.9 - - + -
254B ILE* 5.2 2.2 - - + -
258B HIS 3.3 14.3 + - - +
259B ALA* 3.0 11.5 + - - +
261B MET* 1.3 77.0 - - + +
263B GLY* 1.3 62.7 + - - +
265B ILE* 3.7 6.1 + - - +
266B TYR* 3.1 22.9 + - - +
288B LEU* 5.4 3.6 - - + -
295B LEU* 5.5 8.3 - - + -
297B MET* 3.9 25.8 - - + -
298B ILE* 4.8 12.8 - - + -
301B LEU* 4.9 9.2 - - + -
349B LEU* 4.1 20.1 - - + +
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Residues in contact with GLY 263 (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 GLY* 3.3 24.6 - - - -
244B PHE* 4.2 6.9 - - - +
245B GLY 4.1 9.4 - - - -
259B ALA 2.7 16.3 + - - -
260B VAL 2.8 5.3 + - - -
262B VAL* 1.3 74.6 - - - +
264B ILE* 1.3 57.7 + - - +
266B TYR* 3.7 8.7 - - - +
267B GLN* 3.0 26.5 + - - +
323B MET* 5.5 0.2 - - - +
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Residues in contact with ILE 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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180B TYR* 4.8 6.3 - - + -
181B LYS* 4.4 7.4 - - + -
184B LEU* 3.5 29.8 - - + -
240B LEU* 3.4 42.2 - - + +
241B GLY* 3.9 0.2 - - - -
260B VAL* 2.6 39.4 + - + +
261B MET* 3.1 21.3 + - + +
263B GLY* 1.3 70.9 - - - +
265B ILE* 1.3 68.5 + - + +
266B TYR 3.1 1.1 - - - -
267B GLN* 2.9 31.2 + - - +
268B PHE* 3.0 19.8 + - + -
284B TYR* 5.7 0.4 - - + -
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Residues in contact with ILE 265 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
261B MET 3.1 15.8 + - - +
262B VAL* 4.2 4.0 - - - +
264B ILE* 1.3 77.9 - - + +
266B TYR* 1.3 57.9 + - - +
268B PHE* 3.3 11.4 + - - +
269B ILE* 3.0 30.2 + - - +
281B ILE* 4.1 17.5 - - + -
284B TYR* 3.6 13.7 - - + -
285B ILE* 3.5 44.4 - - + +
288B LEU* 3.3 28.7 - - + -
349B LEU* 3.6 21.5 - - + -
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Residues in contact with TYR 266 (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 PHE* 3.4 55.1 - + + -
262B VAL 3.1 20.0 + - - +
263B GLY 3.7 3.4 - - - +
265B ILE* 1.3 74.8 - - - +
267B GLN* 1.3 66.8 + - - +
269B ILE* 3.3 9.0 + - - +
270B VAL* 3.2 26.5 + - + +
303B PHE* 5.7 0.5 - - - -
310B MET* 4.5 4.2 - - + +
323B MET* 3.8 28.0 - - + -
342B LEU* 2.9 40.6 + - + +
345B ALA* 3.8 16.2 - - + -
346B CYS* 3.8 25.1 - - + -
349B LEU* 3.8 14.8 - - + +
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Residues in contact with GLN 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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240B LEU* 3.8 15.4 - - + +
241B GLY* 4.5 6.3 - - - +
263B GLY 3.0 18.0 + - - +
264B ILE* 2.9 25.0 + - - +
266B TYR* 1.3 79.4 - - - +
268B PHE* 1.3 82.1 + - - +
270B VAL* 3.4 4.3 + - - +
271B ALA* 3.0 23.9 + - - +
323B MET* 4.1 16.2 - - + -
324B VAL 3.2 23.8 - - - +
325B LEU* 3.5 7.6 - - + +
326B MET* 2.6 40.7 + - - +
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Residues in contact with PHE 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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184B LEU* 3.6 20.6 - - + -
240B LEU* 6.4 0.2 - - + -
264B ILE* 3.0 32.4 + - + -
265B ILE* 3.4 11.4 - - - +
266B TYR 3.2 0.2 - - - -
267B GLN* 1.3 94.6 - - - +
269B ILE* 1.3 66.1 + - - +
270B VAL 3.0 0.2 - - - -
271B ALA* 3.1 10.8 + - - -
272B ASN* 3.1 12.9 + - - -
279B HIS* 3.2 46.3 - + + -
281B ILE* 3.7 14.8 - - + -
284B TYR* 3.4 52.0 - + + -
326B MET* 4.1 18.4 - - - -
329B PHE* 5.6 1.1 - + - -
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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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265B ILE 3.0 17.8 + - - +
266B TYR* 3.4 10.5 - - - +
268B PHE* 1.3 76.5 - - - +
270B VAL* 1.3 55.0 + - - +
272B ASN* 3.5 12.8 - - - +
273B ALA* 3.2 23.1 + - + +
281B ILE* 4.0 12.3 - - + +
345B ALA* 3.5 29.2 - - + +
348B GLN* 3.2 29.8 - - - +
349B LEU* 3.4 47.1 - - + +
352B TYR* 3.9 12.3 - - + -
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Residues in contact with VAL 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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266B TYR* 3.2 36.1 + - + +
267B GLN 3.6 7.6 - - - +
268B PHE 3.0 0.6 - - - -
269B ILE* 1.3 74.9 - - - +
271B ALA* 1.3 52.5 + - - +
272B ASN 2.8 14.8 + - - -
273B ALA* 2.8 1.6 + - - +
274B LEU* 2.8 41.6 + - + +
323B MET* 4.3 6.1 - - + -
325B LEU* 3.3 22.0 - - + -
337B VAL* 4.1 9.0 - - + -
341B THR* 3.4 33.9 - - + -
345B ALA* 3.9 8.3 - - + -
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Residues in contact with ALA 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 GLN 3.0 13.9 + - - +
268B PHE* 3.1 4.2 + - - +
270B VAL* 1.3 75.0 - - - +
272B ASN* 1.3 55.5 + - - +
274B LEU 4.2 0.7 - - - -
275B PHE* 3.5 23.6 - - + -
276B ASP 3.0 17.7 + - - -
277B SER* 3.1 12.5 + - - -
279B HIS* 3.1 17.3 - - + +
325B LEU* 4.5 1.1 - - + -
326B MET 2.8 34.1 - - - +
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Residues in contact with ASN 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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268B PHE 3.1 16.8 + - - -
269B ILE* 3.5 9.3 - - - +
271B ALA* 1.3 76.8 - - - +
273B ALA* 1.3 66.6 + - - +
274B LEU 3.0 1.6 - - - -
276B ASP* 2.8 32.6 + - - +
278B LYS* 3.1 13.2 + - - -
279B HIS* 2.6 45.9 + - - +
281B ILE* 3.6 20.2 - - - +
348B GLN* 5.2 5.2 - - - +
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Residues in contact with ALA 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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269B ILE* 3.2 11.2 + - + +
270B VAL 2.8 7.6 + - - +
272B ASN* 1.3 80.2 - - - +
274B LEU* 1.3 62.6 + - - +
340B LEU* 5.7 4.7 - - + +
341B THR* 3.5 28.5 - - + +
345B ALA* 5.6 1.6 - - + -
348B GLN* 5.8 1.3 - - - +
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Residues in contact with LEU 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 VAL* 2.8 27.7 + - + +
272B ASN 2.9 0.5 + - - +
273B ALA* 1.3 79.7 - - - +
275B PHE* 1.3 80.6 + - + +
276B ASP* 3.2 4.5 + - - +
325B LEU* 3.4 33.0 - - + -
335B GLN* 4.0 12.8 - - - +
336B HIS 4.7 1.8 - - - +
337B VAL* 4.5 10.3 - - + -
340B LEU* 5.7 2.2 - - + -
341B THR* 3.2 25.4 - - - +
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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