Contacts of the helix formed by residues 262 - 281 (chain B) in PDB entry 1X7P
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 262 (chain B).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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142A SER* 5.1 8.0 + - - +
145A ARG* 3.6 31.2 + - - +
146A SER* 5.6 0.2 + - - -
139B ASN* 3.4 25.9 + - - +
234B GLU* 5.3 1.2 - - - +
261B LEU* 1.3 76.3 - - - +
263B ALA* 1.3 63.4 + - - +
264B ALA* 3.1 32.5 - - - +
265B ASN* 3.2 33.7 + - - +
266B ALA* 2.9 21.8 + - - +
302B SAM 5.1 1.1 - - - -
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Residues in contact with ALA 263 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
131B PHE* 3.8 34.3 - - + -
139B ASN* 4.3 9.2 - - - +
143B ILE* 4.3 1.6 - - - -
231B ILE* 4.1 6.8 - - + +
232B GLY 3.9 11.2 - - - +
234B GLU* 4.8 6.7 - - + +
261B LEU 3.8 1.2 + - - -
262B ASN* 1.3 75.2 + - - +
264B ALA* 1.3 57.9 + - - +
266B ALA* 3.8 1.9 - - - +
267B ALA* 3.0 31.5 + - - +
302B SAM 3.6 19.6 + - + +
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Residues in contact with ALA 264 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
265A ASN* 3.5 7.2 - - - +
139B ASN* 4.1 12.3 - - - +
142B SER* 3.6 32.3 - - - +
143B ILE* 3.3 19.7 - - + +
146B SER* 5.3 0.2 - - - -
262B ASN* 3.1 11.8 - - - +
263B ALA* 1.3 79.9 - - - +
265B ASN* 1.3 53.6 + - - +
267B ALA* 4.0 0.9 - - - +
268B THR* 2.7 37.2 + - - -
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Residues in contact with ASN 265 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
142A SER* 4.0 18.4 + - - +
145A ARG* 5.8 0.9 - - - -
146A SER* 3.6 12.7 + - - +
264A ALA* 3.6 7.4 - - - +
265A ASN* 2.4 53.0 - - - +
268A THR* 3.5 34.1 - - + +
261B LEU* 5.0 1.3 - - + -
262B ASN* 3.2 32.1 + - + +
264B ALA* 1.3 73.0 - - - +
266B ALA* 1.3 65.1 + - - +
268B THR* 3.5 4.5 + - - -
269B ALA 3.2 17.3 + - - -
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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
----------------------------------------------------------
231B ILE* 5.7 0.2 - - + -
252B ILE* 3.7 4.3 - - + +
261B LEU* 3.9 19.0 - - + +
262B ASN 2.9 17.9 + - - +
263B ALA 3.8 1.1 - - - +
265B ASN* 1.3 77.3 - - - +
267B ALA* 1.3 63.3 + - - +
269B ALA* 3.3 4.7 + - - +
270B ILE* 3.1 29.2 + - + +
302B SAM 3.5 43.7 - - + +
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Residues in contact with ALA 267 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
129B VAL* 5.5 0.4 - - + -
143B ILE* 3.9 21.3 - - + -
146B SER* 6.4 0.2 - - - -
229B LEU* 4.6 1.0 - - + +
231B ILE* 3.4 34.5 - - + -
263B ALA 3.0 18.0 + - - +
264B ALA 4.0 0.2 - - - +
266B ALA* 1.3 74.5 - - - +
268B THR* 1.3 59.5 + - - +
270B ILE* 3.3 3.6 + - - +
271B LEU* 2.9 43.5 + - + +
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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
----------------------------------------------------------
261A LEU* 4.5 7.4 - - + -
265A ASN* 3.4 37.8 - - + +
269A ALA* 4.3 7.9 - - + -
142B SER 5.2 0.2 + - - -
146B SER* 2.6 35.1 + - - +
150B LEU* 3.6 14.7 - - + +
264B ALA 2.7 21.8 + - - -
265B ASN 3.5 6.3 - - - -
267B ALA* 1.3 76.8 - - - +
269B ALA* 1.3 56.7 + - - +
271B LEU* 4.5 2.4 - - - +
272B TYR* 2.9 27.4 + - - +
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Residues in contact with ALA 269 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
268A THR* 4.3 6.7 - - + -
269A ALA* 4.2 17.7 - - - +
272A TYR* 4.1 29.4 - - + -
218B VAL* 6.5 0.2 - - - -
252B ILE* 4.2 13.9 - - + -
265B ASN 3.2 10.6 + - - +
266B ALA 3.5 8.7 - - - +
267B ALA 3.3 0.2 - - - -
268B THR* 1.3 79.2 - - - +
270B ILE* 1.3 57.6 + - - +
272B TYR* 3.4 8.7 + - - +
273B GLU* 3.0 24.9 + - - +
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Residues in contact with ILE 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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210B THR* 3.4 33.9 - - + +
218B VAL* 3.8 14.1 - - + -
223B PHE* 3.7 20.7 - - + -
229B LEU* 3.6 31.9 - - + -
231B ILE* 4.6 3.6 - - + -
250B VAL* 4.5 4.7 - - + -
252B ILE* 4.0 18.8 - - + -
266B ALA* 3.1 20.3 + - + +
267B ALA 3.3 3.3 + - - +
269B ALA* 1.3 70.6 - - - +
271B LEU* 1.3 68.0 + - - +
272B TYR 3.1 1.1 - - - -
273B GLU* 3.0 9.0 + - - +
274B ALA* 3.0 21.0 + - - +
302B SAM 4.4 7.6 - - + +
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Residues in contact with LEU 271 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
127B LEU* 3.9 34.2 - - + +
129B VAL* 4.0 28.5 - - + -
143B ILE* 5.2 3.8 - - + +
146B SER* 4.6 5.2 - - - -
147B ALA* 4.2 27.6 - - + +
150B LEU* 3.9 15.7 - - + -
152B ALA* 4.6 4.9 - - + -
229B LEU* 4.1 11.9 - - + -
267B ALA* 2.9 28.3 + - + +
268B THR* 3.6 7.0 - - - +
270B ILE* 1.3 76.1 - - - +
272B TYR* 1.3 63.5 + - - +
274B ALA* 3.2 6.8 + - + +
275B VAL* 3.1 25.9 + - - +
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Residues in contact with TYR 272 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
218A VAL* 3.2 33.2 - - + +
219A PHE* 3.7 14.7 - + - +
252A ILE* 4.1 22.0 - - + -
253A PRO* 5.1 4.9 - - + -
269A ALA* 3.9 31.0 - - + -
272A TYR* 3.9 18.6 - + - -
273A GLU* 2.6 32.8 + - + -
150B LEU* 4.0 11.6 - - + +
268B THR 2.9 18.8 + - - +
269B ALA 3.5 8.7 - - - +
270B ILE 3.1 0.2 - - - -
271B LEU* 1.3 76.9 - - - +
273B GLU* 1.3 66.6 + - - +
275B VAL* 3.2 10.4 + - + +
276B ARG* 2.9 32.5 + - + +
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Residues in contact with GLU 273 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
272A TYR* 2.7 37.7 + - + +
276A ARG* 3.6 1.4 - - - -
218B VAL* 3.9 15.9 - - + +
219B PHE* 3.4 9.0 - - - -
223B PHE* 4.1 6.3 - - + -
269B ALA 3.0 13.7 + - - +
270B ILE* 3.0 12.1 + - - +
272B TYR* 1.3 79.8 - - - +
274B ALA* 1.3 62.4 + - - +
276B ARG* 3.1 36.6 + - - +
277B GLN* 2.8 50.1 + - - +
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Residues in contact with ALA 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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127B LEU* 4.2 23.8 - - + -
223B PHE* 3.7 37.3 - - + +
270B ILE 3.0 10.8 + - - +
271B LEU* 3.4 11.9 - - + +
272B TYR 3.1 0.2 - - - -
273B GLU* 1.3 73.2 - - - +
275B VAL* 1.3 67.7 + - - +
277B GLN* 3.2 3.8 + - - +
278B ARG* 3.0 30.3 + - - +
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Residues in contact with VAL 275 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
253A PRO* 4.4 18.4 - - + +
127B LEU* 5.5 3.8 - - + +
150B LEU* 3.1 44.0 - - + +
271B LEU 3.1 12.9 + - - +
272B TYR* 3.2 11.0 + - + +
274B ALA* 1.3 78.6 - - + +
276B ARG* 1.3 59.0 + - - +
278B ARG* 3.3 8.2 + - - +
279B ILE* 2.9 52.3 + - + +
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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
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219A PHE* 4.0 28.7 - - + +
273A GLU* 3.6 22.0 - - - -
276A ARG* 3.2 39.8 - - - +
282A ARG* 4.6 13.5 - - - +
219B PHE* 4.6 7.5 + - - +
272B TYR* 2.9 26.7 + - + +
273B GLU* 3.1 41.1 + - - +
274B ALA 3.1 0.2 - - - -
275B VAL* 1.3 79.3 - - - +
277B GLN* 1.3 68.6 + - - +
279B ILE* 3.5 4.1 + - - +
280B SER* 2.8 46.2 + - - -
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Residues in contact with GLN 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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218B VAL 4.0 1.4 + - - -
219B PHE 4.0 9.6 + - - -
221B PHE 2.9 29.0 + - - +
222B ASP* 3.7 5.0 - - - +
223B PHE* 3.0 34.2 + - + -
224B THR* 4.2 14.0 + - + +
273B GLU* 2.8 37.2 + - - +
274B ALA 3.2 6.3 + - - +
276B ARG* 1.3 86.1 - - - +
278B ARG* 1.3 58.9 + - - +
280B SER* 3.5 8.5 + - - +
281B GLY* 2.9 34.9 + - - -
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Residues in contact with ARG 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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125B ASP* 2.7 37.3 + - - +
126B PHE 3.1 22.8 + - - -
127B LEU* 3.9 25.7 - - - +
151B GLY 5.8 0.8 + - - -
153B HIS* 4.8 1.0 + - - -
223B PHE 2.8 19.7 + - - +
224B THR* 4.2 19.9 - - + +
225B GLN 3.1 23.0 + - - -
227B THR* 4.6 1.4 + - - +
274B ALA* 3.0 24.2 + - - +
275B VAL* 3.7 7.4 - - - +
277B GLN* 1.3 77.7 - - - +
279B ILE* 1.3 62.3 + - + +
281B GLY* 4.2 4.2 + - - -
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Residues in contact with ILE 279 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
217A ASP* 5.6 1.3 - - - +
219A PHE* 4.1 22.9 - - + -
253A PRO* 4.1 21.1 - - + -
275B VAL* 2.9 41.9 + - + +
276B ARG* 4.0 3.6 - - - +
278B ARG* 1.3 79.7 - - + +
280B SER* 1.3 61.7 + - - +
281B GLY 3.6 0.2 + - - -
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Residues in contact with SER 280 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
219A PHE* 6.1 6.1 - - - -
276B ARG* 2.8 39.2 + - - -
277B GLN* 3.1 8.5 + - - +
279B ILE* 1.3 75.9 - - - +
281B GLY* 1.3 66.4 + - - +
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Residues in contact with GLY 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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224B THR* 5.2 9.6 - - - -
277B GLN* 2.9 13.4 + - - -
278B ARG 4.2 3.9 + - - -
279B ILE 3.4 2.8 - - - -
280B SER* 1.3 87.9 + - - +
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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
------------------------------------------------------------
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