Contacts of the helix formed by residues 262 - 279 (chain A) in PDB entry 1X7O
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 A).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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139A ASN* 2.9 24.2 + - - +
234A GLU* 5.4 0.7 - - - +
261A LEU* 1.3 74.7 - - - +
263A ALA* 1.3 63.2 + - - +
264A ALA* 2.8 37.7 - - - +
265A ASN* 2.9 33.8 + - - +
266A ALA* 3.0 19.9 + - - +
142B SER* 4.8 6.3 - - - +
145B ARG* 3.4 29.7 + - - +
146B SER* 5.6 0.4 + - - -
265B ASN* 4.9 0.2 + - - -
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Residues in contact with ALA 263 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
131A PHE* 4.1 16.6 - - + -
139A ASN* 4.7 1.3 - - - +
143A ILE* 4.5 1.1 - - - -
231A ILE* 3.9 16.0 - - + +
232A GLY 4.0 20.0 - - - +
234A GLU* 4.2 21.3 - - + +
261A LEU 3.6 2.7 + - - -
262A ASN* 1.3 74.2 + - - +
264A ALA* 1.3 56.9 + - - +
266A ALA* 3.4 7.5 + - - +
267A ALA* 2.9 29.6 + - - +
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Residues in contact with ALA 264 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
139A ASN* 4.0 12.9 + - - +
142A SER* 3.7 30.5 - - - -
143A ILE* 3.7 20.8 - - + +
262A ASN* 2.8 19.4 - - - +
263A ALA* 1.3 72.4 - - - +
265A ASN* 1.3 52.9 + - - +
267A ALA* 3.4 2.4 + - - +
268A THR* 2.8 37.3 + - - -
265B ASN* 4.0 6.5 - - - +
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Residues in contact with ASN 265 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
261A LEU* 4.8 2.0 - - + -
262A ASN* 2.9 31.5 + - + +
264A ALA* 1.3 71.9 - - - +
266A ALA* 1.3 65.5 + - - +
268A THR* 3.4 5.0 + - - -
269A ALA 3.1 16.8 + - - -
142B SER* 3.0 24.4 + - - +
146B SER* 3.5 13.7 + - - +
264B ALA* 3.7 5.1 - - - +
265B ASN* 2.3 47.4 + - - +
268B THR* 3.4 35.3 + - + +
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Residues in contact with ALA 266 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
210A THR* 6.1 1.6 - - - +
231A ILE* 5.7 3.8 - - + -
252A ILE* 4.0 17.7 - - + -
261A LEU* 4.2 16.5 - - + +
262A ASN 3.0 16.0 + - - +
263A ALA* 3.6 8.3 - - - +
265A ASN* 1.3 73.5 - - - +
267A ALA* 1.3 66.9 + - - +
269A ALA* 3.1 3.5 + - - +
270A ILE* 2.9 34.4 + - + +
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Residues in contact with ALA 267 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
129A VAL* 5.4 0.9 - - + -
143A ILE* 4.0 26.9 - - + -
146A SER* 6.1 0.4 - - - -
229A LEU* 4.7 1.4 - - + +
231A ILE* 3.9 26.6 - - + +
263A ALA 2.9 18.2 + - - +
264A ALA 3.6 4.9 - - - +
266A ALA* 1.3 76.1 - - - +
268A THR* 1.3 58.2 + - - +
270A ILE* 3.3 3.0 + - - +
271A LEU* 2.8 41.2 + - + +
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Residues in contact with THR 268 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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146A SER* 2.7 36.5 + - - +
150A LEU* 3.8 10.1 - - + +
264A ALA 2.8 21.7 + - - -
265A ASN 3.6 5.6 - - - -
267A ALA* 1.3 77.0 - - - +
269A ALA* 1.3 57.9 + - - +
271A LEU* 3.4 3.8 + - - +
272A TYR* 2.9 27.9 + - - +
261B LEU* 4.3 10.3 - - + -
265B ASN* 3.4 39.3 + - + +
269B ALA* 4.3 4.9 - - + -
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Residues in contact with ALA 269 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
252A ILE* 4.0 15.0 - - + -
261A LEU* 5.5 0.4 - - + -
265A ASN 3.1 12.6 + - - +
266A ALA 3.1 8.1 + - - +
268A THR* 1.3 76.8 - - - +
270A ILE* 1.3 56.2 + - - +
272A TYR* 3.4 7.7 + - - +
273A GLU* 3.1 25.1 + - - +
268B THR* 4.3 11.0 - - + -
269B ALA* 4.3 11.6 - - - +
272B TYR* 4.0 29.4 - - + -
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Residues in contact with ILE 270 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
210A THR* 3.4 33.2 - - + -
218A VAL* 3.9 21.3 - - + -
223A PHE* 3.9 9.2 - - + -
229A LEU* 3.6 31.4 - - + -
231A ILE* 5.0 2.0 - - + -
250A VAL* 4.7 7.9 - - + +
251A SER* 5.7 0.7 - - - -
252A ILE* 3.7 28.9 - - + +
266A ALA* 2.9 24.7 + - + +
267A ALA 4.0 2.9 - - - +
269A ALA* 1.3 73.6 - - - +
271A LEU* 1.3 65.4 + - - +
273A GLU* 3.3 7.3 + - - +
274A ALA* 3.2 19.8 + - - +
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Residues in contact with LEU 271 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
127A LEU* 3.9 32.0 - - + +
129A VAL* 4.0 28.9 - - + -
143A ILE* 5.2 3.1 - - + +
146A SER* 4.5 4.5 - - - -
147A ALA* 4.0 31.0 - - + +
150A LEU* 3.8 16.2 - - + -
152A ALA* 4.6 2.7 - - + -
229A LEU* 4.0 13.9 - - + -
267A ALA* 2.8 30.3 + - + +
268A THR* 3.7 5.6 - - - +
270A ILE* 1.3 75.3 - - - +
272A TYR* 1.3 64.5 + - - +
274A ALA* 3.1 6.5 + - + +
275A VAL* 3.0 24.7 + - - +
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Residues in contact with TYR 272 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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150A LEU* 3.9 13.9 - - + +
268A THR 2.9 17.6 + - - +
269A ALA 3.5 7.9 - - - +
271A LEU* 1.3 75.5 - - - +
273A GLU* 1.3 62.9 + - - +
275A VAL* 3.3 8.6 + - + +
276A ARG* 2.9 34.4 + - + +
218B VAL* 3.5 27.6 - - + +
219B PHE* 3.6 19.3 - + - +
252B ILE* 4.0 20.6 - - + -
253B PRO* 4.7 4.9 - - + -
269B ALA* 4.1 21.1 - - + -
272B TYR* 3.9 22.4 - + - -
273B GLU* 2.7 44.6 + - + +
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Residues in contact with GLU 273 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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218A VAL* 3.8 26.5 - - + +
219A PHE* 3.5 8.0 - - - -
223A PHE* 4.1 2.0 - - + -
269A ALA 3.1 13.8 + - - +
270A ILE 3.7 8.3 - - - +
271A LEU 3.2 0.2 - - - -
272A TYR* 1.3 79.6 - - - +
274A ALA* 1.3 61.0 + - - +
276A ARG* 2.9 37.3 + - - +
277A GLN* 2.8 47.4 + - - +
272B TYR* 2.8 34.6 + - + +
276B ARG* 3.5 5.7 - - - -
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Residues in contact with ALA 274 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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127A LEU* 4.3 25.1 - - + -
223A PHE* 3.7 37.6 - - + +
270A ILE 3.2 10.2 + - - +
271A LEU* 3.1 10.4 + - + +
273A GLU* 1.3 73.8 - - - +
275A VAL* 1.3 65.6 + - - +
277A GLN* 3.3 4.2 + - - +
278A ARG* 3.0 30.0 + - - +
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Residues in contact with VAL 275 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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127A LEU* 5.5 3.3 - - + +
150A LEU* 2.9 42.0 - - + +
271A LEU 3.0 16.9 + - - +
272A TYR* 3.5 11.7 - - + +
274A ALA* 1.3 75.1 - - + +
276A ARG* 1.3 63.8 + - - +
278A ARG* 3.1 7.9 + - - +
279A ILE* 3.0 48.8 + - + +
253B PRO* 4.1 22.2 - - + +
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Residues in contact with ARG 276 (chain A).
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* 4.6 5.1 + - - +
272A TYR* 2.9 31.7 + - + +
273A GLU* 2.9 40.7 + - - +
274A ALA 3.2 0.6 - - - -
275A VAL* 1.3 76.5 - - - +
277A GLN* 1.3 75.1 + - - +
279A ILE* 3.5 22.1 - - - +
282A ARG* 3.6 34.6 + - + +
283A THR* 3.8 18.7 + - - -
219B PHE* 4.0 25.7 - - + +
273B GLU* 3.7 11.2 - - - -
276B ARG* 3.3 49.6 - - - +
283B THR 4.5 1.6 + - - -
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Residues in contact with GLN 277 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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218A VAL 3.8 4.6 + - - -
219A PHE 4.0 1.2 + - - -
221A PHE 2.7 30.4 + - - +
222A ASP* 4.4 0.2 - - - +
223A PHE* 3.1 29.0 + - + -
224A THR* 3.8 18.2 + - + +
273A GLU* 2.8 40.4 + - - +
274A ALA 3.3 4.0 + - - +
276A ARG* 1.3 81.3 - - - +
278A ARG* 1.3 57.6 + - - +
281A GLY* 2.9 25.3 - - - -
282A ARG 4.4 6.7 - - - +
283A THR 3.0 25.7 + - - +
284A ALA* 3.6 14.9 - - - +
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Residues in contact with ARG 278 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
125A ASP* 2.8 36.3 + - - +
126A PHE 3.2 15.2 + - - -
127A LEU* 3.7 26.8 - - - +
151A GLY 5.7 0.6 + - - -
153A HIS* 4.5 2.0 - - - -
223A PHE 3.0 25.0 + - - +
224A THR* 3.6 28.1 + - + +
225A GLN 3.2 17.0 + - - -
227A THR* 4.8 0.8 + - - +
274A ALA* 3.0 24.2 + - - +
275A VAL* 3.1 8.3 + - - +
277A GLN* 1.3 77.0 - - - +
279A ILE* 1.3 67.9 + - + +
280A SER 3.1 5.0 + - - -
281A GLY* 3.5 5.0 + - - -
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Residues in contact with ILE 279 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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275A VAL* 3.0 29.2 + - + +
276A ARG 3.5 11.0 - - - +
277A GLN 3.6 0.2 - - - -
278A ARG* 1.3 74.9 - - + +
280A SER* 1.3 64.7 + - - +
281A GLY 3.0 8.7 + - - -
282A ARG* 4.8 2.8 + - - +
217B ASP* 5.3 1.3 - - - +
219B PHE* 3.8 27.7 - - + -
253B PRO* 3.8 33.4 - - + -
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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
------------------------------------------------------------
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