Contacts of the helix formed by residues 260 - 275 (chain A) in PDB entry 7D1M
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 ALA 260 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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209A TYR* 3.4 0.7 + - - -
254A SER* 3.5 6.7 - - - -
258A GLY 3.9 3.6 + - - -
259A ILE* 1.3 74.2 - - - +
261A VAL* 1.3 65.9 + - - +
262A LEU* 4.3 3.8 - - + +
263A ASP* 3.0 37.5 + - - +
264A MET 3.0 11.1 + - - -
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Residues in contact with VAL 261 (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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205A LEU* 5.0 0.9 - - + -
209A TYR* 3.2 17.0 + - + +
242A LEU* 4.6 0.4 - - + -
247A VAL* 3.8 50.7 - - + +
250A LEU* 3.8 35.7 - - + +
251A GLY* 4.6 1.3 - - - +
254A SER* 3.7 14.6 + - - +
259A ILE 3.6 0.2 + - - -
260A ALA* 1.3 71.7 - - - +
262A LEU* 1.3 59.5 + - + +
264A MET* 3.1 5.6 + - + +
265A CYS* 2.9 34.4 + - - -
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Residues in contact with LEU 262 (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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224A THR* 3.6 8.8 + - - +
225A THR* 3.4 29.7 - - + +
226A THR* 4.1 3.4 - - - +
227A LEU* 3.7 43.3 - - + +
230A PHE* 5.4 0.2 - - + -
247A VAL* 5.3 9.0 - - + -
260A ALA* 3.2 3.6 - - + +
261A VAL* 1.3 78.5 - - + +
263A ASP* 1.3 57.0 + - - +
265A CYS* 3.3 21.5 + - + +
266A ALA* 3.0 22.3 + - - +
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Residues in contact with ASP 263 (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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220A LEU* 6.1 0.2 - - - -
221A ASN* 4.6 5.6 - - - +
223A PHE 4.4 7.2 - - - +
224A THR* 2.7 35.9 + - - +
259A ILE* 4.1 12.9 - - + -
260A ALA* 3.0 28.4 + - - +
262A LEU* 1.3 74.2 - - - +
264A MET* 1.3 64.2 + - - +
266A ALA* 3.1 9.0 + - - +
267A SER* 3.0 23.7 + - - -
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Residues in contact with MET 264 (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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205A LEU* 3.8 19.3 - - + +
208A LEU* 3.8 22.9 - - + -
209A TYR* 3.6 63.9 - - + +
212A VAL* 4.0 20.6 - - + -
219A PHE* 4.1 4.9 - - - -
220A LEU* 3.9 16.4 - - - -
259A ILE* 4.0 13.6 - - + +
260A ALA 3.0 6.6 + - - +
261A VAL* 3.5 7.6 - - - +
263A ASP* 1.3 75.6 - - - +
265A CYS* 1.3 57.1 + - - +
267A SER* 3.1 6.8 + - - -
268A LEU* 2.9 27.7 + - - +
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Residues in contact with CYS 265 (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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205A LEU* 3.9 14.8 - - - -
225A THR* 3.8 7.6 - - + -
230A PHE* 3.4 40.7 - - + -
242A LEU* 3.6 31.9 - - - -
261A VAL* 2.9 19.1 + - - -
262A LEU* 3.3 21.5 - - + +
263A ASP 3.2 0.2 - - - -
264A MET* 1.3 75.5 - - - +
266A ALA* 1.3 56.8 + - - +
268A LEU 3.2 0.7 + - - -
269A LYS* 2.8 26.0 + - - +
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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
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221A ASN* 3.2 12.2 + - - +
223A PHE* 3.1 41.2 - - + +
224A THR* 3.7 15.0 - - - -
225A THR* 3.7 8.0 - - + +
262A LEU 3.0 8.6 + - - +
263A ASP 3.1 5.6 + - - +
265A CYS* 1.3 75.3 - - - +
267A SER* 1.3 62.5 + - - +
269A LYS* 3.4 8.2 + - - +
270A GLU* 3.2 21.1 + - - +
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Residues in contact with SER 267 (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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208A LEU* 5.4 0.7 - - - -
219A PHE* 3.4 25.8 + - - +
220A LEU* 3.4 10.7 - - - +
221A ASN* 3.3 34.0 + - - +
263A ASP 3.0 13.2 + - - -
264A MET* 3.1 15.7 + - - -
266A ALA* 1.3 73.4 - - - +
268A LEU* 1.3 64.6 + - - +
270A GLU* 3.2 5.5 + - - +
271A LEU* 3.1 26.3 + - - +
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Residues in contact with LEU 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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201A THR* 4.2 3.8 - - + -
204A VAL* 3.9 17.9 - - + -
205A LEU* 3.8 22.2 - - + -
208A LEU* 4.1 11.6 - - + +
230A PHE* 3.8 25.6 - - + -
239A TYR* 4.1 18.4 - - + -
264A MET 2.9 13.7 + - - +
265A CYS 3.6 7.0 - - - +
267A SER* 1.3 70.8 - - - +
269A LYS* 1.3 65.7 + - - +
271A LEU* 3.0 9.1 + - + -
272A LEU* 2.9 37.7 + - + +
287A LEU* 3.8 29.2 - - + -
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Residues in contact with LYS 269 (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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224A THR 5.3 0.6 + - - -
225A THR* 2.8 37.7 + - - -
229A ASP* 4.2 11.7 + - - +
230A PHE* 4.0 19.5 - - + +
233A VAL* 3.7 37.8 - - + +
265A CYS 2.8 15.6 + - - +
266A ALA* 3.6 7.6 - - - +
267A SER 3.3 0.4 - - - -
268A LEU* 1.3 76.9 - - - +
270A GLU* 1.3 63.9 + - - +
272A LEU* 3.2 10.4 + - - +
273A GLN* 3.0 47.9 + - - +
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Residues in contact with GLU 270 (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 5.7 1.3 - - - +
221A ASN* 3.1 31.6 - - - +
223A PHE* 3.7 27.2 - - + +
266A ALA 3.2 5.9 + - - +
267A SER 3.6 3.6 - - - +
268A LEU 3.2 0.4 - - - -
269A LYS* 1.3 84.5 - - - +
271A LEU* 1.3 57.4 + - - +
273A GLN* 3.2 20.7 - - - +
274A ASN* 2.8 60.0 + - - +
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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
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208A LEU* 4.2 19.3 - - + -
218A TRP* 3.7 33.0 - - + -
219A PHE* 4.0 23.8 - - + +
267A SER 3.1 16.2 + - - +
268A LEU* 3.0 9.9 + - - +
270A GLU* 1.3 75.9 - - + +
272A LEU* 1.3 58.3 + - - +
275A GLY* 2.8 40.1 + - - +
276A MET* 4.0 17.1 - - + +
281A ILE* 4.2 6.1 - - + -
287A LEU* 4.1 32.2 - - + +
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Residues in contact with LEU 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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230A PHE* 5.4 2.9 - - + -
233A VAL* 4.9 3.4 - - + -
234A ALA* 4.6 12.1 - - + +
237A TYR* 3.4 53.9 - - + -
239A TYR* 3.5 46.7 - - + +
268A LEU* 2.9 32.2 + - + +
269A LYS* 3.6 9.4 - - - +
271A LEU* 1.3 77.2 - - - +
273A GLN* 1.3 63.0 + - - +
274A ASN 3.7 0.2 + - - -
275A GLY* 4.2 2.8 + - - -
287A LEU* 4.2 11.4 - - + -
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Residues in contact with GLN 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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233A VAL* 4.0 24.7 - - + +
236A LYS* 6.1 1.4 - - - +
237A TYR* 3.6 25.6 + - + +
269A LYS* 3.0 26.2 + - - +
270A GLU* 3.2 29.5 - - - +
272A LEU* 1.3 78.9 - - - +
274A ASN* 1.3 68.0 + - - +
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Residues in contact with ASN 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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270A GLU* 2.8 44.1 + - - +
273A GLN* 1.3 82.0 - - - +
275A GLY* 1.3 59.0 + - - +
277A ASN* 2.8 28.6 + - - +
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Residues in contact with GLY 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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218A TRP* 5.1 1.9 - - - -
271A LEU* 2.8 31.2 + - - +
272A LEU 4.2 2.5 + - - -
273A GLN 3.7 1.2 - - - -
274A ASN* 1.3 87.3 - - - +
276A MET* 1.3 63.1 + - - -
277A ASN* 3.4 5.2 - - - +
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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