Contacts of the helix formed by residues 263 - 277 (chain A) in PDB entry 3MOS
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 263 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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257A TRP* 4.7 6.1 - - + -
261A PRO 3.6 7.1 - - - +
262A LEU* 1.3 85.5 - - + +
264A LYS* 1.3 57.3 + - - +
265A ASN* 3.2 14.4 - - - +
266A MET* 3.1 29.3 + - + -
267A ALA* 2.8 31.0 + - - +
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Residues in contact with LYS 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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31A THR* 3.4 41.8 + - + +
32A ALA* 4.4 8.7 + - - +
262A LEU 3.6 1.2 + - - -
263A PRO* 1.3 70.7 - - - +
265A ASN* 1.3 63.6 + - - +
267A ALA* 3.3 1.6 + - - +
268A GLU* 2.9 37.9 + - - +
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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
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263A PRO* 3.8 18.5 - - - +
264A LYS* 1.3 79.6 - - - +
266A MET* 1.3 75.0 + - - +
268A GLU* 3.6 9.4 + - - +
269A GLN* 3.3 20.6 + - - +
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Residues in contact with MET 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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248A ILE* 4.5 8.7 - - + -
249A THR 4.8 5.6 - - - +
250A GLY* 5.9 0.4 - - - -
251A VAL* 3.6 31.9 - - + -
257A TRP* 4.0 23.1 - - + -
262A LEU* 4.1 9.9 - - + -
263A PRO* 3.1 27.3 + - + +
265A ASN* 1.3 86.7 - - - +
267A ALA* 1.3 66.7 + - - +
269A GLN* 3.2 8.1 + - - +
270A ILE* 2.9 37.0 + - + +
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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
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27A ILE* 3.8 13.0 - - + -
28A GLN* 5.9 0.2 - - - -
31A THR* 3.5 33.0 - - + +
262A LEU* 3.9 13.3 - - + +
263A PRO 2.8 17.1 + - - +
264A LYS 3.5 5.2 - - - +
266A MET* 1.3 72.6 - - - +
268A GLU* 1.3 58.8 + - + +
270A ILE* 3.3 0.7 + - - +
271A ILE* 2.8 43.3 + - + +
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Residues in contact with GLU 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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264A LYS* 2.9 28.1 + - - +
265A ASN* 3.8 8.1 - - - +
266A MET 3.3 0.4 - - - -
267A ALA* 1.3 77.9 - - + +
269A GLN* 1.3 55.3 + - - +
271A ILE* 3.9 8.4 - - + +
272A GLN* 3.0 28.9 + - - +
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Residues in contact with GLN 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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249A THR* 4.6 4.6 + - - -
265A ASN 3.3 10.9 + - - +
266A MET* 3.2 11.5 + - - +
268A GLU* 1.3 75.2 - - - +
270A ILE* 1.3 88.6 + - - +
272A GLN* 3.4 8.0 + - - +
273A GLU* 3.2 25.0 + - - +
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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
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27A ILE* 3.9 15.3 - - + -
247A GLY 4.4 0.7 - - - +
248A ILE* 3.8 35.9 - - + -
249A THR* 3.5 28.0 - - - +
262A LEU* 4.1 9.9 - - + -
266A MET* 2.9 29.2 + - + +
267A ALA 3.9 2.2 - - - +
269A GLN* 1.3 93.3 - - - +
271A ILE* 1.3 59.3 + - - +
273A GLU* 3.0 8.6 + - - +
274A ILE* 2.9 48.9 + - + +
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Residues in contact with ILE 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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24A ILE* 3.7 35.8 - - + +
27A ILE* 4.0 24.5 - - + -
28A GLN* 3.6 34.3 - - + +
267A ALA* 2.8 32.7 + - + +
268A GLU* 3.9 8.3 - - + +
270A ILE* 1.3 76.7 - - - +
272A GLN* 1.3 58.3 + - - +
274A ILE* 3.2 3.5 + - - +
275A TYR* 2.8 36.4 + - + +
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Residues in contact with GLN 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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268A GLU 3.0 18.0 + - - +
269A GLN* 3.7 8.0 - - - +
270A ILE 3.3 0.2 - - - -
271A ILE* 1.3 79.0 - - - +
273A GLU* 1.3 62.4 + - - +
275A TYR* 3.4 7.1 + - + +
276A SER* 3.1 23.7 + - - -
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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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247A GLY 4.6 6.0 - - - +
249A THR* 3.1 42.2 + - - +
269A GLN* 3.2 20.0 + - - +
270A ILE* 3.0 12.6 + - - +
272A GLN* 1.3 74.6 - - - +
274A ILE* 1.3 67.7 + - + +
276A SER* 2.7 27.3 + - - +
277A GLN* 3.5 13.5 + - + +
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Residues in contact with ILE 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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20A ASN* 3.5 46.9 - - + +
23A ARG* 4.0 18.8 - - + -
24A ILE* 3.8 12.1 - - + -
27A ILE* 4.0 17.3 - - + -
247A GLY* 3.7 22.9 - - - +
248A ILE* 5.0 0.4 - - + -
270A ILE* 2.9 37.3 + - + +
271A ILE* 3.8 3.4 - - - +
273A GLU* 1.3 78.7 - - + +
275A TYR* 1.3 62.0 + - - +
277A GLN* 2.8 25.8 + - + +
278A ILE* 3.7 5.2 + - - +
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Residues in contact with TYR 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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21A ARG* 6.3 0.7 - - + -
24A ILE* 3.8 15.8 - - + +
271A ILE* 2.8 25.9 + - + +
272A GLN* 3.8 6.3 - - + +
274A ILE* 1.3 72.0 - - - +
276A SER* 1.3 64.2 + - - +
278A ILE* 3.0 43.5 + - + +
281A LYS* 2.9 35.8 + - + +
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Residues in contact with SER 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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272A GLN* 3.1 14.1 + - - -
273A GLU* 2.7 23.8 + - - +
274A ILE 3.1 0.6 - - - -
275A TYR* 1.3 78.1 - - - +
277A GLN* 1.3 72.9 + - - +
278A ILE 3.3 2.6 + - - +
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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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13A GLN* 4.2 5.4 + - - -
17A ASP* 4.0 4.0 - - - +
20A ASN* 4.0 20.4 + - - +
273A GLU* 3.6 18.0 + - + +
274A ILE* 2.8 14.9 + - - +
276A SER* 1.3 98.7 + - - +
278A ILE* 1.3 60.9 + - - +
279A GLN* 3.6 13.1 + - - +
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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