Contacts of the helix formed by residues 269 - 279 (chain A) in PDB entry 1O0C
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 SER 269 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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260A ARG* 5.7 0.7 - - - -
267A VAL* 3.7 1.2 - - - +
268A MET* 1.3 77.8 - - - +
270A LYS* 1.3 61.0 + - - +
271A ARG* 4.3 6.5 - - - +
272A LYS* 2.8 43.5 + - - +
273A LEU* 2.8 16.2 + - - +
1394A SO4 4.1 4.0 - - - -
1395A SO4 2.6 34.2 + - - -
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Residues in contact with LYS 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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33A PRO* 5.6 0.6 - - - +
34A GLU 3.7 5.3 + - - -
36A ASN* 2.8 38.6 + - - +
37A GLY* 3.6 25.6 - - - -
38A TYR 3.4 27.8 - - - +
39A LEU* 5.2 2.7 - - - -
40A HIS* 4.7 3.8 - - + -
43A HIS* 3.5 17.3 - - + -
81A ILE* 6.0 0.2 - - - -
268A MET 4.2 0.2 - - - -
269A SER* 1.3 70.2 - - - +
271A ARG* 1.3 56.8 + - - +
273A LEU* 4.3 8.7 - - + +
274A ASN* 2.8 34.4 + - - +
285A TRP* 3.9 5.4 - - + -
998A AMP 2.5 28.7 + - - -
1394A SO4 3.3 24.6 + - - +
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Residues in contact with ARG 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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269A SER* 3.0 6.1 + - - +
270A LYS* 1.3 79.4 - - - +
272A LYS* 1.3 82.2 + - - +
274A ASN* 3.7 5.8 - - - +
275A LEU* 3.2 53.4 + - - +
487A PHE* 4.3 5.5 - - - -
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Residues in contact with LYS 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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267A VAL* 3.7 25.1 - - + -
269A SER* 2.8 22.3 + - - +
271A ARG* 1.3 90.2 - - - +
273A LEU* 1.3 63.9 + - - +
274A ASN 3.1 1.6 - - - -
275A LEU* 3.0 14.1 + - - +
276A LEU* 3.1 13.9 + - - +
482A GLY* 3.9 20.9 + - - -
487A PHE* 3.6 38.9 - - + -
1395A SO4 2.9 39.0 + - - +
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Residues in contact with LEU 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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38A TYR 5.5 0.7 - - - +
40A HIS* 4.0 34.8 - - + -
267A VAL* 3.8 19.7 - - + +
268A MET* 4.4 2.9 - - - -
269A SER 2.8 25.6 + - - +
270A LYS* 4.0 4.5 - - + +
272A LYS* 1.3 75.2 - - - +
274A ASN* 1.3 62.8 + - - +
276A LEU* 3.3 7.8 + - + +
277A VAL* 3.2 27.1 + - - +
285A TRP* 3.8 22.0 - - + -
290A MET* 3.6 17.3 - - + +
291A PRO* 3.6 35.4 - - + -
292A THR* 4.6 4.9 - - + -
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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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36A ASN 5.3 5.6 + - - +
77A TYR* 4.4 8.1 + - - -
270A LYS 2.8 21.8 + - - +
271A ARG* 3.7 7.1 - - - +
273A LEU* 1.3 76.9 - - - +
275A LEU* 1.3 52.6 + - - +
277A VAL* 3.3 3.7 + - - +
278A THR* 2.8 50.5 + - - -
285A TRP* 3.3 30.0 + - + -
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Residues in contact with LEU 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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271A ARG* 3.2 42.7 + - - +
272A LYS 3.0 10.9 + - - +
274A ASN* 1.3 76.0 - - - +
276A LEU* 1.3 60.1 + - - +
278A THR* 4.4 7.2 - - + +
279A ASP* 2.9 64.1 + - - +
281A HIS* 4.7 0.3 + - - -
487A PHE* 3.6 24.2 - - + -
488A LEU* 4.2 13.7 - - + -
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Residues in contact with LEU 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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267A VAL* 4.2 18.8 - - + -
272A LYS 3.1 17.9 + - - +
273A LEU* 3.3 15.9 + - + +
275A LEU* 1.3 75.2 - - - +
277A VAL* 1.3 62.0 + - - +
280A LYS 3.3 1.9 + - - -
281A HIS* 2.8 39.5 + - + +
282A VAL* 3.7 22.8 + - + -
290A MET* 4.3 15.7 - - + -
475A LEU* 4.3 9.9 - - + -
476A PHE* 4.3 11.4 - - + -
487A PHE* 4.1 9.6 - - + -
488A LEU* 3.6 24.2 - - + -
491A ILE* 3.9 18.4 - - + -
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Residues in contact with VAL 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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273A LEU 3.2 14.6 + - - +
274A ASN* 3.4 8.5 - - - +
275A LEU 3.2 0.2 - - - -
276A LEU* 1.3 77.6 - - - +
278A THR* 1.3 65.7 + - - +
280A LYS* 3.1 23.4 + - - +
282A VAL* 4.1 8.3 - - + +
283A GLU 5.7 0.7 - - - +
284A GLY* 4.0 8.3 - - - -
285A TRP* 3.8 50.9 - - + +
290A MET* 3.5 20.9 - - + -
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Residues in contact with THR 278 (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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274A ASN* 2.8 37.4 + - - -
275A LEU* 4.2 8.1 - - + -
277A VAL* 1.3 77.0 - - - +
279A ASP* 1.3 64.6 + - - +
280A LYS* 3.1 12.7 + - - +
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Residues in contact with ASP 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 LEU* 2.9 44.8 + - - +
278A THR* 1.3 77.7 - - - +
280A LYS* 1.3 70.9 + - - +
281A HIS* 3.4 31.1 + - + +
488A LEU* 3.7 14.2 - - - +
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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