Contacts of the helix formed by residues 250 - 262 (chain A) in PDB entry 1R5O
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 GLY 250 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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248A ASP 3.3 3.6 + - - -
249A ALA* 1.3 78.6 - - - +
251A LYS* 1.3 57.2 + - - +
252A SER 3.1 3.1 - - - -
253A THR* 3.4 14.3 - - - +
254A LEU* 2.7 38.4 + - - +
346A VAL* 4.3 2.2 - - - -
384A ASN* 3.8 8.2 - - - +
1986A GNP 3.0 21.5 + - - -
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Residues in contact with LYS 251 (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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243A PHE* 3.4 43.9 - - + +
244A ILE 4.0 0.4 - - - -
245A GLY* 2.7 46.5 + - - +
246A HIS 2.7 17.4 + - - -
249A ALA* 3.4 7.8 - - + +
250A GLY* 1.3 77.5 - - - +
252A SER* 1.3 57.1 + - - +
254A LEU* 4.1 1.9 - - - +
255A GLY* 3.2 19.2 + - - -
346A VAL* 4.3 16.8 - - + -
1986A GNP 3.2 30.3 + - - +
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Residues in contact with SER 252 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
250A GLY 3.1 0.4 - - - -
251A LYS* 1.3 78.2 - - - +
253A THR* 1.3 61.6 + - - +
254A LEU 3.2 1.3 - - - -
255A GLY* 3.1 2.1 + - - -
256A GLY* 2.7 27.9 + - - -
273A ILE* 3.8 30.0 + - - +
274A GLU* 4.7 2.4 - - - -
277A ALA* 4.0 9.3 - - - +
1986A GNP 3.4 36.4 + - - -
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Residues in contact with THR 253 (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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250A GLY* 3.4 15.7 - - - +
252A SER* 1.3 76.4 - - - +
254A LEU* 1.3 50.6 + - - +
256A GLY* 3.3 1.8 + - - +
257A ASN* 2.7 35.7 + - - +
270A MET* 5.8 0.2 - - - +
274A GLU* 3.9 34.6 + - - +
428A ALA* 3.6 21.3 + - + +
429A TYR* 4.0 5.5 + - - +
1986A GNP 3.1 43.4 + - + +
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Residues in contact with LEU 254 (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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243A PHE* 3.9 26.9 - - + -
250A GLY 2.7 22.4 + - - +
251A LYS 4.1 2.7 - - - +
253A THR* 1.3 71.4 + - - +
255A GLY* 1.3 68.3 + - - +
257A ASN* 3.2 3.1 + - + +
258A ILE* 3.0 41.1 + - + +
346A VAL* 4.2 16.4 - - + -
382A VAL* 4.2 12.8 - - + -
384A ASN* 4.9 1.6 - - - +
426A VAL* 4.7 9.4 - - + -
428A ALA* 3.4 25.7 - - + +
434A VAL* 4.3 14.1 - - + -
451A LEU* 4.2 22.7 - - + -
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Residues in contact with GLY 255 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
243A PHE* 5.2 6.3 - - - -
251A LYS 3.2 12.2 + - - -
252A SER* 3.1 6.7 + - - -
254A LEU* 1.3 84.2 - - - +
256A GLY* 1.3 62.2 + - - +
257A ASN 2.9 0.3 + - - -
258A ILE* 2.9 17.1 + - - +
259A LEU* 3.1 17.8 + - - +
320A LEU* 5.1 14.8 - - - -
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Residues in contact with GLY 256 (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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252A SER 2.7 18.7 + - - -
253A THR* 3.6 2.0 - - - -
255A GLY* 1.3 70.7 - - - -
257A ASN* 1.3 56.0 + - - +
259A LEU* 3.5 12.2 + - - +
260A PHE* 3.1 21.8 + - - +
270A MET* 3.6 23.4 - - - +
273A ILE* 4.4 21.6 - - - +
274A GLU* 5.8 0.7 - - - -
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Residues in contact with ASN 257 (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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253A THR* 2.7 21.6 + - - +
254A LEU* 3.6 6.7 - - + +
255A GLY 2.9 0.4 + - - -
256A GLY* 1.3 71.7 - - - +
258A ILE* 1.3 58.4 + - + +
260A PHE* 4.1 2.6 - - - +
261A LEU* 2.7 71.5 + - - +
270A MET* 3.9 21.6 - - - +
428A ALA* 3.1 26.4 + - - +
429A TYR 4.2 7.1 - - - +
430A THR 5.3 0.2 - - - -
431A GLY* 3.4 13.3 - - - -
434A VAL* 3.4 9.3 - - - +
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Residues in contact with ILE 258 (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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243A PHE* 4.2 21.3 - - + -
254A LEU* 3.0 36.7 + - + +
255A GLY* 2.9 8.6 + - - +
257A ASN* 1.3 76.3 - - - +
259A LEU* 1.3 60.3 + - - +
261A LEU* 3.8 4.4 - - - -
262A THR* 2.8 32.9 + - + -
311A PHE* 3.6 44.0 - - + -
434A VAL* 3.5 25.4 - - + -
451A LEU* 4.7 7.4 - - + -
452A LEU* 4.0 16.4 - - + -
455A LEU* 5.9 2.0 - - + -
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Residues in contact with LEU 259 (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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255A GLY 3.1 14.3 + - - +
256A GLY* 3.7 9.0 - - - +
257A ASN 3.3 0.2 - - - -
258A ILE* 1.3 80.1 - - - +
260A PHE* 1.3 63.1 + - - +
262A THR* 3.2 3.9 - - - +
264A MET* 2.9 37.7 + - + -
265A VAL* 3.7 22.0 - - + -
273A ILE* 4.4 22.0 - - + -
309A ALA* 4.6 15.9 - - + -
310A TYR* 3.2 37.5 - - - +
311A PHE* 3.9 11.2 - - + -
320A LEU* 5.2 7.9 - - + -
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Residues in contact with PHE 260 (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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256A GLY 3.1 5.6 + - - +
257A ASN* 4.7 2.7 - - - -
259A LEU* 1.3 77.8 - - - +
261A LEU* 1.3 75.1 + - + +
262A THR 2.7 11.8 + - - -
263A GLY* 2.9 14.4 + - - -
265A VAL* 3.1 25.3 - - - +
266A ASP* 3.8 10.8 - - - -
267A LYS* 4.3 18.8 - - + -
270A MET* 3.7 43.1 - - + -
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Residues in contact with LEU 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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257A ASN* 2.7 51.1 + - - +
258A ILE* 4.0 4.0 - - - +
260A PHE* 1.3 87.7 - - + +
262A THR* 1.3 56.9 + - - +
263A GLY 3.4 1.4 + - - -
431A GLY* 4.1 9.9 - - - +
434A VAL* 3.3 22.0 - - + -
435A LYS* 3.8 40.8 + - + +
436A ASP* 5.5 3.6 - - - +
452A LEU* 5.5 2.5 - - + -
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Residues in contact with THR 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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258A ILE* 2.8 25.7 + - - +
259A LEU* 3.2 11.0 - - - +
260A PHE 2.7 6.1 + - - -
261A LEU* 1.3 74.5 - - - +
263A GLY* 1.3 53.9 + - - -
264A MET* 3.0 34.6 - - + +
311A PHE* 3.5 21.0 - - + +
312A GLU* 2.9 24.4 + - - +
435A LYS* 5.1 9.3 - - - +
452A LEU* 5.1 9.7 - - - +
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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