Contacts of the helix formed by residues 276 - 289 (chain A) in PDB entry 2CHR
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 VAL 276 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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105A GLU* 3.1 6.8 + - + -
106A MET* 5.2 2.2 - - + -
109A LEU* 3.8 27.8 - - + -
120A ILE* 5.3 2.2 - - + -
124A LEU* 4.1 20.4 - - + -
270A LEU* 3.4 31.0 - - + -
275A GLY* 1.3 70.5 - - - -
277A SER* 1.3 67.0 + - - +
278A ALA 3.2 0.2 - - - -
279A THR* 3.4 1.9 + - - -
280A GLN* 3.1 26.2 + - - +
307A VAL* 3.6 19.7 - - + -
311A LEU* 3.8 26.9 - - + +
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Residues in contact with SER 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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83A VAL* 4.2 6.4 - - - +
87A LEU* 3.4 26.5 - - - +
105A GLU* 2.9 17.6 + - - -
109A LEU* 4.9 4.0 - - - +
276A VAL* 1.3 79.3 - - - +
278A ALA* 1.3 61.7 + - - +
280A GLN* 3.6 15.5 + - - +
281A LYS* 3.6 26.7 + - - +
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Residues in contact with ALA 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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87A LEU* 5.0 2.8 - - + +
105A GLU* 4.3 1.0 + - - -
251A LEU* 5.8 0.7 - - - +
273A MET 3.0 28.9 - - - +
274A GLY* 3.8 16.4 - - - +
275A GLY 3.9 1.0 + - - -
276A VAL 3.2 0.2 - - - -
277A SER* 1.3 77.7 - - - +
279A THR* 1.3 64.0 + - - +
281A LYS* 3.2 20.6 + - - +
282A ILE* 3.3 18.2 + - + +
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Residues in contact with THR 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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268A LEU* 3.9 37.4 - - + +
270A LEU* 3.2 22.3 + - + +
273A MET* 3.8 19.4 - - - +
275A GLY 2.8 21.9 + - - -
276A VAL 3.4 5.1 + - - -
278A ALA* 1.3 78.3 - - - +
280A GLN* 1.3 56.3 + - - +
282A ILE* 3.1 5.1 + - - +
283A ALA* 2.9 26.1 + - + +
311A LEU* 3.6 20.2 - - + -
312A TYR* 4.9 0.2 - - + -
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Residues in contact with GLN 280 (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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124A LEU* 4.1 32.7 + - - +
276A VAL* 3.1 22.5 + - - +
277A SER* 3.7 16.9 + - - +
278A ALA 3.3 0.2 - - - -
279A THR* 1.3 76.2 - - - +
281A LYS* 1.3 59.6 + - + +
283A ALA* 3.2 10.3 + - - +
284A ALA* 3.0 25.2 + - - +
311A LEU* 3.5 24.3 - - + +
314A THR* 5.3 2.4 + - - -
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Residues in contact with LYS 281 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
251A LEU* 3.7 33.9 - - + +
277A SER* 3.6 16.4 + - - +
278A ALA* 3.2 13.2 + - - +
280A GLN* 1.3 74.6 - - + +
282A ILE* 1.3 62.0 + - - +
284A ALA* 3.0 21.4 + - - +
285A VAL* 3.0 18.7 + - - +
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Residues in contact with ILE 282 (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 LEU* 4.7 0.9 - - + -
249A SER 4.6 2.5 - - - +
250A THR* 4.2 21.1 - - - +
251A LEU* 4.0 13.0 - - + +
254A ALA* 3.7 25.1 - - + -
266A PHE* 3.9 15.3 - - + -
268A LEU* 4.4 6.3 - - + -
273A MET* 3.6 53.2 - - + +
278A ALA* 3.3 10.7 + - + +
279A THR 3.1 8.2 + - - +
281A LYS* 1.3 72.6 - - - +
283A ALA* 1.3 57.5 + - - +
284A ALA 3.0 4.5 - - - -
285A VAL* 3.3 8.2 + - - +
286A ALA* 3.0 26.9 + - - +
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Residues in contact with ALA 283 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
268A LEU* 4.4 22.2 - - + +
279A THR* 2.9 13.7 + - + +
280A GLN* 3.4 14.4 - - - +
282A ILE* 1.3 76.8 - - - +
284A ALA* 1.3 56.5 + - - +
286A ALA* 4.0 8.4 - - - +
287A GLU* 3.4 25.8 + - - +
293A SER* 4.4 10.2 + - - +
315A VAL* 5.2 13.4 - - + +
316A PRO* 5.9 2.5 - - + +
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Residues in contact with ALA 284 (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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280A GLN 3.0 10.4 + - - +
281A LYS* 3.1 14.8 - - - +
282A ILE 3.0 0.4 - - - -
283A ALA* 1.3 77.3 - - - +
285A VAL* 1.3 62.8 + - + +
286A ALA 3.2 1.6 - - - -
287A GLU* 3.4 8.2 + - - +
288A ALA* 3.1 27.4 + - - +
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Residues in contact with VAL 285 (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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251A LEU* 3.8 17.5 - - + -
254A ALA* 3.9 32.5 - - + +
255A PHE* 4.3 20.2 - - + +
258A ALA* 4.3 2.3 - - + +
266A PHE* 4.1 8.3 - - + -
281A LYS 3.0 13.8 + - - +
282A ILE 3.3 11.0 - - - +
284A ALA* 1.3 76.6 - - + +
286A ALA* 1.3 61.7 + - - +
288A ALA* 4.0 5.8 - - - +
289A SER* 2.8 30.9 + - - -
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Residues in contact with ALA 286 (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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266A PHE* 3.5 27.1 - - + -
268A LEU* 6.2 0.2 - - + -
282A ILE 3.0 17.4 + - - +
283A ALA* 4.1 3.1 - - - +
285A VAL* 1.3 77.4 - - - +
287A GLU* 1.3 59.4 + - - +
289A SER* 3.1 4.7 + - - -
290A GLY 2.9 7.8 + - - -
291A ILE* 2.7 45.4 + - + +
293A SER* 4.1 16.4 - - - +
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Residues in contact with GLU 287 (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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283A ALA 3.4 18.1 + - - +
284A ALA* 3.7 8.2 - - - +
285A VAL 3.4 0.4 - - - -
286A ALA* 1.3 79.1 - - - +
288A ALA* 1.3 62.5 + - - +
290A GLY* 3.5 10.1 + - - -
291A ILE 4.2 2.7 + - - -
293A SER* 5.5 0.2 + - - -
316A PRO* 3.7 29.3 - - - +
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Residues in contact with ALA 288 (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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284A ALA 3.1 17.5 + - - +
285A VAL* 4.0 6.7 - - - +
287A GLU* 1.3 79.3 - - - +
289A SER* 1.3 60.4 + - - +
290A GLY 3.6 0.2 + - - -
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Residues in contact with SER 289 (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 ALA* 3.5 36.7 - - - +
261A ARG* 4.5 6.2 + - - -
285A VAL 2.8 20.3 + - - -
286A ALA* 3.1 11.6 + - - -
288A ALA* 1.3 78.7 - - - +
290A GLY* 1.3 58.7 + - - +
291A ILE* 3.6 9.9 + - - +
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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