Contacts of the helix formed by residues 277 - 291 (chain A) in PDB entry 2H31
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 ASP 277 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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272A MSE 5.1 1.1 - - + -
274A SER* 3.0 23.3 + - - +
276A SER* 1.3 85.8 + - - +
278A LEU* 1.3 56.2 + - - +
279A GLY 3.0 3.6 - - - -
280A HIS* 2.7 31.3 + - + +
281A CYS* 3.0 14.5 + - - -
328A VAL* 4.2 20.4 - - + +
329A ALA* 5.3 0.2 - - - -
330A GLY* 4.3 10.7 + - - -
352A PRO* 3.7 31.9 - - - +
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Residues in contact with LEU 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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272A MSE 3.5 30.6 - - + -
275A THR* 3.0 24.8 + - + +
276A SER 3.4 0.4 - - - -
277A ASP* 1.3 76.5 - - - +
279A GLY* 1.3 57.3 + - - +
281A CYS* 3.2 1.6 + - - +
282A GLU* 2.9 60.3 + - - +
297A LEU* 3.9 16.2 - - + -
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Residues in contact with GLY 279 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
276A SER 5.1 1.6 + - - -
277A ASP 3.0 1.2 - - - -
278A LEU* 1.3 79.8 - - - +
280A HIS* 1.3 62.9 + - - +
282A GLU* 3.3 21.3 + - - +
283A LYS* 3.3 21.1 + - - +
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Residues in contact with HIS 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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277A ASP* 2.7 21.6 + - + +
279A GLY* 1.3 72.2 - - - +
281A CYS* 1.3 61.3 + - - +
283A LYS* 3.2 23.7 + - + +
284A ILE* 3.5 14.5 + - + +
328A VAL* 3.6 18.2 - - + +
350A CYS* 3.1 43.7 - - - -
351A PRO 3.7 5.7 + - - -
352A PRO* 3.6 33.2 - - + +
378A LEU 4.5 0.6 + - - -
380A PRO* 3.2 28.4 - - + +
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Residues in contact with CYS 281 (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 VAL* 3.7 20.2 - - + -
272A MSE 3.4 54.1 - - + -
277A ASP 3.0 11.1 + - - -
278A LEU 3.6 3.4 - - - +
280A HIS* 1.3 76.4 - - - +
282A GLU* 1.3 56.7 + - - +
284A ILE* 3.2 14.3 + - - +
285A LYS* 2.9 25.3 + - - +
297A LEU* 3.8 9.5 - - + +
328A VAL* 4.0 16.6 - - - -
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Residues in contact with GLU 282 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
278A LEU* 2.9 44.5 + - - +
279A GLY* 3.7 13.2 - - - +
280A HIS 3.2 0.4 - - - -
281A CYS* 1.3 74.1 - - - +
283A LYS* 1.3 59.6 + - - +
285A LYS* 3.6 8.8 - - + +
286A LYS* 2.8 32.4 + - - +
297A LEU* 3.8 17.3 - - + +
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Residues in contact with LYS 283 (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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279A GLY 3.3 15.4 + - - +
280A HIS* 3.2 12.4 + - - +
282A GLU* 1.3 77.0 - - - +
284A ILE* 1.3 62.6 + - - +
286A LYS* 3.9 6.3 - - - +
287A ALA* 3.0 24.6 + - - +
380A PRO* 4.0 18.7 - - + +
381A GLU* 4.0 25.5 + - - +
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Residues in contact with ILE 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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270A VAL* 4.2 17.7 - - + -
280A HIS* 3.6 16.2 - - - +
281A CYS* 3.2 9.4 + - - +
282A GLU 3.2 0.4 - - - -
283A LYS* 1.3 78.0 - - - +
285A LYS* 1.3 56.6 + - - +
287A ALA* 3.1 4.8 + - - +
288A CYS* 2.8 35.0 + - - -
326A VAL* 3.8 23.3 - - + -
328A VAL* 4.1 20.0 - - + -
350A CYS* 4.1 9.6 - - - -
380A PRO* 3.5 24.2 - - + +
383A SER* 3.7 22.4 - - - +
384A ALA* 4.0 12.1 - - + +
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Residues in contact with LYS 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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281A CYS 2.9 13.2 + - - +
282A GLU* 3.3 11.9 + - + +
284A ILE* 1.3 76.7 - - - +
286A LYS* 1.3 63.5 + - - +
288A CYS* 3.2 4.5 + - - +
289A GLY* 3.0 18.2 + - - -
295A CYS* 3.2 46.8 - - + +
296A GLU* 4.9 1.6 - - - +
297A LEU* 3.7 30.1 - - + +
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Residues in contact with LYS 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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282A GLU 2.8 21.1 + - - +
283A LYS* 3.9 7.0 - - - +
285A LYS* 1.3 73.3 - - - +
287A ALA* 1.3 59.2 + - - +
289A GLY* 2.9 17.7 + - - -
290A ASN* 3.2 27.9 + - - +
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Residues in contact with ALA 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 LYS 3.0 20.0 + - - +
284A ILE 3.1 4.7 + - - +
286A LYS* 1.3 78.6 - - - +
288A CYS* 1.3 57.8 + - - +
290A ASN* 2.8 37.7 + - - +
291A PHE* 3.6 12.7 + - + -
381A GLU* 3.9 22.0 - - + +
384A ALA* 3.3 19.3 - - + -
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Residues in contact with CYS 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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268A VAL* 3.9 39.0 - - - -
284A ILE* 2.8 18.1 + - - +
285A LYS 3.2 9.4 + - - +
287A ALA* 1.3 76.4 - - - +
289A GLY* 1.3 62.7 + - - +
291A PHE* 3.0 13.5 + - - +
293A ILE* 3.0 43.4 + - + +
295A CYS* 3.8 12.1 - - + -
384A ALA* 3.7 22.2 - - - +
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Residues in contact with GLY 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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285A LYS 3.0 10.3 + - - -
286A LYS* 2.9 12.4 + - - -
288A CYS* 1.3 78.4 - - - +
290A ASN* 1.3 59.7 + - - +
292A GLY* 3.2 14.1 + - - -
293A ILE 4.2 5.1 + - - -
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Residues in contact with ASN 290 (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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286A LYS* 3.2 27.6 + - - +
287A ALA* 2.8 20.0 + - - +
289A GLY* 1.3 77.9 - - - +
291A PHE* 1.3 67.9 + - + +
292A GLY 3.3 0.9 - - - -
401A LYS* 3.4 17.7 - - - +
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Residues in contact with PHE 291 (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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287A ALA* 3.7 22.2 - - + -
288A CYS* 3.0 8.2 + - - +
290A ASN* 1.3 86.3 - - + +
292A GLY* 1.3 63.9 + - - +
293A ILE* 3.2 14.3 + - + +
381A GLU 5.4 0.7 - - - -
384A ALA* 4.4 4.3 - - + -
385A GLN* 3.7 39.0 - - + -
388A ALA* 3.6 24.0 - - + -
398A VAL* 3.7 14.9 - - + +
401A LYS* 3.4 34.0 - - + +
402A LEU* 3.1 35.0 - - + -
405A SER* 4.9 11.4 - - - -
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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