Contacts of the helix formed by residues 283 - 293 (chain D) in PDB entry 3JXI
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 GLN 283 (chain D).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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232D ILE* 2.8 32.9 + - - +
233D GLU 4.7 0.8 + - - -
235D ARG* 3.3 46.7 + - - +
278D ALA 2.9 14.0 + - - +
281D THR* 2.9 34.6 + - - +
282D ASN* 1.3 70.7 - - - +
284D PRO* 1.3 61.6 - - - +
285D HIS* 3.2 3.1 - - - -
286D ILE* 3.1 29.1 + - + +
287D VAL* 3.0 27.9 + - - +
331D MET* 3.5 3.5 - - - +
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Residues in contact with PRO 284 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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282D ASN* 3.2 22.0 - - - +
283D GLN* 1.3 89.1 - - - +
285D HIS* 1.3 71.3 + - + +
286D ILE 3.3 0.2 - - - -
287D VAL* 3.5 7.2 + - + +
288D HIS* 2.9 39.8 + - + +
330D LYS* 6.4 3.4 - - - -
331D MET* 3.8 16.4 - - + -
334D LEU* 5.3 5.8 - - + -
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Residues in contact with HIS 285 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
237D LYS* 3.5 38.1 + - + +
283D GLN 3.2 1.0 - - - -
284D PRO* 1.3 88.7 - - + +
286D ILE* 1.3 60.1 + - + +
288D HIS* 3.4 14.1 + + - +
289D TYR* 2.9 28.2 + - - +
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Residues in contact with ILE 286 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
232D ILE* 4.3 15.5 - - + -
236D CYS 4.6 1.6 - - - +
237D LYS* 4.2 30.1 - - + +
240D VAL* 3.7 32.5 - - + -
278D ALA* 3.6 20.0 - - + -
283D GLN* 3.1 38.8 + - + +
285D HIS* 1.3 73.6 - - + +
287D VAL* 1.3 60.0 + - - +
289D TYR* 3.9 5.6 - - + +
290D LEU* 3.0 43.6 + - + +
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Residues in contact with VAL 287 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
275D LEU* 4.2 13.8 - - + +
278D ALA* 3.9 6.1 - - + -
279D ALA* 3.6 40.8 - - + +
283D GLN 3.0 14.5 + - - +
284D PRO* 3.6 9.4 - - + +
285D HIS 3.4 0.2 - - - -
286D ILE* 1.3 77.1 - - - +
288D HIS* 1.3 59.4 + - - +
290D LEU* 3.6 1.6 + - - +
291D THR* 2.8 30.7 + - + +
331D MET* 4.0 5.4 - - - -
334D LEU* 3.4 30.7 - - + -
335D LEU* 4.0 18.4 - - + -
338D LYS* 6.2 1.6 - - - -
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Residues in contact with HIS 288 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
284D PRO* 2.9 26.9 + - + +
285D HIS* 3.6 16.2 - + - +
286D ILE 3.3 0.2 - - - -
287D VAL* 1.3 75.5 - - - +
289D TYR* 1.3 55.5 + - - +
291D THR* 3.3 1.8 + - - -
292D GLU* 2.6 74.5 + - - +
334D LEU* 3.3 41.1 - - + +
338D LYS* 4.9 8.4 - - + -
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Residues in contact with TYR 289 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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237D LYS* 5.0 7.2 - - + +
240D VAL* 5.0 7.4 - - + -
241D GLU* 3.6 50.3 + - + +
244D VAL* 3.5 31.6 - - + +
245D GLU* 3.5 31.2 + - - +
285D HIS 2.9 19.0 + - - +
286D ILE* 3.4 7.2 + - + +
288D HIS* 1.3 76.0 - - - +
290D LEU* 1.3 55.7 + - + +
292D GLU* 4.5 1.6 - - - +
293D ASN* 2.7 65.9 + - + +
295D HIS* 4.0 6.4 - + - -
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Residues in contact with LEU 290 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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228D LEU* 4.7 9.2 - - + -
232D ILE* 4.4 4.9 - - + -
240D VAL* 4.5 10.5 - - + -
244D VAL* 4.0 26.2 - - + -
250D VAL* 4.1 17.0 - - + +
274D PRO* 4.0 23.1 - - + +
275D LEU* 4.1 17.9 - - + +
278D ALA* 4.2 2.5 - - + -
286D ILE* 3.0 39.4 + - + +
287D VAL 4.1 3.4 - - - +
288D HIS 3.4 0.2 - - - -
289D TYR* 1.3 78.0 - - + +
291D THR* 1.3 54.9 + - - +
293D ASN* 3.5 4.6 + - - +
296D LYS 4.0 0.5 - - - +
297D GLN* 3.1 8.0 - - - -
298D ALA* 2.6 40.2 + - + -
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Residues in contact with THR 291 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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275D LEU* 4.2 16.8 - - + -
287D VAL* 2.8 20.8 + - + +
288D HIS* 3.3 4.7 + - - -
289D TYR 3.2 0.2 - - - -
290D LEU* 1.3 79.3 - - - +
292D GLU* 1.3 56.9 + - - +
293D ASN 3.7 1.3 - - - -
297D GLN* 3.3 28.0 - - - +
298D ALA* 3.4 21.3 - - + +
300D LEU* 3.4 22.4 - - + -
335D LEU* 5.7 1.1 - - + -
338D LYS* 3.2 29.6 + - - -
342D LEU* 5.0 6.9 - - - +
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Residues in contact with GLU 292 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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288D HIS* 2.6 62.9 + - - +
289D TYR* 3.9 1.8 - - - -
291D THR* 1.3 71.2 - - - +
293D ASN* 1.3 65.5 + - - +
294D GLY 3.9 0.3 + - - -
297D GLN* 4.7 2.0 - - - +
338D LYS* 3.0 29.0 + - - +
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Residues in contact with ASN 293 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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244D VAL* 3.9 5.5 - - - +
289D TYR* 2.7 64.1 + - + +
290D LEU* 3.5 13.3 + - - +
292D GLU* 1.3 79.1 - - - +
294D GLY* 1.3 54.8 + - - +
295D HIS* 3.0 12.6 + - + +
296D LYS 2.6 50.4 + - - +
297D GLN* 2.7 38.2 + - - +
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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