Contacts of the helix formed by residues 256 - 260 (chain D) in PDB entry 1EJI
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 HIS 256 (chain D).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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70C ASN 5.8 1.8 - - - +
73C TYR* 3.3 40.5 + + - -
53D SER 4.8 0.7 - - - -
119D SER* 4.1 1.1 - - - -
233D SER* 4.0 2.8 + - - -
254D THR* 3.4 27.8 + - + -
255D THR* 1.3 85.8 + - - +
257D LYS* 1.3 87.5 + - + +
259D LEU* 3.4 8.3 + - - +
260D ARG* 4.9 0.2 - - - +
261D GLY 3.8 21.3 - - - +
262D CYS 4.3 3.8 - - - +
263D ARG* 3.5 44.9 + - + +
264D ALA 3.9 8.5 - - - -
503D PLG 3.6 12.5 + - - -
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Residues in contact with LYS 257 (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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73C TYR* 3.4 13.2 - - - -
52D ALA 5.3 1.3 - - - +
53D SER* 3.1 39.0 + - - +
54D GLU 4.8 1.5 - - - -
55D ASN* 3.6 20.0 + - - +
230D ALA* 3.8 17.5 - - - +
231D HIS* 4.0 9.8 + - + +
254D THR* 3.5 16.4 - - - +
256D HIS* 1.3 87.5 - - + +
258D THR* 1.3 56.0 + - + +
259D LEU 2.6 15.2 + - - -
260D ARG* 2.8 14.7 + - - -
406D PRO* 5.5 0.2 - - - -
503D PLG 1.5 91.9 + - - -
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Residues in contact with THR 258 (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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52D ALA 5.3 1.9 + - - +
55D ASN* 4.3 9.9 - - - +
231D HIS* 3.1 28.6 + - - +
232D ILE 3.5 1.2 - - - -
233D SER* 3.3 6.4 + - - -
234D GLY* 2.8 40.1 + - - -
235D LEU* 4.3 9.6 - - + -
257D LYS* 1.3 74.8 - - + +
259D LEU* 1.3 56.2 + - - +
260D ARG 3.4 0.7 - - - -
324D PHE* 3.9 2.6 - - - -
327D TYR* 4.8 2.3 - - - -
328D GLN* 3.4 21.2 + - - +
357D HIS* 3.9 13.5 - - + +
406D PRO* 3.8 26.6 - - + +
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Residues in contact with LEU 259 (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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104D TYR* 3.6 23.3 - - + +
233D SER* 3.4 18.8 + - - +
234D GLY* 3.9 17.9 - - - -
237D ALA* 4.7 2.5 - - + -
254D THR 4.3 0.4 - - - +
255D THR* 3.3 31.0 - - + +
256D HIS 3.4 2.4 + - - +
257D LYS 2.6 7.7 + - - -
258D THR* 1.3 75.1 + - - +
260D ARG* 1.3 66.7 + - - +
261D GLY* 3.2 1.8 + - - -
266D MSE 4.2 17.5 - - + -
315D ALA* 4.3 13.6 - - + +
316D LEU* 4.9 9.4 - - + -
319D ALA* 4.1 25.6 - - + -
324D PHE* 4.2 9.3 - - + -
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Residues in contact with ARG 260 (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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18C HIS* 3.0 35.5 + - - -
21C MSE 3.6 17.4 - - - +
22C LEU* 3.6 20.0 - - - +
55D ASN* 3.2 31.4 - - - +
56D PHE 3.0 26.7 - - - +
57D ALA* 4.0 12.8 - - - +
58D SER* 4.3 4.7 + - - +
61D VAL* 4.5 3.3 - - - +
255D THR 4.0 0.2 + - - -
256D HIS* 4.9 1.1 - - - +
257D LYS 2.8 11.3 + - - -
258D THR 3.4 1.3 - - - +
259D LEU* 1.3 80.7 - - - +
261D GLY* 1.3 60.1 + - - +
315D ALA* 4.2 5.4 - - - +
318D GLN* 4.8 7.6 + - - +
324D PHE* 3.6 27.1 - - + -
327D TYR* 3.5 16.9 - - + -
410D SER* 3.1 19.6 + - - -
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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