Contacts of the helix formed by residues 256 - 260 (chain B) 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 B).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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70A ASN* 6.0 2.0 - - - +
73A TYR* 3.4 29.5 + + - -
53B SER 4.8 0.7 - - - -
119B SER* 4.2 1.3 - - - -
233B SER* 4.1 1.4 + - - -
254B THR* 3.4 33.6 + - + +
255B THR* 1.3 86.4 + - - +
257B LYS* 1.3 88.9 + - + +
259B LEU* 3.4 7.6 + - - +
260B ARG* 4.1 0.4 - - - +
261B GLY 3.8 20.6 - - - +
262B CYS 4.3 4.5 - - - +
263B ARG* 3.5 50.1 + - + +
264B ALA 3.9 9.6 - - - -
501B PLG 3.7 10.5 + - - -
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Residues in contact with LYS 257 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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73A TYR* 3.9 7.9 - - - -
52B ALA 5.4 1.1 - - - +
53B SER* 3.1 45.8 + - - +
54B GLU 4.7 2.2 - - - -
55B ASN* 3.3 26.6 + - - +
230B ALA* 3.5 22.4 - - - +
231B HIS* 3.8 10.4 + - + +
254B THR* 3.2 20.5 + - - +
256B HIS* 1.3 83.3 - - + +
258B THR* 1.3 56.1 + - + +
259B LEU 2.6 17.5 + - - -
260B ARG* 2.8 14.6 + - - +
406B PRO* 5.3 0.4 - - - -
501B PLG 2.8 59.9 + - - -
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Residues in contact with THR 258 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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52B ALA 5.5 0.9 - - - +
55B ASN* 4.4 8.5 - - - +
231B HIS 3.1 28.3 + - - +
232B ILE 3.4 0.9 - - - -
233B SER* 3.2 7.6 + - - -
234B GLY* 2.8 38.9 + - - -
235B LEU* 4.1 10.3 - - + -
256B HIS 3.6 0.2 + - - -
257B LYS* 1.3 76.4 - - - +
259B LEU* 1.3 57.5 + - - +
260B ARG 3.5 0.4 - - - -
324B PHE* 3.9 2.4 - - - -
327B TYR* 4.8 1.6 - - - -
328B GLN* 3.3 23.0 + - - +
357B HIS* 3.8 15.3 - - + +
406B PRO* 3.8 25.3 - - + +
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Residues in contact with LEU 259 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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104B TYR* 3.6 22.9 - - + +
233B SER* 3.4 20.6 + - - +
234B GLY* 3.9 16.4 - - - -
237B ALA* 4.6 2.7 - - + -
254B THR 4.4 0.2 - - - +
255B THR* 3.3 30.3 - - - +
256B HIS 3.4 2.4 + - - +
257B LYS 2.6 7.7 + - - -
258B THR* 1.3 76.3 + - - +
260B ARG* 1.3 68.0 + - - +
261B GLY* 3.3 1.6 + - - -
266B MSE 4.3 16.6 - - + -
315B ALA* 4.3 14.5 - - + +
316B LEU* 4.9 10.5 - - + -
319B ALA* 4.0 25.4 - - + -
324B PHE* 4.1 9.0 - - + -
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Residues in contact with ARG 260 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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18A HIS* 2.9 27.9 + - - -
21A MSE 3.6 29.5 - - - +
22A LEU* 3.7 19.7 - - - +
55B ASN* 3.3 21.1 - - - +
56B PHE 3.0 26.2 - - - +
57B ALA* 4.0 12.5 - - - +
58B SER* 4.3 5.0 + - - +
61B VAL* 4.5 2.8 - - - +
255B THR 4.0 0.6 + - - -
256B HIS 4.8 1.3 - - - -
257B LYS 2.8 12.6 + - - +
258B THR 5.0 0.4 - - - -
259B LEU* 1.3 81.2 - - - +
261B GLY* 1.3 60.6 + - - +
315B ALA* 4.2 5.8 - - - +
318B GLN* 4.8 6.7 + - - +
324B PHE* 3.6 22.2 - - + -
327B TYR* 3.4 17.2 - - + -
410B SER* 3.1 29.0 + - - -
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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