Contacts of the helix formed by residues 256 - 260 (chain C) 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 C).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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53C SER 4.8 0.9 - - - -
119C SER* 4.3 0.4 - - - -
233C SER* 4.1 1.4 + - - -
254C THR* 3.3 29.0 + - + +
255C THR* 1.3 86.2 + - - +
257C LYS* 1.3 92.6 + - + +
259C LEU* 3.4 8.9 + - - +
260C ARG* 4.2 0.7 - - - +
261C GLY 3.8 21.1 - - - +
262C CYS 4.3 4.0 - - - +
263C ARG* 3.6 39.7 + - + +
264C ALA 3.9 9.9 - - - -
502C PLG 3.5 14.5 + - - -
70D ASN* 5.9 1.8 - - - +
73D TYR* 3.3 34.1 + + - -
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Residues in contact with LYS 257 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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52C ALA 5.3 1.8 - - - +
53C SER* 3.3 39.1 + - - +
54C GLU 4.7 2.2 - - - -
55C ASN* 3.1 28.0 + - - +
230C ALA 3.9 15.7 - - - +
231C HIS* 4.1 8.4 - - + +
254C THR* 3.6 14.8 - - - +
256C HIS* 1.3 88.6 - - + +
258C THR* 1.3 62.5 + - + +
259C LEU 2.8 11.0 + - - -
260C ARG 3.1 8.9 + - - +
406C PRO* 5.3 1.3 - - - -
502C PLG 1.5 92.9 + - - -
73D TYR* 3.4 13.5 - - - -
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Residues in contact with THR 258 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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52C ALA 5.3 1.1 - - - +
55C ASN* 4.6 6.1 - - - +
231C HIS* 2.8 32.3 + - + +
232C ILE* 3.4 0.2 - - - -
233C SER* 3.1 10.0 + - - -
234C GLY* 2.6 44.9 + - - -
235C LEU* 4.3 14.4 - - + -
256C HIS 3.4 0.4 + - - -
257C LYS* 1.3 78.8 - - + +
259C LEU* 1.3 52.5 + - - +
260C ARG* 3.6 0.9 - - - -
324C PHE* 4.2 0.9 - - - -
327C TYR* 5.9 1.3 - - - -
328C GLN* 3.7 15.7 - - - +
357C HIS* 3.8 25.1 - - + +
406C PRO* 3.9 13.5 - - + -
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Residues in contact with LEU 259 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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104C TYR* 3.6 22.4 - - + +
233C SER* 3.5 18.2 - - - +
234C GLY* 3.8 18.6 - - - +
237C ALA* 4.6 2.9 - - + -
254C THR 4.4 0.2 - - - +
255C THR* 3.3 29.8 - - + +
256C HIS 3.4 2.2 + - - +
257C LYS 2.8 1.6 + - - -
258C THR* 1.3 77.5 + - - +
260C ARG* 1.3 70.6 + - - +
261C GLY* 3.2 1.8 + - - -
266C MSE 4.3 17.3 - - + -
315C ALA* 4.3 13.5 - - + +
316C LEU* 4.8 10.3 - - + -
319C ALA* 4.1 25.1 - - + -
324C PHE* 4.2 11.1 - - + -
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Residues in contact with ARG 260 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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55C ASN* 3.2 31.9 - - - +
56C PHE 3.0 26.7 - - - +
57C ALA* 4.0 13.2 - - - +
58C SER* 4.3 4.3 + - - +
61C VAL* 4.5 3.3 - - - +
255C THR 4.0 0.8 + - - -
256C HIS* 4.2 1.5 - - - +
257C LYS 3.1 10.4 + - - -
258C THR 5.3 0.4 - - - -
259C LEU* 1.3 80.0 - - - +
261C GLY* 1.3 61.3 + - - +
315C ALA* 4.2 5.4 - - - +
318C GLN* 4.8 8.5 + - - +
324C PHE* 3.5 28.6 - - + -
327C TYR* 3.4 18.6 - - + -
410C SER* 3.1 20.3 + - - -
18D HIS* 2.9 28.5 + - - -
21D MSE 3.6 24.4 - - - +
22D LEU* 3.8 17.9 - - - +
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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