Contacts of the helix formed by residues 14 - 22 (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 LEU 14 (chain C).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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10C ARG 5.3 2.2 - - - +
11C ASP* 3.4 18.2 - - + +
13C THR* 1.3 79.3 - - + +
15C TRP* 1.3 52.7 + - - +
16C ALA 2.6 6.4 + - - -
17C SER* 2.5 37.1 + - - +
18C HIS* 2.9 12.3 + - - +
322D THR* 3.2 42.2 - - + +
323D GLU* 4.6 9.2 - - + -
326D ILE* 4.2 21.5 - - + -
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Residues in contact with TRP 15 (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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7C MET* 4.2 24.4 - - - +
12C ALA* 3.4 19.2 + - + +
13C THR 2.8 4.4 + - - -
14C LEU* 1.3 73.4 - - - +
16C ALA* 1.3 55.6 + - - +
18C HIS* 3.7 34.8 - + + -
19C GLU* 3.1 30.8 + - + +
326D ILE* 3.5 33.2 - - + +
327D TYR* 4.7 9.9 - + - -
330D GLN* 3.8 30.4 + - + +
409D THR* 3.6 28.9 - - + -
410D SER 5.3 0.7 - - - -
412D GLY* 4.3 19.5 - - - -
414D LEU* 4.5 9.0 - - + +
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Residues in contact with ALA 16 (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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12C ALA 4.3 0.8 + - - +
13C THR* 2.7 14.3 + - + +
14C LEU 2.6 4.6 + - - -
15C TRP* 1.3 75.6 - - - +
17C SER* 1.3 61.6 + - - +
19C GLU* 2.9 24.1 - - - +
20C LYS* 3.1 10.2 + - - +
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Residues in contact with SER 17 (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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14C LEU* 2.5 21.7 + - - +
16C ALA* 1.3 68.7 - - - +
18C HIS* 1.3 55.8 + - - -
19C GLU 2.8 4.0 - - - -
20C LYS* 2.7 28.7 + - - +
21C MSE 2.8 14.6 + - - +
323D GLU* 3.2 28.5 + - - -
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Residues in contact with HIS 18 (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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14C LEU 2.9 8.0 + - - +
15C TRP* 3.7 37.3 - + + +
17C SER* 1.3 79.2 - - - +
19C GLU* 1.3 65.7 + - - +
21C MSE 3.7 12.4 + - + +
22C LEU* 3.4 37.0 + - + +
260D ARG* 3.0 38.5 + - - -
323D GLU* 3.2 41.3 - - + +
326D ILE* 5.2 2.0 - - + -
327D TYR* 3.4 20.0 - + + +
410D SER 4.4 8.1 - - - -
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Residues in contact with GLU 19 (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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15C TRP* 3.1 20.8 + - + +
16C ALA* 2.9 16.8 - - - +
17C SER 2.8 0.4 + - - -
18C HIS* 1.3 85.7 + - - +
20C LYS* 1.3 61.6 + - - +
22C LEU* 3.5 13.0 + - - +
23C SER* 3.6 10.0 + - - -
412D GLY* 6.1 0.5 - - - -
477D SER* 4.0 28.1 + - - -
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Residues in contact with LYS 20 (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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16C ALA 3.1 6.5 + - - +
17C SER* 2.7 13.9 + - - +
19C GLU* 1.3 74.3 - - - +
21C MSE 1.3 54.0 + - - +
22C LEU 3.0 2.7 - - - -
23C SER* 2.7 16.1 + - - +
24C GLN* 2.6 59.0 + - + +
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Residues in contact with MSE 21 (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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17C SER 2.8 18.4 + - - +
18C HIS* 3.7 21.1 - - + +
20C LYS* 1.3 73.5 - - - +
22C LEU* 1.3 64.5 + - + +
23C SER 3.5 0.7 + - - -
24C GLN* 3.9 27.9 + - - +
29C SER* 4.5 2.4 + - - +
58D SER* 4.1 1.4 - - - -
60D ALA* 4.7 0.2 - - - +
260D ARG* 3.6 27.4 - - - +
318D GLN* 3.9 45.2 + - + +
321D THR* 3.7 38.1 - - - +
323D GLU* 4.2 13.5 - - + +
324D PHE 4.6 2.0 - - - +
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Residues in contact with LEU 22 (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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18C HIS* 3.4 35.2 - - + +
19C GLU* 3.5 9.6 + - - +
20C LYS 2.9 1.4 + - - -
21C MSE 1.3 80.5 - - + +
23C SER* 1.3 59.0 + - - +
58D SER* 3.6 26.1 - - - +
59D ARG 3.1 20.3 + - - -
260D ARG* 3.6 37.2 - - - +
318D GLN* 4.0 6.7 - - - +
410D SER* 4.1 7.2 - - - +
479D PRO* 3.7 33.8 - - + +
480D GLY 3.7 12.1 + - - -
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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