Contacts of the helix formed by residues 13 - 22 (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 THR 13 (chain D).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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9D ASP* 3.0 29.1 + - + +
12D ALA* 1.3 76.7 - - - +
14D LEU* 1.3 73.3 + - + +
15D TRP 3.0 1.3 - - - -
16D ALA* 2.6 32.6 + - - +
17D SER* 3.1 19.2 + - - +
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Residues in contact with LEU 14 (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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322C THR* 3.3 36.6 - - + +
323C GLU* 3.4 37.4 - - + +
326C ILE* 3.2 27.7 - - + +
9D ASP* 3.3 14.6 + - + +
10D ARG* 3.9 5.2 - - + +
13D THR* 1.3 94.2 - - + +
15D TRP* 1.3 56.8 + - - +
17D SER* 3.9 4.0 - - - -
18D HIS* 3.0 30.7 + - - +
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Residues in contact with TRP 15 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
326C ILE* 3.7 28.1 - - + +
327C TYR* 4.8 9.0 - + - -
330C GLN* 3.6 33.9 + - + +
409C THR* 3.5 27.4 - - + -
410C SER 5.3 0.9 - - - -
412C GLY* 4.1 21.5 - - - -
414C LEU* 4.3 9.1 - - + +
10D ARG* 3.1 21.1 + - - +
11D ASP* 3.4 37.2 + - - +
13D THR 2.8 3.8 + - - -
14D LEU* 1.3 72.8 - - - +
16D ALA* 1.3 60.1 + - - +
18D HIS* 3.7 29.6 - + + -
19D GLU* 3.1 29.5 + - - +
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Residues in contact with ALA 16 (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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12D ALA 3.3 15.2 + - - +
13D THR* 2.6 18.0 + - - +
15D TRP* 1.3 71.8 - - - +
17D SER* 1.3 60.1 + - - +
19D GLU* 2.9 24.1 - - - +
20D LYS* 3.1 10.2 + - - +
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Residues in contact with SER 17 (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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323C GLU* 3.3 32.0 + - - -
13D THR* 3.1 20.5 + - - +
14D LEU* 3.9 4.0 - - - +
16D ALA* 1.3 71.7 - - - +
18D HIS* 1.3 65.3 + - - +
19D GLU 2.9 4.0 - - - -
20D LYS* 2.7 21.3 + - - +
21D MSE 2.8 14.6 + - - +
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Residues in contact with HIS 18 (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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260C ARG* 2.9 30.5 + - - -
323C GLU* 3.3 35.5 - - + +
326C ILE* 5.2 1.6 - - + -
327C TYR* 3.4 19.9 - + + +
410C SER 4.2 7.9 - - - -
14D LEU 3.0 17.2 + - - +
15D TRP* 3.7 32.8 - + + +
17D SER* 1.3 79.2 - - - +
19D GLU* 1.3 64.7 + - - +
21D MSE 3.7 19.4 - - + +
22D LEU* 3.4 38.5 + - + +
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Residues in contact with GLU 19 (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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411C ARG 6.1 0.2 - - - -
412C GLY* 6.1 0.9 - - - -
477C SER* 3.9 29.4 + - - -
15D TRP* 3.1 20.4 + - - +
16D ALA* 2.9 17.2 + - - +
17D SER 2.8 0.4 + - - -
18D HIS* 1.3 84.8 + - - +
20D LYS* 1.3 60.0 + - - +
22D LEU* 3.5 12.0 + - - +
23D SER* 3.5 12.6 + - - +
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Residues in contact with LYS 20 (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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16D ALA 3.1 6.7 + - - +
17D SER* 2.7 14.0 + - - +
19D GLU* 1.3 74.1 - - + +
21D MSE 1.3 54.0 + - - +
22D LEU 3.0 2.5 - - - -
23D SER* 2.7 15.6 + - - +
24D GLN* 2.7 59.9 + - + +
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Residues in contact with MSE 21 (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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58C SER* 4.1 2.1 - - - -
60C ALA* 4.8 0.2 - - - +
260C ARG* 3.6 28.0 - - - +
318C GLN* 4.0 46.1 + - + +
321C THR* 3.7 29.8 - - - +
323C GLU* 4.2 17.3 - - + +
324C PHE* 4.6 2.7 - - - +
17D SER 2.8 18.8 + - - +
18D HIS* 3.7 19.7 - - + +
20D LYS* 1.3 72.2 - - - +
22D LEU* 1.3 65.4 + - + +
23D SER 3.3 0.9 + - - -
24D GLN* 3.9 28.6 + - - +
29D SER* 4.5 2.0 + - - +
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Residues in contact with LEU 22 (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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58C SER* 3.7 24.1 - - - +
59C ARG 3.2 19.1 + - - -
260C ARG* 3.8 36.3 - - - +
318C GLN* 4.1 6.1 - - - +
410C SER* 4.0 8.3 - - - +
479C PRO* 3.5 35.1 - - + +
480C GLY 3.6 14.2 + - - -
18D HIS* 3.4 34.3 - - + +
19D GLU* 3.5 9.1 + - - +
20D LYS 2.9 1.4 + - - -
21D MSE 1.3 80.4 - - + +
23D SER* 1.3 60.0 + - - +
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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