Contacts of the helix formed by residues 27 - 35 (chain B) in PDB entry 2E9D
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 GLY 27 (chain B).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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26B ASP* 1.3 90.4 + - - +
28B ASN* 1.3 62.9 + - - +
29B GLY 3.5 1.3 - - - -
30B ARG* 4.1 12.1 - - - -
31B TRP* 3.1 26.9 + - - +
196B GLY* 4.7 1.6 - - - -
220B LEU* 3.6 20.0 - - - +
222B PRO* 3.6 7.0 - - - +
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Residues in contact with ASN 28 (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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25B MET* 6.0 1.5 - - - +
26B ASP* 5.5 1.6 - - - -
27B GLY* 1.3 73.9 - - - +
29B GLY* 1.3 66.2 + - - +
31B TRP* 3.2 4.2 - - - +
32B ALA* 3.1 17.0 + - - +
39B ARG 5.6 0.4 - - - -
42B GLY* 3.7 28.2 - - - +
43B HIS* 4.3 20.1 + - + +
46B GLY* 3.8 11.8 - - - -
221B TRP* 3.6 23.0 - - - +
222B PRO* 3.2 30.9 - - - +
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Residues in contact with GLY 29 (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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28B ASN* 1.3 77.7 - - - +
30B ARG* 1.3 65.9 + - - +
32B ALA* 3.0 17.5 + - - +
33B LYS* 3.0 14.6 + - - +
39B ARG* 5.0 18.3 - - - -
43B HIS* 5.6 2.1 - - - -
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Residues in contact with ARG 30 (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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27B GLY* 4.1 14.1 - - - +
29B GLY* 1.3 74.2 - - - +
31B TRP* 1.3 63.6 - - - +
33B LYS* 3.4 11.0 + - + +
34B LYS* 3.1 36.0 + - + +
196B GLY 4.6 10.0 + - - -
198B GLU* 5.5 5.5 + - - +
220B LEU* 3.6 31.8 - - + +
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Residues in contact with TRP 31 (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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27B GLY 3.1 19.5 + - - +
28B ASN 3.2 5.8 - - - +
30B ARG* 1.3 77.3 - - - +
32B ALA* 1.3 82.9 + - - +
34B LYS* 3.2 17.2 + - + +
35B GLN* 3.4 31.2 + - + +
41B PHE* 3.5 41.7 - + - -
42B GLY* 3.6 16.6 - - - -
45B ALA* 3.5 27.6 - - + -
220B LEU* 4.1 13.9 - - + +
222B PRO* 3.4 26.9 - - + +
223B ASP* 3.0 39.2 + - - -
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Residues in contact with ALA 32 (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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28B ASN 3.1 11.5 + - - +
29B GLY 3.0 9.9 + - - +
31B TRP* 1.3 84.4 - - - +
33B LYS* 1.3 55.4 + - - +
35B GLN* 2.5 33.8 + - - +
36B GLY 2.9 6.6 + - - -
37B LYS* 3.1 14.9 + - + +
38B ILE 3.3 29.4 - - - +
39B ARG* 4.3 4.3 - - - +
42B GLY* 4.0 11.0 - - - +
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Residues in contact with LYS 33 (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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29B GLY 3.0 8.4 + - - +
30B ARG* 3.5 13.5 - - + +
32B ALA* 1.3 77.5 - - - +
34B LYS* 1.3 57.1 + - + +
36B GLY* 2.5 28.3 + - - +
37B LYS 3.8 8.8 + - - -
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Residues in contact with LYS 34 (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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30B ARG* 3.1 23.2 + - + +
31B TRP* 3.3 13.2 - - + +
32B ALA 2.9 0.8 + - - -
33B LYS* 1.3 79.9 - - + +
35B GLN* 1.3 66.3 + - + +
36B GLY 3.1 0.4 + - - -
220B LEU* 3.8 30.3 - - + +
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Residues in contact with GLN 35 (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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31B TRP* 3.4 52.2 + - + +
32B ALA 2.5 11.5 + - - +
34B LYS* 1.3 80.2 + - - +
36B GLY* 1.3 60.2 + - - +
37B LYS* 3.6 30.5 + - + +
41B PHE* 4.5 5.6 - - + -
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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