Contacts of the helix formed by residues 27 - 39 (chain B) in PDB entry 5BNG
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 SER 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 PRO* 1.3 73.5 - - - +
28B GLU* 1.3 55.1 + - - +
29B GLU* 3.6 10.3 + - - +
30B GLN* 3.0 30.7 + - - +
31B LYS* 2.8 38.6 + - - +
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Residues in contact with GLU 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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27B SER* 1.3 74.2 - - - +
29B GLU* 1.3 60.6 + - - +
31B LYS* 3.7 32.5 + - - +
32B LYS* 3.3 34.7 + - - +
42B ILE* 5.1 7.8 - - - +
28L A 3.4 25.3 + - - +
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Residues in contact with GLU 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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27B SER* 3.0 11.5 + - - +
28B GLU* 1.3 79.7 - - - +
30B GLN* 1.3 60.3 + - + +
32B LYS* 3.2 34.4 + - - +
33B GLN* 3.2 31.4 + - - +
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Residues in contact with GLN 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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16B TRP* 3.1 42.5 - - + +
20B HIS* 4.8 6.1 + - - -
26B PRO* 3.2 8.9 - - + +
27B SER* 3.0 33.1 + - - +
29B GLU* 1.3 79.7 - - + +
31B LYS* 1.3 59.3 + - - +
33B GLN* 3.7 14.2 - - - +
34B LEU* 2.8 37.5 + - + +
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Residues in contact with LYS 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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26B PRO* 3.7 35.2 + - + -
27B SER 2.8 17.5 + - - +
28B GLU* 3.7 36.5 + - - +
30B GLN* 1.3 78.5 - - - +
32B LYS* 1.3 56.1 + - - +
34B LEU* 3.5 5.3 + - - +
35B ALA* 3.1 24.8 + - - +
42B ILE* 4.5 10.8 - - + +
45B VAL* 3.8 20.8 - - + +
46B ASN* 3.5 28.6 + - - +
53B ARG* 6.1 0.9 - - - +
28L A 4.2 7.5 + - - -
29L G 2.7 29.9 + - - -
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Residues in contact with LYS 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 GLU* 3.3 20.9 + - - +
29B GLU* 3.2 28.5 + - - +
31B LYS* 1.3 77.2 - - - +
33B GLN* 1.3 65.0 + - + +
35B ALA* 3.1 2.6 + - - +
36B GLN* 2.9 35.9 + - + +
42B ILE* 4.0 20.6 - - + +
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Residues in contact with GLN 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 GLU* 3.2 32.3 + - - +
30B GLN* 3.7 14.7 - - - +
32B LYS* 1.3 83.4 - - + +
34B LEU* 1.3 57.5 + - + +
36B GLN* 4.0 6.1 - - + +
37B ASP* 2.9 45.9 + - - +
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Residues in contact with LEU 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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12B ILE* 4.0 33.9 - - + +
13B MET* 4.2 14.6 - - - -
16B TRP* 4.5 23.8 - - + -
26B PRO* 5.0 4.0 - - + -
30B GLN* 2.8 23.1 + - + +
31B LYS* 3.7 5.8 - - - +
33B GLN* 1.3 75.9 - - - +
35B ALA* 1.3 53.7 + - - +
37B ASP* 3.2 5.3 + - - +
38B THR* 2.6 42.8 + - - +
45B VAL* 4.4 6.1 - - + -
49B PHE* 3.4 38.6 - - + -
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Residues in contact with ALA 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 LYS 3.1 14.6 + - - +
32B LYS 3.1 8.7 + - - +
34B LEU* 1.3 78.3 - - - +
36B GLN* 1.3 54.6 + - + +
38B THR* 3.4 5.6 - - - -
39B GLY* 2.5 37.4 + - - -
40B LEU 3.2 20.8 + - - +
41B THR 4.5 0.2 - - - -
42B ILE* 4.0 18.8 - - + -
45B VAL* 3.9 14.1 - - + +
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Residues in contact with GLN 36 (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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32B LYS* 2.9 20.6 + - + +
33B GLN* 4.0 7.4 - - + +
35B ALA* 1.3 73.3 - - + +
37B ASP* 1.3 64.0 + - - +
38B THR 3.1 5.8 + - - -
39B GLY* 3.8 6.5 + - - +
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Residues in contact with ASP 37 (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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12B ILE* 4.1 28.0 - - + +
33B GLN* 2.9 34.7 + - - +
34B LEU* 3.2 7.9 + - - +
36B GLN* 1.3 78.8 - - - +
38B THR* 1.3 62.3 + - - +
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Residues in contact with THR 38 (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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6B PRO* 5.5 2.9 - - - +
8B VAL* 5.8 3.7 - - - +
9B ALA* 4.0 27.0 - - - +
12B ILE* 3.9 24.9 - - + -
13B MET* 4.3 10.5 - - + -
34B LEU 2.6 22.3 + - - +
35B ALA* 3.3 8.8 + - - -
37B ASP* 1.3 85.6 - - - +
39B GLY* 1.3 58.0 + - - +
40B LEU* 3.1 33.9 + - - +
45B VAL* 4.6 1.9 - - - +
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Residues in contact with GLY 39 (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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35B ALA 2.5 18.4 + - - -
36B GLN* 3.8 8.1 + - - -
38B THR* 1.3 72.9 - - - +
40B LEU* 1.3 65.3 + - - +
41B THR* 5.4 1.2 - - - +
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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