Contacts of the helix formed by residues 26 - 36 (chain B) in PDB entry 1JBR
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 GLN 26 (chain B).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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1B ALA* 2.7 31.6 + - + +
3B TRP* 3.1 27.3 + - - +
24B TYR 3.8 0.6 + - - -
25B SER* 1.3 68.7 - - - +
27B ALA* 1.3 67.6 + - - +
29B ALA* 3.7 5.8 - - - +
30B GLU* 2.9 47.7 + - - +
130B PHE* 3.3 32.6 - - + -
133B ILE* 4.8 0.7 - - - -
149B HIS* 4.9 4.9 + - - -
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Residues in contact with ALA 27 (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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1B ALA* 5.5 5.1 - - + +
25B SER* 3.2 8.5 + - - +
26B GLN* 1.3 80.3 - - - +
28B LYS* 1.3 65.3 + - + +
30B GLU* 3.4 9.8 + - - +
31B SER* 3.1 21.2 + - - -
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Residues in contact with LYS 28 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
25B SER* 3.0 27.0 + - - +
27B ALA* 1.3 75.9 - - + +
29B ALA* 1.3 66.0 + - - +
31B SER* 2.9 10.3 + - - -
32B ASN* 2.8 27.6 + - - +
100B PRO 5.0 4.2 + - - +
101B ASP* 4.0 13.4 + - - +
102B GLY* 3.8 32.8 - - - +
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Residues in contact with ALA 29 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
24B TYR* 5.6 0.2 - - + -
25B SER 2.8 20.7 + - - +
26B GLN* 3.7 4.5 - - - +
28B LYS* 1.3 74.3 - - - +
30B GLU* 1.3 64.2 + - - +
32B ASN* 3.2 11.8 + - - +
33B SER 3.2 9.4 + - - -
98B THR* 3.6 21.5 - - - +
121B VAL* 3.7 19.4 - - + +
130B PHE* 4.6 2.5 - - + -
133B ILE* 3.5 31.4 - - + -
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Residues in contact with GLU 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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26B GLN* 2.9 37.4 + - - +
27B ALA* 3.7 8.6 - - - +
29B ALA* 1.3 76.2 - - - +
31B SER* 1.3 61.2 + - - +
33B SER* 2.6 25.6 + - - +
34B HIS* 3.1 27.4 + - + +
121B VAL* 4.8 1.3 - - - -
130B PHE* 3.0 47.6 - - + +
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Residues in contact with SER 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 ALA 3.1 13.5 + - - -
28B LYS* 2.9 14.3 + - - -
30B GLU* 1.3 74.0 - - - +
32B ASN* 1.3 68.9 + - - +
34B HIS* 2.9 20.2 + - - +
35B HIS* 2.8 44.3 + - - -
104B ASP* 4.3 2.3 + - - -
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Residues in contact with ASN 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 LYS 2.8 17.5 + - - +
29B ALA* 3.2 7.8 + - - +
31B SER* 1.3 77.8 - - - +
33B SER* 1.3 56.7 + - - +
35B HIS* 3.3 3.5 + - - +
36B ALA* 3.0 27.0 + - - +
96B PHE* 4.0 21.4 - - + -
97B PRO 4.7 5.2 - - - +
98B THR* 3.0 26.1 + - - +
99B PHE 4.6 0.2 + - - -
102B GLY* 2.7 31.3 + - - +
103B HIS 3.1 13.4 + - - +
104B ASP* 2.9 23.0 + - - +
121B VAL* 4.7 2.0 - - + -
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Residues in contact with SER 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 ALA 3.2 6.8 + - - -
30B GLU* 2.6 26.0 + - - +
32B ASN* 1.3 76.5 - - - +
34B HIS* 1.3 69.3 + - - +
36B ALA* 3.5 16.7 + - - +
96B PHE* 4.8 1.8 - - - -
121B VAL* 4.3 6.0 - - - +
123B TYR* 3.6 45.3 - - - +
128B LYS* 3.2 23.1 + - - +
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Residues in contact with HIS 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 GLU* 3.1 36.0 + - + +
31B SER* 2.9 12.1 + - - +
33B SER* 1.3 82.6 + - - +
35B HIS* 1.3 68.5 + + + +
36B ALA 3.0 1.7 - - - +
128B LYS* 3.0 44.8 + - + +
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Residues in contact with HIS 35 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
31B SER* 2.8 45.9 + - - -
32B ASN 3.8 1.6 - - - +
34B HIS* 1.3 79.9 - + + +
36B ALA* 1.3 59.0 + - - +
37B PRO* 3.9 3.3 - - - +
104B ASP* 3.4 37.7 + - + +
107B PHE* 4.2 9.9 - - - -
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Residues in contact with ALA 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 ASN 3.0 15.9 + - - +
33B SER* 3.6 9.6 - - - +
34B HIS 3.0 2.9 - - - +
35B HIS* 1.3 79.0 - - - +
37B PRO* 1.3 68.7 - - + +
48B PRO* 4.5 1.6 - - + -
96B PHE* 3.8 25.8 - - + -
107B PHE* 4.6 1.3 - - - -
123B TYR* 3.7 18.2 - - - +
128B LYS* 2.9 26.0 + - - -
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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