Contacts of the helix formed by residues 51 - 56 (chain A) in PDB entry 2JBG
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 51 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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38A LEU* 4.0 33.4 - - + +
41A PHE* 4.5 6.7 - - + -
42A VAL* 3.7 21.4 - - + +
49A ASP 3.2 2.0 + - - -
50A GLY* 1.3 68.8 - - - -
52A ASP* 1.3 67.6 + - - +
53A LEU 3.0 0.4 - - - -
54A ILE* 2.8 17.7 + - - +
55A TYR* 3.1 26.5 + - - -
528B LYS* 5.9 3.0 - - - +
529B THR 4.9 4.9 + - - -
531B THR* 3.5 16.8 + - - -
534B VAL* 6.0 1.4 - - - +
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Residues in contact with ASP 52 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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49A ASP* 3.0 35.4 + - + +
51A THR* 1.3 77.9 + - - +
53A LEU* 1.3 57.4 + - - +
55A TYR 4.4 0.2 - - - +
56A TYR* 2.6 56.8 + - + +
529B THR 4.3 1.4 - - - +
530B ARG* 3.4 23.6 + - - +
531B THR* 2.8 34.2 + - - -
532B GLN* 4.7 5.5 - - - +
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Residues in contact with LEU 53 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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41A PHE* 4.1 22.2 - - + -
45A THR* 4.9 0.9 - - - +
47A HIS* 3.7 46.4 - - + +
49A ASP* 4.9 3.4 - - + -
50A GLY 3.6 14.4 - - - +
51A THR 3.0 1.0 + - - -
52A ASP* 1.3 77.0 - - - +
54A ILE* 1.3 58.6 + - - +
56A TYR 5.0 1.1 - - - -
57A PRO* 4.2 3.5 - - - +
61A ARG* 3.2 24.7 + - - +
68A ILE* 3.5 16.7 - - + +
71A GLU* 3.4 41.3 - - + +
72A ILE* 4.1 16.6 - - + -
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Residues in contact with ILE 54 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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19A LEU* 4.2 9.9 - - + -
22A ILE* 4.2 10.3 - - + -
38A LEU* 4.0 24.0 - - + -
41A PHE* 4.0 39.7 - - + -
51A THR* 2.8 9.9 + - - +
53A LEU* 1.3 82.0 - - - +
55A TYR* 1.3 78.7 + - + +
56A TYR 3.6 0.8 + - - -
57A PRO* 3.9 8.0 - - - +
63A ASP* 4.4 5.7 - - - +
68A ILE* 3.9 21.6 - - + +
514B SER* 4.1 1.7 + - - -
516B ASN* 3.6 40.5 - - - +
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Residues in contact with TYR 55 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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22A ILE* 4.4 2.1 - - - +
26A ASN* 2.6 42.4 + - - -
34A LEU* 3.7 16.6 - - - +
38A LEU* 3.8 24.5 - - + +
51A THR* 3.1 24.8 + - - +
54A ILE* 1.3 90.2 - - + +
56A TYR* 1.3 79.0 + - + +
57A PRO* 3.5 1.6 - - - -
514B SER* 2.7 24.7 + - - -
516B ASN* 3.7 15.0 - - + -
517B ASN* 3.5 30.9 + - - +
520B ARG* 3.8 4.7 - - - -
528B LYS* 3.7 28.7 - - + -
529B THR 5.3 0.7 - - - +
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Residues in contact with TYR 56 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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52A ASP* 2.6 34.9 + - + +
53A LEU* 5.0 0.2 - - - -
55A TYR* 1.3 86.6 - - + +
57A PRO* 1.3 68.3 - - - +
58A SER* 3.6 1.7 + - - -
512B GLN 6.0 1.8 - - - -
513B PHE* 5.1 8.9 - + - -
514B SER* 5.0 0.4 - - - -
517B ASN* 3.8 10.2 + - - -
528B LYS 2.8 29.8 + - - -
529B THR* 3.4 17.1 - - - -
530B ARG* 3.5 61.2 + - + +
541B PHE* 3.4 21.5 - + - -
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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