Contacts of the helix formed by residues 51 - 56 (chain C) 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 C).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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38C LEU* 4.1 34.5 - - + +
41C PHE* 4.6 7.2 - - + -
42C VAL* 3.7 20.5 - - + +
49C ASP 3.1 1.2 + - - -
50C GLY* 1.3 69.2 - - - -
52C ASP* 1.3 61.2 + - - +
53C LEU 3.1 0.2 - - - -
54C ILE* 2.8 22.4 + - - +
55C TYR* 3.0 27.9 + - - -
528D LYS* 6.0 2.8 - - + +
529D THR 4.9 4.9 + - - -
531D THR* 3.4 18.2 + - - +
534D VAL* 6.0 1.0 - - - +
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Residues in contact with ASP 52 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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49C ASP* 2.9 35.3 + - + +
51C THR* 1.3 79.4 + - - +
53C LEU* 1.3 58.5 + - - +
55C TYR 4.4 0.2 - - - +
56C TYR* 2.7 53.3 + - + +
529D THR 4.3 0.7 - - - +
530D ARG* 3.4 28.7 + - - +
531D THR* 2.9 34.3 + - - -
532D GLN* 5.1 1.9 + - - +
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Residues in contact with LEU 53 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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41C PHE* 4.1 18.4 - - + -
45C THR* 4.8 0.7 - - - +
47C HIS* 3.6 47.6 - - + +
49C ASP* 4.9 3.8 - - + +
50C GLY 3.6 13.7 - - - +
51C THR 3.1 0.2 - - - -
52C ASP* 1.3 78.7 - - - +
54C ILE* 1.3 62.1 + - - +
56C TYR 4.9 0.9 - - - -
57C PRO* 4.0 2.8 - - - +
61C ARG* 2.7 28.0 + - - +
68C ILE* 3.8 12.4 - - + +
71C GLU* 3.5 39.3 - - + +
72C ILE* 3.8 23.8 - - + -
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Residues in contact with ILE 54 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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19C LEU* 4.5 4.9 - - + -
22C ILE* 4.2 13.0 - - + -
38C LEU* 3.8 20.9 - - + -
41C PHE* 3.7 46.7 - - + -
51C THR* 2.8 10.6 + - - +
53C LEU* 1.3 81.3 - - - +
55C TYR* 1.3 78.6 + - + +
56C TYR 3.5 0.6 + - - -
57C PRO* 3.8 8.0 - - - +
63C ASP* 4.4 5.4 - - - +
68C ILE* 4.1 19.9 - - + +
514D SER* 4.1 1.2 + - - -
516D ASN* 3.7 40.8 - - - +
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Residues in contact with TYR 55 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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22C ILE* 4.3 2.4 - - - +
26C ASN* 2.7 45.3 + - - -
34C LEU* 3.7 5.9 - - - +
38C LEU* 3.6 34.6 - - + +
51C THR* 3.0 25.3 + - - +
54C ILE* 1.3 87.3 - - + +
56C TYR* 1.3 83.2 + - + +
57C PRO* 3.6 0.7 - - - -
514D SER* 2.8 24.2 + - - -
516D ASN* 3.7 15.5 - - + -
517D ASN* 3.6 29.6 + - - +
520D ARG* 3.8 4.0 - - - -
528D LYS* 3.7 28.3 - - + -
529D THR 5.3 0.4 - - - +
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Residues in contact with TYR 56 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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52C ASP* 2.7 38.0 + - + +
53C LEU* 4.9 0.2 - - - -
55C TYR* 1.3 96.3 - - + +
57C PRO* 1.3 68.9 - - - +
58C SER* 3.6 1.7 + - - -
512D GLN 6.2 0.4 - - - -
513D PHE* 5.4 6.2 - + - -
514D SER* 4.9 0.2 - - - -
517D ASN* 3.7 10.6 + - - -
528D LYS 2.7 28.5 + - - -
529D THR* 3.5 17.4 - - - -
530D ARG* 3.7 57.0 + - + +
541D PHE* 3.5 20.4 - - - -
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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