Contacts of the helix formed by residues 52 - 62 (chain o) in PDB entry 6QXT
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 52 (chain o).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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51o THR* 1.3 70.0 - - - +
53o MET* 1.3 60.4 + - - +
55o VAL* 3.1 11.4 + - - +
56o LYS* 2.9 27.2 + - - +
43p LEU* 5.5 6.5 - - - -
45p THR 3.9 21.5 - - - -
46p THR* 4.0 7.1 + - - -
48p ILE* 3.4 23.9 + - - -
67p PHE* 5.7 8.5 - - - +
68p CYS 5.2 4.1 - - - +
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Residues in contact with MET 53 (chain o).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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17o TYR* 4.8 9.2 - - + +
51o THR* 3.2 6.6 - - - -
52o THR* 1.3 74.7 - - - +
54o LEU* 1.3 59.4 + - - +
56o LYS* 3.1 6.2 + - - +
57o ARG* 2.9 28.1 + - - +
46p THR* 3.1 34.9 + - - +
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Residues in contact with LEU 54 (chain o).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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15o LEU* 5.0 6.7 - - + +
16o SER* 4.5 14.8 - - - +
17o TYR* 4.0 22.2 - - + +
50o LEU* 5.9 1.6 - - + -
51o THR* 3.2 19.5 + - - +
53o MET* 1.3 78.2 - - - +
55o VAL* 1.3 57.2 + - - +
57o ARG* 3.5 5.0 + - - +
58o LEU* 2.9 28.1 + - - +
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Residues in contact with VAL 55 (chain o).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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51o THR 3.1 12.1 + - - +
52o THR* 3.3 15.7 - - - +
53o MET 3.1 0.4 - - - -
54o LEU* 1.3 76.8 - - - +
56o LYS* 1.3 56.3 + - - +
58o LEU* 3.3 8.5 + - - +
59o VAL* 2.9 25.6 + - - +
67p PHE* 5.3 12.1 - - + -
76p ALA* 5.9 0.9 - - - +
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Residues in contact with LYS 56 (chain o).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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52o THR 2.9 12.9 + - - +
53o MET* 3.5 9.9 - - - +
55o VAL* 1.3 73.9 - - - +
57o ARG* 1.3 59.6 + - - +
59o VAL* 3.0 9.7 + - - +
60o ASP* 2.9 27.2 + - - +
46p THR* 5.4 4.7 - - - -
68p CYS 4.7 13.0 - - - +
69p ASP* 5.0 10.5 - - + -
70p ASP 5.8 0.7 - - - +
75p THR* 5.3 7.6 - - - -
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Residues in contact with ARG 57 (chain o).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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17o TYR* 4.8 10.8 - - + -
53o MET 2.9 16.7 + - - +
54o LEU* 3.8 8.5 - - - +
56o LYS* 1.3 74.8 - - - +
58o LEU* 1.3 57.5 + - - +
60o ASP* 3.3 9.5 + - - +
61o GLU* 2.9 28.2 + - - +
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Residues in contact with LEU 58 (chain o).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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54o LEU 2.9 18.3 + - - +
55o VAL* 3.5 8.7 - - - +
56o LYS 3.2 0.2 - - - -
57o ARG* 1.3 73.6 - - - +
59o VAL* 1.3 59.6 - - - +
61o GLU* 4.2 7.2 - - - -
62o ASN* 2.8 24.9 + - - -
63o ILE* 3.3 26.1 + - + +
65o VAL* 5.8 7.4 - - + -
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Residues in contact with VAL 59 (chain o).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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55o VAL 2.9 13.4 + - - +
56o LYS* 3.0 12.3 + - - +
58o LEU* 1.3 76.6 - - - +
60o ASP* 1.3 61.9 + - - +
62o ASN* 3.4 11.0 + - - +
80o PRO* 5.1 13.8 - - + +
82o TYR 5.2 4.0 - - - +
83o ALA* 5.2 8.3 - - - +
75p THR* 4.6 17.9 - - - -
76p ALA* 4.8 13.5 - - + -
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Residues in contact with ASP 60 (chain o).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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56o LYS 2.9 11.5 + - - +
57o ARG* 3.7 10.5 - - - +
59o VAL* 1.3 77.2 - - - +
61o GLU* 1.3 59.7 + - - +
62o ASN* 3.6 1.0 + - - +
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Residues in contact with GLU 61 (chain o).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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35o LEU* 5.2 18.8 - - + +
57o ARG 2.9 17.6 + - - +
58o LEU* 3.3 7.8 + - - +
59o VAL 3.2 0.2 - - - -
60o ASP* 1.3 76.0 - - - +
62o ASN* 1.3 63.0 + - - +
63o ILE* 3.0 17.2 + - + +
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Residues in contact with ASN 62 (chain o).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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58o LEU 2.8 7.5 + - - -
59o VAL* 3.4 8.4 + - - +
60o ASP 3.3 4.9 - - - +
61o GLU* 1.3 77.5 - - - +
63o ILE* 1.3 65.8 + - - +
64o LEU* 3.4 1.9 + - - -
83o ALA* 4.2 20.9 - - + +
84o ARG 5.4 1.1 - - - +
85o HIS* 4.0 23.6 - - - +
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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