Contacts of the helix formed by residues 52 - 61 (chain S) 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 S).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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43R LEU* 5.4 6.3 - - - -
45R THR 3.9 17.5 - - - -
46R THR* 3.8 11.4 + - - -
48R ILE* 3.2 26.1 + - - -
67R PHE* 6.0 6.1 - - - -
68R CYS 5.0 5.3 - - - +
51S THR* 1.3 72.6 - - - +
53S MET* 1.3 56.4 + - - +
55S VAL* 3.5 10.6 - - - +
56S LYS* 2.9 27.7 + - - +
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Residues in contact with MET 53 (chain S).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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46R THR* 3.0 35.3 + - - +
17S TYR* 4.7 7.3 - - + +
51S THR* 3.2 6.2 - - - -
52S THR* 1.3 73.7 - - - +
54S LEU* 1.3 59.5 + - - +
56S LYS* 3.2 5.6 + - - +
57S ARG* 2.9 27.9 + - - +
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Residues in contact with LEU 54 (chain S).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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15S LEU* 4.9 4.9 - - + +
16S SER* 4.4 7.4 - - - +
17S TYR* 3.8 32.3 - - + +
50S LEU* 5.7 2.9 - - + -
51S THR* 3.1 19.5 + - - +
53S MET* 1.3 79.5 - - - +
55S VAL* 1.3 57.4 + - - +
57S ARG* 3.8 3.3 - - - +
58S LEU* 2.9 28.2 + - - +
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Residues in contact with VAL 55 (chain S).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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67R PHE* 5.4 11.4 - - + -
50S LEU* 6.4 0.7 - - + -
51S THR 3.1 12.7 + - - +
52S THR* 3.5 13.2 - - - +
53S MET 3.2 0.2 - - - -
54S LEU* 1.3 74.1 - - - +
56S LYS* 1.3 59.8 + - - +
58S LEU* 3.3 7.1 + - - +
59S VAL* 2.9 27.7 + - - +
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Residues in contact with LYS 56 (chain S).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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46R THR* 5.5 3.4 - - - -
68R CYS 4.6 4.5 - - - +
69R ASP* 4.5 26.7 - - + -
70R ASP 5.6 0.4 - - - +
75R THR* 5.7 4.7 - - - -
52S THR 2.9 14.0 + - - +
53S MET* 3.2 9.8 + - - +
55S VAL* 1.3 76.6 - - - +
57S ARG* 1.3 56.9 + - - +
59S VAL* 3.2 7.4 + - - +
60S ASP* 2.9 29.6 + - - +
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Residues in contact with ARG 57 (chain S).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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17S TYR* 4.8 9.9 - - + -
53S MET 2.9 17.1 + - - +
54S LEU* 3.8 8.1 - - - +
55S VAL 3.3 0.2 - - - -
56S LYS* 1.3 75.2 - - - +
58S LEU* 1.3 58.4 + - - +
60S ASP* 3.5 6.3 + - - +
61S GLU* 2.9 29.3 + - - +
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Residues in contact with LEU 58 (chain S).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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54S LEU 2.9 18.1 + - - +
55S VAL* 3.6 8.1 - - - +
56S LYS 3.2 0.2 - - - -
57S ARG* 1.3 75.9 - - - +
59S VAL* 1.3 59.5 + - - +
61S GLU* 3.6 4.9 - - - -
62S ASN 3.0 21.0 + - - -
63S ILE* 3.0 34.0 + - + +
65S VAL* 5.6 7.6 - - + -
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Residues in contact with VAL 59 (chain S).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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75R THR* 4.4 22.2 - - - -
76R ALA* 4.6 15.9 - - + -
55S VAL 2.9 16.5 + - - +
56S LYS* 3.2 6.3 + - - +
58S LEU* 1.3 76.3 - - - +
60S ASP* 1.3 63.8 + - - +
62S ASN* 3.2 14.1 + - - +
63S ILE 5.5 0.7 - - - -
80S PRO* 4.9 16.2 - - + +
83S ALA* 6.2 0.2 - - - -
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Residues in contact with ASP 60 (chain S).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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56S LYS 2.9 16.3 + - - +
57S ARG* 3.9 7.0 - - - +
59S VAL* 1.3 77.3 - - - +
61S GLU* 1.3 60.7 + - - +
62S ASN* 3.2 2.8 + - - +
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Residues in contact with GLU 61 (chain S).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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35S LEU* 5.1 19.7 - - + +
57S ARG 2.9 18.6 + - - +
58S LEU* 3.4 7.2 + - - +
59S VAL 3.3 0.2 - - - -
60S ASP* 1.3 73.7 - - - +
62S ASN* 1.3 71.1 + - - +
63S ILE* 3.5 7.9 + - + +
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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