Contacts of the helix formed by residues 52 - 62 (chain y) 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 y).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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51y THR* 1.3 70.0 - - - +
53y MET* 1.3 60.8 + - - +
55y VAL* 3.2 11.3 + - - +
56y LYS* 2.9 27.4 + - - +
43z LEU* 5.5 7.0 - - - -
45z THR 3.9 21.3 - - - -
46z THR* 3.9 6.6 + - - -
48z ILE* 3.4 23.0 + - - -
67z PHE* 5.7 8.3 - - - +
68z CYS 5.2 5.1 - - - +
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Residues in contact with MET 53 (chain y).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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187G LEU* 4.1 20.6 - - + +
17y TYR* 4.8 8.7 - - + +
51y THR* 3.2 6.4 - - - -
52y THR* 1.3 74.7 - - - +
54y LEU* 1.3 59.6 + - - +
56y LYS* 3.1 5.8 + - - +
57y ARG* 2.9 27.7 + - - +
46z THR* 3.1 34.5 + - - +
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Residues in contact with LEU 54 (chain y).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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15y LEU* 4.9 6.7 - - + +
16y SER* 4.5 13.9 - - - +
17y TYR* 4.0 22.9 - - + +
50y LEU* 5.9 1.6 - - + -
51y THR* 3.2 19.7 + - - +
53y MET* 1.3 79.1 - - - +
55y VAL* 1.3 57.2 + - - +
57y ARG* 3.8 4.2 - - - +
58y LEU* 2.9 28.4 + - - +
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Residues in contact with VAL 55 (chain y).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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51y THR 3.1 12.7 + - - +
52y THR* 3.4 15.0 - - - +
53y MET 3.1 0.2 - - - -
54y LEU* 1.3 74.5 - - - +
56y LYS* 1.3 60.5 + - - +
58y LEU* 3.3 7.8 + - - +
59y VAL* 2.9 26.0 + - - +
67z PHE* 5.3 12.3 - - + -
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Residues in contact with LYS 56 (chain y).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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52y THR 2.9 13.2 + - - +
53y MET* 3.1 10.5 + - - +
55y VAL* 1.3 73.7 - - - +
57y ARG* 1.3 59.7 + - - +
59y VAL* 3.0 9.9 + - - +
60y ASP* 2.9 26.7 + - - +
46z THR* 5.3 4.3 - - - -
68z CYS 4.6 13.7 - - - +
69z ASP* 5.0 11.0 - - + -
70z ASP 5.7 0.7 - - - +
75z THR* 5.3 6.7 - - - -
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Residues in contact with ARG 57 (chain y).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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17y TYR* 4.8 11.2 - - + -
53y MET 2.9 16.0 + - - +
54y LEU* 3.8 8.7 - - - +
56y LYS* 1.3 75.4 - - - +
58y LEU* 1.3 56.9 - - - +
60y ASP* 3.3 8.3 + - - +
61y GLU* 2.8 28.9 + - - +
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Residues in contact with LEU 58 (chain y).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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54y LEU 2.9 18.0 + - - +
55y VAL* 3.5 9.2 - - - +
56y LYS 3.2 0.2 - - - -
57y ARG* 1.3 73.6 - - - +
59y VAL* 1.3 59.5 + - - +
61y GLU* 4.1 7.2 - - - -
62y ASN* 2.8 24.3 + - - -
63y ILE* 3.3 26.8 + - + +
65y VAL* 5.8 7.0 - - + -
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Residues in contact with VAL 59 (chain y).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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55y VAL 2.9 13.7 + - - +
56y LYS* 3.0 12.3 + - - +
58y LEU* 1.3 76.6 - - - +
60y ASP* 1.3 60.4 + - - +
62y ASN* 3.4 11.2 + - - +
80y PRO* 5.0 10.8 - - + -
82y TYR 5.2 4.3 - - - +
83y ALA* 5.2 7.8 - - - +
75z THR* 4.6 18.6 - - - +
76z ALA* 4.8 13.2 - - + -
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Residues in contact with ASP 60 (chain y).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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56y LYS 2.9 12.0 + - - +
57y ARG* 3.7 10.1 - - - +
59y VAL* 1.3 77.1 - - - +
61y GLU* 1.3 59.4 + - - +
62y ASN* 3.6 1.4 + - - +
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Residues in contact with GLU 61 (chain y).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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35y LEU* 5.2 18.4 - - + +
57y ARG 2.8 18.2 + - - +
58y LEU* 3.9 8.3 - - - +
59y VAL 3.2 0.4 - - - -
60y ASP* 1.3 76.0 - - - +
62y ASN* 1.3 63.5 + - - +
63y ILE* 3.0 16.6 + - + +
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Residues in contact with ASN 62 (chain y).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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58y LEU 2.8 8.3 + - - -
59y VAL* 3.4 7.5 + - - +
60y ASP 3.3 4.9 - - - +
61y GLU* 1.3 77.2 - - - +
63y ILE* 1.3 64.8 + - - +
64y LEU* 3.4 1.9 + - - -
83y ALA* 4.2 21.5 - - + +
84y ARG 5.3 0.7 - - - +
85y HIS* 4.0 23.5 - - - +
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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