Contacts of the helix formed by residues 52 - 61 (chain m) in PDB entry 6QY3
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 m).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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43l LEU* 5.5 6.3 - - - -
45l THR 3.9 17.9 - - - -
46l THR* 3.7 11.1 + - - -
48l ILE* 3.1 26.7 + - - -
67l PHE* 6.1 4.5 - - - -
68l CYS 5.0 5.0 - - - +
50m LEU 4.4 0.2 + - - -
51m THR* 1.3 71.5 - - - +
53m MET* 1.3 57.3 + - - +
55m VAL* 3.2 10.3 + - - +
56m LYS* 2.9 28.1 + - - +
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Residues in contact with MET 53 (chain m).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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46l THR* 3.0 34.4 + - - +
17m TYR* 4.6 7.6 - - + +
51m THR* 3.2 6.4 - - - -
52m THR* 1.3 77.3 - - - +
54m LEU* 1.3 56.9 + - - +
56m LYS* 3.3 5.2 + - - +
57m ARG* 2.9 28.8 + - - +
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Residues in contact with LEU 54 (chain m).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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15m LEU* 4.9 4.3 - - + +
16m SER* 4.3 7.6 - - - +
17m TYR* 3.8 32.6 - - + +
50m LEU* 5.7 2.7 - - + -
51m THR* 3.2 19.5 + - - +
53m MET* 1.3 78.5 - - - +
55m VAL* 1.3 58.0 + - - +
57m ARG* 3.8 3.4 - - - +
58m LEU* 2.9 28.2 + - - +
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Residues in contact with VAL 55 (chain m).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
67l PHE* 5.5 11.0 - - + -
76l ALA* 5.9 0.5 - - - +
50m LEU* 6.4 0.9 - - + -
51m THR 3.1 12.1 + - - +
52m THR* 3.5 12.8 - - - +
53m MET 3.2 0.2 - - - -
54m LEU* 1.3 75.8 - - - +
56m LYS* 1.3 60.0 + - - +
58m LEU* 3.3 7.5 + - - +
59m VAL* 2.9 28.2 + - - +
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Residues in contact with LYS 56 (chain m).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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46l THR* 5.4 3.8 - - - -
68l CYS 4.6 4.5 - - - +
69l ASP* 4.4 26.7 - - + +
70l ASP 5.5 0.7 - - - +
75l THR* 5.7 4.7 - - - -
52m THR 2.9 16.3 + - - +
53m MET* 3.6 7.6 - - - +
55m VAL* 1.3 74.3 - - - +
57m ARG* 1.3 60.1 + - - +
59m VAL* 3.2 7.9 + - - +
60m ASP* 2.9 29.1 + - - +
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Residues in contact with ARG 57 (chain m).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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17m TYR* 4.8 10.1 - - + -
35m LEU* 6.1 0.2 - - - +
53m MET 2.9 16.7 + - - +
54m LEU* 3.8 8.1 - - - +
56m LYS* 1.3 76.1 - - - +
58m LEU* 1.3 57.1 + - - +
60m ASP* 3.5 6.5 + - - +
61m GLU* 2.9 30.0 + - - +
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Residues in contact with LEU 58 (chain m).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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54m LEU 2.9 18.5 + - - +
55m VAL* 3.6 8.7 - - - +
56m LYS 3.2 0.2 - - - -
57m ARG* 1.3 76.1 - - - +
59m VAL* 1.3 59.5 + - - +
61m GLU* 3.6 5.3 - - - -
62m ASN 3.0 21.1 + - - -
63m ILE* 3.0 32.2 + - + +
65m VAL* 5.6 7.9 - - + -
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Residues in contact with VAL 59 (chain m).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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75l THR* 4.4 20.6 - - - -
76l ALA* 4.6 15.3 - - + -
55m VAL 2.9 17.8 + - - +
56m LYS* 3.2 8.0 + - - +
58m LEU* 1.3 75.0 - - - +
60m ASP* 1.3 63.8 + - - +
62m ASN* 3.3 13.0 + - - +
63m ILE 5.5 0.9 - - - -
80m PRO* 4.9 16.2 - - + +
83m ALA* 6.2 0.2 - - - -
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Residues in contact with ASP 60 (chain m).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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56m LYS 2.9 16.9 + - - +
57m ARG* 3.9 7.0 - - - +
59m VAL* 1.3 76.0 - - - +
61m GLU* 1.3 60.0 + - - +
62m ASN* 3.2 3.3 + - - +
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Residues in contact with GLU 61 (chain m).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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35m LEU* 5.1 20.2 - - + +
57m ARG 2.9 18.4 + - - +
58m LEU* 3.9 6.3 - - - +
60m ASP* 1.3 74.3 - - - +
62m ASN* 1.3 70.3 + - - +
63m ILE* 3.5 7.5 + - + +
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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