Contacts of the helix formed by residues 52 - 62 (chain U) 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 U).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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51U THR* 1.3 70.2 - - - +
53U MET* 1.3 61.4 + - - +
55U VAL* 3.2 11.1 + - - +
56U LYS* 2.9 27.4 + - - +
43V LEU* 5.5 6.3 - - - -
45V THR 3.8 22.0 - - - -
46V THR* 3.9 6.1 - - - -
48V ILE* 3.4 23.5 + - - -
67V PHE* 5.7 7.9 - - - +
68V CYS 5.2 5.1 - - - +
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Residues in contact with MET 53 (chain U).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
17U TYR* 4.8 8.7 - - + +
51U THR* 3.2 6.2 - - - -
52U THR* 1.3 77.1 - - - +
54U LEU* 1.3 57.5 + - - +
56U LYS* 3.1 6.1 + - - +
57U ARG* 2.9 28.2 + - - +
46V THR* 3.1 33.1 + - - +
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Residues in contact with LEU 54 (chain U).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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15U LEU* 5.0 6.3 - - + +
16U SER* 4.5 13.9 - - - +
17U TYR* 4.0 25.4 - - + +
50U LEU* 6.0 1.3 - - + -
51U THR* 3.2 19.3 + - - +
53U MET* 1.3 76.8 - - - +
55U VAL* 1.3 59.9 + - - +
57U ARG* 3.8 3.9 - - - +
58U LEU* 2.9 28.1 + - - +
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Residues in contact with VAL 55 (chain U).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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51U THR 3.1 12.6 + - - +
52U THR* 3.3 14.1 - - - +
53U MET 3.1 0.4 - - - -
54U LEU* 1.3 79.0 - - - +
56U LYS* 1.3 56.8 + - - +
58U LEU* 3.3 7.7 + - - +
59U VAL* 2.9 25.3 + - - +
67V PHE* 5.3 13.0 - - + -
76V ALA* 5.8 1.2 - - - +
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Residues in contact with LYS 56 (chain U).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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52U THR 2.9 12.9 + - - +
53U MET* 3.1 10.5 + - - +
55U VAL* 1.3 75.0 - - - +
57U ARG* 1.3 59.3 + - - +
59U VAL* 3.1 9.2 + - - +
60U ASP* 2.9 26.7 + - - +
46V THR* 5.4 4.7 - - - -
68V CYS 4.6 14.1 - - - +
69V ASP* 4.9 11.0 - - + -
70V ASP 5.7 0.9 - - - +
75V THR* 5.3 6.7 - - - -
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Residues in contact with ARG 57 (chain U).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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17U TYR* 4.8 10.8 - - + -
53U MET 2.9 15.6 + - - +
54U LEU* 3.9 8.7 - - - +
56U LYS* 1.3 75.4 - - - +
58U LEU* 1.3 57.3 + - - +
60U ASP* 3.4 8.9 + - - +
61U GLU* 2.9 29.0 + - - +
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Residues in contact with LEU 58 (chain U).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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54U LEU 2.9 17.2 + - - +
55U VAL* 3.5 9.0 - - - +
56U LYS 3.2 0.2 - - - -
57U ARG* 1.3 75.9 - - - +
59U VAL* 1.3 59.2 + - - +
61U GLU* 4.2 6.1 - - - +
62U ASN* 2.8 25.3 + - - -
63U ILE* 3.3 26.8 + - + +
65U VAL* 5.8 6.7 - - + -
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Residues in contact with VAL 59 (chain U).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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55U VAL 2.9 14.5 + - - +
56U LYS* 3.1 12.7 + - - +
58U LEU* 1.3 76.1 - - - +
60U ASP* 1.3 61.4 + - - +
62U ASN* 3.5 10.9 + - - +
80U PRO* 5.1 13.3 - - + +
82U TYR 5.2 5.5 - - - +
83U ALA* 5.2 7.1 - - - +
75V THR* 4.6 18.2 - - - +
76V ALA* 4.8 13.7 - - + -
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Residues in contact with ASP 60 (chain U).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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56U LYS 2.9 13.3 + - - +
57U ARG* 3.8 10.1 - - - +
59U VAL* 1.3 76.9 - - - +
61U GLU* 1.3 58.9 + - - +
62U ASN* 3.4 1.3 + - - +
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Residues in contact with GLU 61 (chain U).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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35U LEU* 5.2 19.1 - - + +
57U ARG 2.9 17.8 + - - +
58U LEU* 3.2 8.2 + - - +
60U ASP* 1.3 75.7 - - - +
62U ASN* 1.3 63.1 + - - +
63U ILE* 2.9 18.7 + - + +
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Residues in contact with ASN 62 (chain U).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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58U LEU 2.8 7.7 + - - -
59U VAL* 3.5 7.5 + - - +
60U ASP 3.4 5.1 - - - +
61U GLU* 1.3 76.8 - - - +
63U ILE* 1.3 64.2 + - - +
64U LEU* 3.4 1.7 + - - -
83U ALA* 4.2 21.3 - - + +
84U ARG 5.4 0.9 - - - +
85U HIS* 4.0 23.7 - - - +
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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