Contacts of the helix formed by residues 61 - 72 (chain P) in PDB entry 1TQE
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 ASP 61 (chain P).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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58P ALA* 3.6 6.2 - - - +
60P THR* 1.3 85.1 + - - +
62P MET* 1.3 66.3 + - - +
63P ASP* 2.9 20.1 + - - +
64P ARG* 2.6 73.3 + - - +
65P VAL* 3.4 12.8 + - - +
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Residues in contact with MET 62 (chain P).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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44P ALA* 3.6 21.5 - - + -
45P LEU 4.2 2.9 - - - +
46P ILE* 4.8 5.8 - - + -
56P GLN* 3.6 18.8 - - + +
57P TYR 2.8 31.2 - - - +
58P ALA* 3.3 11.1 - - + +
61P ASP* 1.3 71.1 - - - +
63P ASP* 1.3 63.2 + - - +
65P VAL* 4.9 2.2 - - - +
66P LEU* 3.0 69.9 + - + +
69Q TYR* 2.9 29.8 - - - +
109X ALA* 3.4 17.9 - - + +
110X SER* 4.8 0.2 - - - +
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Residues in contact with ASP 63 (chain P).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
61P ASP* 2.9 17.8 - - - +
62P MET* 1.3 79.2 + - - +
64P ARG* 1.3 65.2 + - - +
67P LEU* 3.0 29.6 + - + +
109X ALA 3.6 11.3 - - - +
110X SER* 2.6 35.1 + - - -
113X VAL* 3.3 22.1 - - + +
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Residues in contact with ARG 64 (chain P).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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42P GLU* 4.2 21.3 + - - +
60P THR* 3.5 31.7 + - - +
61P ASP* 2.6 41.3 + - - +
63P ASP* 1.3 73.3 - - - +
65P VAL* 1.3 53.5 + - - +
67P LEU* 3.1 7.7 + - + +
68P LYS* 2.6 42.0 + - + +
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Residues in contact with VAL 65 (chain P).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
42P GLU* 4.0 33.7 - - + +
43P ILE* 4.4 14.8 - - - +
44P ALA* 3.6 28.5 - - + +
58P ALA* 5.6 1.6 - - + -
59P SER* 5.2 2.5 - - - +
60P THR* 5.3 2.2 - - - +
61P ASP 3.4 11.5 + - - +
62P MET* 4.1 5.2 - - - +
63P ASP 3.4 0.6 - - - -
64P ARG* 1.3 78.4 - - + +
66P LEU* 1.3 55.6 + - - +
68P LYS* 2.9 8.8 + - - +
69P TYR* 2.7 36.7 + - - +
46Q ILE* 3.6 23.3 - - + +
48Q PHE* 3.9 7.6 - - + -
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Residues in contact with LEU 66 (chain P).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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44P ALA* 5.0 1.8 - - + -
46P ILE* 4.6 2.2 - - + -
62P MET* 3.0 55.2 + - + +
63P ASP 4.1 0.9 - - - +
65P VAL* 1.3 79.4 - - - +
67P LEU* 1.3 61.8 + - - +
69P TYR* 3.2 20.8 + - + +
70P THR* 3.4 10.6 + - - -
46Q ILE* 4.7 11.4 - - + -
66Q LEU* 4.3 17.9 - - + -
69Q TYR* 3.4 22.7 - - + +
110X SER* 4.7 7.6 - - - +
113X VAL* 4.2 12.6 - - + -
114X LYS* 5.5 2.2 - - + +
117X LEU* 4.0 30.3 - - + +
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Residues in contact with LEU 67 (chain P).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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63P ASP* 3.0 21.9 + - + +
64P ARG* 3.3 5.6 - - - +
66P LEU* 1.3 72.2 - - - +
68P LYS* 1.3 55.6 + - - +
69P TYR 2.9 4.3 - - - -
70P THR* 2.7 33.4 + - - +
71P GLU* 3.7 3.3 + - - +
113X VAL* 3.7 30.2 - - + +
116X LYS* 4.0 27.6 - - + -
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Residues in contact with LYS 68 (chain P).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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42P GLU* 2.5 31.6 + - - +
64P ARG* 2.6 25.8 + - + +
65P VAL* 3.3 7.6 - - - +
67P LEU* 1.3 71.5 - - - +
69P TYR* 1.3 56.0 + - - +
70P THR 3.2 1.7 + - - -
71P GLU* 4.0 6.1 + - + +
72P TYR* 3.7 26.5 + - + -
48Q PHE* 3.2 42.9 - - + +
52Q ASN* 3.6 35.4 + - - +
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Residues in contact with TYR 69 (chain P).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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65P VAL 2.7 13.9 + - - +
66P LEU* 3.3 13.7 - - + +
67P LEU 2.9 0.4 - - - -
68P LYS* 1.3 76.3 - - - +
70P THR* 1.3 62.7 + - - +
71P GLU* 3.3 1.3 - - - -
72P TYR 4.6 2.5 - - - -
73P SER* 4.0 17.4 + - - -
46Q ILE* 3.5 25.8 - - + -
48Q PHE* 3.8 8.5 - + + -
54Q LEU* 3.5 31.2 - - + -
56Q GLN* 3.1 28.6 + - - -
62Q MET* 3.8 12.1 - - + +
63Q ASP* 5.0 0.9 + - - -
66Q LEU* 3.9 24.6 - - + +
117X LEU* 4.8 6.5 - - + -
120X PHE* 3.9 20.8 - + - -
121X LEU* 4.9 5.1 - - + +
124X LYS* 4.3 14.9 + - - -
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Residues in contact with THR 70 (chain P).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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66P LEU 3.4 9.9 + - - -
67P LEU* 2.7 20.3 + - - +
69P TYR* 1.3 80.5 - - - +
71P GLU* 1.3 62.2 + - - +
73P SER* 4.6 0.5 - - - -
116X LYS* 3.6 38.6 - - - +
117X LEU* 4.6 10.9 - - - +
120X PHE* 4.1 40.9 - - + -
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Residues in contact with GLU 71 (chain P).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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67P LEU 3.7 3.0 + - - +
68P LYS* 4.0 9.6 + - + +
69P TYR 3.3 0.2 - - - -
70P THR* 1.3 81.4 - - - +
72P TYR* 1.3 105.2 + - + +
73P SER* 2.9 9.5 + - - -
74P GLU* 5.5 1.0 - - - +
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Residues in contact with TYR 72 (chain P).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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68P LYS* 3.7 25.5 + - + -
69P TYR 4.4 4.4 - - - +
71P GLU* 1.3 105.6 + - + +
73P SER* 1.3 58.1 + - - +
74P GLU* 3.3 14.9 + - + +
48Q PHE* 4.2 13.9 - + + -
52Q ASN* 3.0 49.6 + - + +
54Q LEU* 3.4 22.3 - - + +
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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