Contacts of the helix formed by residues 61 - 71 (chain Q) 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 Q).
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
58Q ALA* 3.7 3.6 - - - -
60Q THR* 1.3 86.1 + - - +
62Q MET* 1.3 74.5 + - - +
63Q ASP* 3.2 18.8 + - - +
64Q ARG* 3.6 26.9 + - + +
65Q VAL* 3.5 24.8 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with MET 62 (chain Q).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
69P TYR* 3.8 15.7 - - - +
44Q ALA* 4.0 17.3 - - - -
45Q LEU 3.8 6.5 - - - +
46Q ILE* 4.1 10.5 - - + -
56Q GLN* 3.1 61.5 - - + +
57Q TYR 3.2 22.0 - - - +
58Q ALA* 3.4 12.3 - - + +
61Q ASP* 1.3 76.0 + - - +
63Q ASP* 1.3 67.9 + - - +
65Q VAL* 3.6 2.4 + - - +
66Q LEU* 3.3 36.0 + - + +
124X LYS* 6.0 0.2 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with ASP 63 (chain Q).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
69P TYR* 5.0 0.9 + - - -
61Q ASP* 3.2 13.1 + - - +
62Q MET* 1.3 83.5 - - - +
64Q ARG* 1.3 63.1 + - - +
66Q LEU* 4.9 1.5 - - - +
67Q LEU* 3.1 25.0 + - - +
121X LEU* 4.0 23.9 - - + +
124X LYS* 3.1 44.5 + - - +
125X SER* 5.7 1.4 + - - -
----------------------------------------------------------
Back to top of page
Residues in contact with ARG 64 (chain Q).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
42Q GLU* 2.9 34.9 + - - +
60Q THR* 3.4 23.2 + - - +
61Q ASP* 3.6 25.3 + - + +
62Q MET 3.3 0.8 - - - -
63Q ASP* 1.3 78.7 - - - +
65Q VAL* 1.3 64.5 + - + +
67Q LEU* 3.0 16.9 + - + +
68Q LYS* 3.1 15.4 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with VAL 65 (chain Q).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
46P ILE* 3.7 21.8 - - + +
48P PHE* 3.8 10.9 - - + -
42Q GLU* 4.2 29.6 - - + +
43Q ILE* 4.4 14.4 - - - +
44Q ALA* 3.5 31.4 - - + +
58Q ALA* 5.4 0.9 - - + -
59Q SER* 5.4 1.8 - - - +
60Q THR* 5.3 3.1 - - - +
61Q ASP 3.5 15.5 + - - +
62Q MET* 4.0 4.0 - - - +
63Q ASP 3.5 0.2 - - - -
64Q ARG* 1.3 77.2 - - + +
66Q LEU* 1.3 63.3 + - - +
68Q LYS* 3.6 7.2 + - - +
69Q TYR* 3.1 20.1 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with LEU 66 (chain Q).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
46P ILE* 3.6 28.5 - - + -
66P LEU* 4.3 15.3 - - + -
69P TYR* 3.9 33.0 - - + +
44Q ALA* 4.6 8.7 - - + -
46Q ILE* 4.4 10.3 - - + -
62Q MET* 3.3 33.2 + - + +
63Q ASP* 4.1 1.3 - - - +
65Q VAL* 1.3 77.2 - - - +
67Q LEU* 1.3 70.0 + - - +
69Q TYR* 3.0 6.2 - - + +
70Q THR* 2.9 22.5 + - - +
117X LEU* 4.6 9.0 - - + -
121X LEU* 3.6 21.8 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with LEU 67 (chain Q).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
63Q ASP 3.1 11.8 + - - +
64Q ARG* 3.0 12.9 + - + +
66Q LEU* 1.3 73.5 - - - +
68Q LYS* 1.3 59.1 + - - +
70Q THR* 2.5 38.4 + - - +
71Q GLU* 3.3 15.2 + - - +
118X GLN* 4.3 10.3 - - + -
121X LEU* 3.4 23.5 - - + +
122X LEU* 3.4 34.8 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with LYS 68 (chain Q).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
48P PHE* 3.8 23.8 - - + -
52P ASN* 3.9 25.3 - - - +
42Q GLU* 5.8 3.6 - - - +
64Q ARG 3.1 8.1 + - - +
65Q VAL* 3.7 9.9 - - - +
67Q LEU* 1.3 78.1 - - - +
69Q TYR* 1.3 64.6 + - - +
71Q GLU* 3.4 32.0 + - + +
72Q TYR* 3.5 18.2 + - + +
----------------------------------------------------------
Back to top of page
Residues in contact with TYR 69 (chain Q).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
46P ILE* 3.5 27.8 - - + -
48P PHE* 4.0 8.7 - - + -
54P LEU* 3.6 29.2 - - + -
56P GLN* 2.8 17.1 + - - -
62P MET* 2.9 11.8 - - + +
66P LEU* 3.4 22.4 - - + -
65Q VAL 3.1 14.0 + - - +
66Q LEU* 3.0 17.3 - - + +
67Q LEU 2.7 3.6 + - - -
68Q LYS* 1.3 75.2 - - - +
70Q THR* 1.3 67.6 + - - +
72Q TYR* 2.9 19.9 + - - +
76Q HIS* 5.2 0.4 - - - -
109X ALA* 2.4 37.0 - - + +
114X LYS* 3.7 24.1 - - + +
117X LEU* 4.6 9.6 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with THR 70 (chain Q).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
66Q LEU 2.9 20.6 + - - +
67Q LEU* 2.5 27.6 + - - +
69Q TYR* 1.3 72.8 - - + +
71Q GLU* 1.3 59.1 + - - +
72Q TYR 3.0 6.1 + - - -
73Q SER* 5.2 1.7 + - - -
114X LYS* 3.3 49.7 - - - +
117X LEU* 3.7 25.6 - - + -
118X GLN* 2.6 39.2 + - + +
121X LEU* 4.4 0.9 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with GLU 71 (chain Q).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
67Q LEU* 3.6 24.6 - - - +
68Q LYS* 3.6 33.3 + - + +
69Q TYR 3.2 0.2 - - - -
70Q THR* 1.3 75.9 + - - +
72Q TYR* 1.3 59.9 + - - +
73Q SER* 3.8 4.2 + - - -
118X GLN* 4.5 12.4 + - - +
----------------------------------------------------------
Back to top of page
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
------------------------------------------------------------
Atomic class I II III IV V VI VII VIII
------------------------------------------------------------
I (Hydrophilic) + + + - + + + +
II (Acceptor) + - + - + + + -
III (Donor) + + - - + + - +
IV (Hydrophobic) - - - + + + + +
V (Aromatic) + + + + + + + +
VI (Neutral) + + + + + + + +
VII (Neutral-donor) + + - + + + - +
VIII (Neutral-acceptor) + - + + + + + -
------------------------------------------------------------
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