Contacts of the helix formed by residues 68 - 80 (chain A) in PDB entry 3LRQ
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 TRP 68 (chain A).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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13A PHE* 3.5 28.9 - + - -
34A LEU* 5.2 0.2 - - + -
66A CYS* 3.0 26.9 - - - -
67A ARG* 1.3 73.2 - - + +
69A ALA* 1.3 74.7 + - - +
70A GLU 3.3 2.0 - - - -
71A GLU* 3.2 10.7 + - + +
72A VAL* 3.1 33.6 + - + +
12D VAL* 3.6 30.7 - - + +
13D PHE* 4.0 7.4 - + - -
27D LEU* 4.3 8.3 - - + +
31D CYS 5.1 0.7 - - - -
32D SER* 2.6 38.4 + - - -
33D LYS* 5.1 5.2 - - + -
34D LEU* 4.2 13.7 - - + +
68D TRP* 3.4 33.9 - + - -
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Residues in contact with ALA 69 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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13A PHE* 5.5 3.4 - - + -
22A LEU* 5.0 9.6 - - + -
25A ALA* 3.5 27.4 - - + +
34A LEU* 5.1 0.7 - - + -
66A CYS* 3.1 27.0 + - - +
68A TRP* 1.3 94.7 - - + +
70A GLU* 1.3 58.0 + - - +
72A VAL* 3.3 2.8 + - - +
73A THR* 2.8 34.1 + - - +
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Residues in contact with GLU 70 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
22A LEU 6.0 1.1 - - - -
24A ASP* 5.0 10.6 - - - +
66A CYS 4.6 0.8 + - - -
67A ARG 4.4 5.9 + - - +
68A TRP 3.3 0.8 - - - -
69A ALA* 1.3 74.2 - - - +
71A GLU* 1.3 61.2 + - - +
73A THR* 3.6 10.2 - - + -
74A GLN* 2.9 58.0 + - + +
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Residues in contact with GLU 71 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
67A ARG 5.2 0.6 + - - +
68A TRP* 3.2 13.4 + - + +
70A GLU* 1.3 75.8 + - - +
72A VAL* 1.3 72.3 + - + +
74A GLN* 3.1 14.4 + - - +
75A GLN* 2.9 48.8 + - + +
8D SER* 3.7 24.9 + - - +
12D VAL* 5.0 10.3 - - + -
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Residues in contact with VAL 72 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
9A ILE* 5.0 0.2 - - + -
13A PHE* 4.0 25.8 - - + -
68A TRP* 3.1 31.0 + - + +
69A ALA* 3.7 8.1 - - - +
71A GLU* 1.3 76.2 - - + +
73A THR* 1.3 57.8 + - - +
75A GLN* 3.3 6.3 + - - +
76A LEU* 2.8 47.8 + - + +
9D ILE* 4.3 19.9 - - + +
12D VAL* 3.9 25.8 - - + -
13D PHE* 4.3 6.5 - - + -
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Residues in contact with THR 73 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
13A PHE* 4.4 21.0 + - - +
21A LYS* 3.6 31.1 - - + +
22A LEU* 4.3 20.4 + - - +
69A ALA 2.8 18.9 + - - -
70A GLU* 3.6 11.9 - - + +
72A VAL* 1.3 79.1 - - - +
74A GLN* 1.3 67.1 + - + +
76A LEU* 3.4 9.8 + - - +
77A ASP* 3.1 24.5 + - - +
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Residues in contact with GLN 74 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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70A GLU* 2.9 45.8 + - + +
71A GLU* 3.6 14.5 - - - +
73A THR* 1.3 76.9 - - + +
75A GLN* 1.3 73.7 + - - +
77A ASP* 3.0 13.5 + - - +
78A THR* 3.0 23.5 + - - -
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Residues in contact with GLN 75 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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71A GLU* 2.9 43.9 + - + +
72A VAL 3.6 4.0 - - - +
74A GLN* 1.3 81.3 + - - +
76A LEU* 1.3 61.3 + - - +
78A THR* 3.0 18.0 + - - +
79A LEU* 3.0 18.8 + - - +
5D SER* 2.8 38.6 + - - +
8D SER* 4.0 25.0 + - - -
9D ILE* 3.7 19.7 - - + -
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Residues in contact with LEU 76 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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6A VAL* 4.0 20.9 - - + +
9A ILE* 3.8 36.1 - - + -
10A ALA* 3.7 26.0 - - + +
13A PHE* 4.1 9.0 - - + -
72A VAL* 2.8 31.4 + - + +
73A THR* 3.7 9.4 - - - +
75A GLN* 1.3 75.6 - - - +
77A ASP* 1.3 63.7 + - - +
79A LEU* 3.2 7.6 + - + +
80A GLN* 3.0 38.0 + - - +
9D ILE* 3.8 17.0 - - + -
79D LEU* 6.2 0.4 - - + -
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Residues in contact with ASP 77 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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21A LYS* 3.1 38.0 + - - +
73A THR* 3.1 18.5 + - - +
74A GLN* 3.0 16.3 + - - +
76A LEU* 1.3 78.4 - - - +
78A THR* 1.3 60.5 - - - +
79A LEU 3.3 0.5 + - - -
80A GLN* 3.3 30.4 + - - +
81A LEU 3.8 4.7 - - - +
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Residues in contact with THR 78 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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74A GLN 3.0 12.9 + - - -
75A GLN* 3.0 14.3 + - - -
77A ASP* 1.3 77.0 - - - +
79A LEU* 1.3 63.8 + - + +
81A LEU* 3.4 18.9 + - - +
2D ASP* 4.9 10.8 - - + +
5D SER* 3.4 21.5 + - - +
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Residues in contact with LEU 79 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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6A VAL* 3.8 24.9 - - + +
75A GLN 3.0 17.3 + - - +
76A LEU* 3.5 10.8 - - + +
77A ASP 3.1 0.2 - - - -
78A THR* 1.3 75.6 - - - +
80A GLN* 1.3 52.8 + - - +
81A LEU* 2.6 33.6 + - - +
1D MSE 3.6 26.2 - - + +
2D ASP* 4.3 20.2 - - + +
5D SER* 3.2 33.4 - - - +
6D VAL* 4.2 11.4 - - + -
9D ILE* 3.9 25.1 - - + -
79D LEU* 5.1 2.5 - - + -
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Residues in contact with GLN 80 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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6A VAL* 3.5 23.3 - - + +
7A GLU* 2.5 37.4 + - - +
10A ALA* 4.0 16.1 - - - +
14A ARG* 5.1 4.3 + - - +
76A LEU* 3.0 21.5 + - - +
77A ASP* 3.3 17.3 + - - +
79A LEU* 1.3 71.1 - - - +
81A LEU* 1.3 71.2 + - - +
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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