Contacts of the helix formed by residues 68 - 82 (chain D) 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 D).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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12A VAL* 3.7 33.0 - - + -
13A PHE* 4.1 3.6 - + - -
27A LEU* 3.8 21.3 - - + -
32A SER* 2.9 40.0 + - - -
33A LYS* 5.2 6.5 - - + -
34A LEU* 4.0 14.5 - - + +
68A TRP* 3.4 30.7 - + - -
13D PHE* 3.4 28.9 - + - -
34D LEU* 4.7 2.0 - - + -
66D CYS* 3.9 21.5 - - + -
67D ARG* 1.3 72.2 - - + +
69D ALA* 1.3 75.3 + - + +
70D GLU 3.3 2.4 + - - -
71D GLU* 3.4 9.6 + - + +
72D VAL* 3.2 26.6 + - + +
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Residues in contact with ALA 69 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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13D PHE* 5.1 3.3 - - + -
22D LEU* 4.9 9.0 - - + -
25D ALA* 3.4 29.2 - - + +
34D LEU* 5.5 0.9 - - + -
66D CYS* 3.1 24.0 + - + +
68D TRP* 1.3 95.2 - - + +
70D GLU* 1.3 57.8 + - - +
72D VAL* 3.2 4.2 + - - +
73D THR* 2.8 32.7 + - - +
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Residues in contact with GLU 70 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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22D LEU 6.0 1.1 - - - -
66D CYS 4.7 0.4 + - - -
67D ARG 4.5 5.5 + - - +
68D TRP 3.3 0.4 - - - -
69D ALA* 1.3 75.2 - - - +
71D GLU* 1.3 68.0 + - - +
73D THR* 3.0 9.9 + - + -
74D GLN* 2.8 54.7 + - + +
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Residues in contact with GLU 71 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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8A SER* 4.1 10.0 - - - +
9A ILE* 6.4 0.2 - - - -
12A VAL* 4.1 21.3 - - + -
67D ARG 5.2 1.5 + - - +
68D TRP* 3.4 15.3 + - + +
70D GLU* 1.3 80.4 - - - +
72D VAL* 1.3 65.4 + - - +
74D GLN* 3.0 16.3 + - - +
75D GLN* 3.0 52.7 + - + +
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Residues in contact with VAL 72 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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9A ILE* 4.4 19.7 - - + +
12A VAL* 3.9 31.9 - - + -
13A PHE* 4.0 11.4 - - + -
9D ILE* 5.4 0.2 - - + -
13D PHE* 4.0 26.2 - - + -
68D TRP* 3.2 19.6 + - + +
69D ALA 3.6 7.0 - - - +
71D GLU* 1.3 80.3 - - - +
73D THR* 1.3 63.5 + - - +
75D GLN* 3.2 8.0 + - - +
76D LEU* 2.9 40.6 + - + +
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Residues in contact with THR 73 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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13D PHE* 4.9 7.5 + - - +
21D LYS* 3.8 43.9 + - + +
22D LEU* 4.5 25.6 + - - +
69D ALA 2.8 20.4 + - - -
70D GLU* 3.4 12.4 - - + -
72D VAL* 1.3 78.2 - - - +
74D GLN* 1.3 64.3 + - + +
76D LEU* 3.3 11.9 + - + +
77D ASP* 3.0 21.3 + - - +
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Residues in contact with GLN 74 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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21D LYS* 5.8 0.7 - - - +
70D GLU* 2.8 49.4 + - + +
71D GLU* 3.4 18.2 - - - +
73D THR* 1.3 79.0 - - + +
75D GLN* 1.3 64.8 + - + +
77D ASP* 3.2 10.2 - - - +
78D THR* 3.2 22.4 + - - -
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Residues in contact with GLN 75 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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5A SER* 3.0 31.8 + - - +
8A SER* 3.6 25.9 + - - -
9A ILE* 3.7 26.5 - - + +
71D GLU* 3.0 42.5 + - + +
72D VAL 3.2 2.4 + - - +
74D GLN* 1.3 76.5 + - - +
76D LEU* 1.3 59.7 + - - +
78D THR* 3.1 9.0 + - - +
79D LEU* 2.8 28.3 + - - +
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Residues in contact with LEU 76 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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9A ILE* 3.6 21.8 - - + -
6D VAL* 4.7 7.6 - - + +
9D ILE* 3.9 17.9 - - + -
10D ALA* 4.1 22.4 - - + +
13D PHE* 3.9 27.6 - - + -
72D VAL* 2.9 32.5 + - + +
73D THR* 3.4 11.4 - - - +
75D GLN* 1.3 74.3 - - - +
77D ASP* 1.3 53.5 + - - +
79D LEU* 3.1 13.9 + - + +
80D GLN* 2.7 44.0 + - + +
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Residues in contact with ASP 77 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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21D LYS* 3.1 26.7 + - - +
73D THR 3.0 12.7 + - - +
74D GLN* 3.2 13.5 - - - +
76D LEU* 1.3 76.3 - - - +
78D THR* 1.3 57.5 + - - +
80D GLN* 3.3 7.6 + - - +
81D LEU* 3.0 40.2 + - - +
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Residues in contact with THR 78 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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1A MSE 4.5 24.5 - - + +
5A SER* 3.2 24.5 - - - +
74D GLN 3.2 9.9 + - - -
75D GLN* 3.1 8.2 + - - -
77D ASP* 1.3 80.7 + - - +
79D LEU* 1.3 61.3 + - - +
81D LEU* 3.3 12.9 + - + +
82D CYS* 3.1 21.9 + - - -
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Residues in contact with LEU 79 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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2A ASP* 4.0 24.0 - - + +
5A SER* 4.0 13.2 - - - -
6A VAL* 4.1 17.5 - - + +
9A ILE* 4.0 26.9 - - + -
76A LEU* 6.2 0.4 - - + -
79A LEU* 5.1 4.0 - - + -
1D MSE 4.0 27.1 - - + -
6D VAL* 4.1 25.0 - - + +
9D ILE* 5.8 1.6 - - + -
75D GLN 2.8 11.3 + - - +
76D LEU* 3.1 17.9 + - + +
78D THR* 1.3 73.5 - - - +
80D GLN* 1.3 64.0 + - - +
82D CYS* 3.0 23.6 + - + +
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Residues in contact with GLN 80 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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6D VAL* 3.7 20.7 - - + +
7D GLU* 3.4 18.2 - - - +
10D ALA* 3.7 15.0 - - - +
14D ARG* 3.7 23.6 - - - +
76D LEU* 2.7 39.6 + - - +
77D ASP* 3.7 6.5 - - - +
79D LEU* 1.3 71.8 - - - +
81D LEU* 1.3 62.6 + - - +
82D CYS 3.3 0.3 + - - -
83D SER* 3.4 17.5 + - - -
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Residues in contact with LEU 81 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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77D ASP* 3.0 27.3 + - - +
78D THR* 3.3 16.6 - - + +
80D GLN* 1.3 71.6 - - - +
82D CYS* 1.3 53.8 + - - +
83D SER* 2.6 19.6 + - - -
84D LEU* 3.3 13.0 + - - +
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Residues in contact with CYS 82 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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1A MSE 3.7 30.3 - - - -
2A ASP* 3.6 39.1 - - + +
1D MSE 5.8 4.8 - - + +
78D THR* 3.1 17.5 + - - -
79D LEU* 3.0 17.4 + - + +
81D LEU* 1.3 74.0 - - - +
83D SER* 1.3 60.9 + - - +
84D LEU* 3.4 22.6 - - + +
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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