Contacts of the helix formed by residues 69 - 84 (chain S) in PDB entry 1RZR
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 69 (chain S).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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29S PHE* 3.3 25.9 - - - +
30S ASP* 3.5 13.7 + - - +
31S SER* 3.2 23.4 + - - -
68S SER* 1.3 75.1 - - - +
70S GLU* 1.3 65.0 + - - +
71S ALA 3.6 1.1 - - - -
72S ASP* 3.3 22.0 + - + +
73S ALA* 2.9 20.3 + - - +
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Residues in contact with GLU 70 (chain S).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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2S ALA* 4.0 17.4 + - - +
31S SER* 2.8 18.1 + - - -
65S ALA* 3.0 33.7 - - - +
66S GLU* 3.8 2.6 - - - +
67S GLY 2.9 29.2 + - - +
68S SER 3.9 4.5 - - - +
69S ASP* 1.3 71.0 - - - +
71S ALA* 1.3 72.5 + - + +
73S ALA* 2.8 9.0 + - - +
74S LEU 2.8 23.2 + - - -
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Residues in contact with ALA 71 (chain S).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
2S ALA 4.5 11.2 - - - +
70S GLU* 1.3 85.6 - - + +
72S ASP* 1.3 65.4 + - - +
73S ALA 2.8 6.7 + - - -
74S LEU* 2.9 9.5 + - + +
75S ALA* 2.8 26.5 + - - +
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Residues in contact with ASP 72 (chain S).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
29S PHE* 3.6 23.9 - - - -
69S ASP* 3.3 27.9 + - + +
71S ALA* 1.3 78.5 - - - +
73S ALA* 1.3 58.9 + - - +
75S ALA* 4.0 6.7 + - - +
76S ALA* 3.8 9.7 + - - +
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Residues in contact with ALA 73 (chain S).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
29S PHE* 3.4 41.0 - - + -
31S SER* 5.2 0.2 - - - -
33S ILE* 4.0 19.1 - - + -
69S ASP 2.9 8.7 + - - +
70S GLU 2.8 11.8 + - - +
71S ALA 2.8 1.6 + - - -
72S ASP* 1.3 76.2 - - - +
74S LEU* 1.3 55.7 + - - +
75S ALA 2.8 11.3 + - - -
76S ALA* 2.9 3.5 + - - +
77S LEU* 2.8 29.8 + - + +
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Residues in contact with LEU 74 (chain S).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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2S ALA 3.5 10.8 - - - +
3S GLN* 3.2 41.7 - - - +
4S LYS* 4.1 28.6 + - + +
6S PHE* 4.8 3.6 - - + -
63S ILE* 3.6 32.3 - - + -
65S ALA* 3.9 11.6 - - + +
70S GLU 2.8 14.3 + - - +
71S ALA* 2.9 8.7 + - - +
73S ALA* 1.3 73.2 - - - +
75S ALA* 1.3 59.7 + - - +
77S LEU* 4.1 6.1 - - + -
78S GLU* 3.6 15.8 + - - +
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Residues in contact with ALA 75 (chain S).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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71S ALA 2.8 15.6 + - - +
72S ASP* 4.0 9.2 - - - +
73S ALA 2.8 0.2 + - - -
74S LEU* 1.3 80.1 - - - +
76S ALA* 1.3 59.1 + - - +
78S GLU* 3.3 11.0 + - - +
79S ASP* 3.0 22.1 + - - +
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Residues in contact with ALA 76 (chain S).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
25S ALA* 5.6 3.6 - - + +
29S PHE* 3.7 28.5 - - + -
72S ASP 3.8 3.5 + - - +
73S ALA 2.9 6.5 + - - +
75S ALA* 1.3 76.8 - - - +
77S LEU* 1.3 52.3 + - - +
78S GLU 2.9 4.9 - - - -
79S ASP* 2.7 19.1 + - + +
80S THR* 2.7 38.5 + - - +
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Residues in contact with LEU 77 (chain S).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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6S PHE* 4.6 1.4 - - - -
22S LEU* 4.1 19.2 - - + +
25S ALA* 4.3 6.3 - - + -
26S ALA* 3.0 39.3 - - + +
29S PHE* 5.3 0.9 - - + -
33S ILE* 3.3 30.3 - - + -
44S LEU* 3.9 6.7 - - + -
63S ILE* 3.1 37.4 - - + +
65S ALA* 5.3 0.4 - - + -
73S ALA* 2.8 24.5 + - + +
74S LEU* 4.3 3.8 - - - -
76S ALA* 1.3 76.0 - - - +
78S GLU* 1.3 55.3 + - - +
80S THR* 4.0 3.8 - - - +
81S MET* 2.9 29.1 + - - +
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Residues in contact with GLU 78 (chain S).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
4S LYS* 2.4 36.5 + - - +
6S PHE* 3.6 17.3 - - + -
74S LEU 3.6 7.7 + - - +
75S ALA* 3.3 13.0 + - - +
76S ALA 2.9 0.6 - - - -
77S LEU* 1.3 77.3 - - - +
79S ASP* 1.3 67.3 + - - +
80S THR 3.3 0.2 - - - -
81S MET* 3.1 18.7 - - + +
82S SER* 3.2 14.1 + - - -
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Residues in contact with ASP 79 (chain S).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
75S ALA 3.0 8.3 + - - +
76S ALA* 2.7 25.8 + - - +
78S GLU* 1.3 74.3 - - - +
80S THR* 1.3 64.5 + - - -
82S SER* 3.6 4.3 + - - -
83S LYS* 2.9 58.2 + - - +
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Residues in contact with THR 80 (chain S).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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21S THR* 3.8 26.0 - - - +
22S LEU* 3.9 26.7 - - + +
25S ALA* 3.2 23.4 - - - +
76S ALA 2.7 16.3 + - - -
77S LEU* 4.3 4.9 - - - -
79S ASP* 1.3 77.4 + - - +
81S MET* 1.3 56.0 + - - +
82S SER 2.8 6.1 + - - -
83S LYS* 2.9 8.6 + - - +
84S GLU* 2.6 40.9 + - + +
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Residues in contact with MET 81 (chain S).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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6S PHE* 3.6 28.9 - - + -
8S VAL* 6.3 1.1 - - + -
14S ILE* 4.9 2.7 - - + -
22S LEU* 3.3 34.1 - - + -
61S ILE* 3.4 33.2 - - + -
63S ILE* 4.8 8.5 - - + -
77S LEU 2.9 21.0 + - - +
78S GLU* 3.1 17.3 - - + +
80S THR* 1.3 78.4 - - - +
82S SER* 1.3 55.6 + - - -
84S GLU* 5.2 0.2 - - - -
86S LEU* 3.0 44.4 + - + +
87S GLY 3.2 18.0 + - - +
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Residues in contact with SER 82 (chain S).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
78S GLU* 3.2 12.8 + - - -
79S ASP* 3.6 5.2 + - - -
80S THR 2.8 1.4 + - - -
81S MET* 1.3 76.0 - - - +
83S LYS* 1.3 63.2 + - - +
84S GLU 3.1 1.8 - - - -
85S GLY* 2.6 26.4 + - - +
87S GLY 4.5 7.0 - - - +
88S GLU* 5.8 7.6 - - - -
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Residues in contact with LYS 83 (chain S).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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79S ASP* 2.9 49.4 + - - +
80S THR* 2.9 7.3 + - - +
82S SER* 1.3 78.8 + - - +
84S GLU* 1.3 59.5 + - - +
85S GLY 3.1 4.2 + - - -
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Residues in contact with GLU 84 (chain S).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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17S ARG* 3.9 1.9 - - - +
18S PRO* 3.0 41.8 - - + +
21S THR* 2.8 43.3 + - - +
80S THR* 2.6 25.2 + - + +
83S LYS* 1.3 73.8 - - - +
85S GLY* 1.3 58.3 + - - +
86S LEU* 2.8 22.0 + - + +
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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