Contacts of the helix formed by residues 69 - 84 (chain Y) 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 Y).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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29Y PHE* 3.2 24.9 - - + +
30Y ASP* 2.1 37.3 + - - +
31Y SER* 2.3 31.0 + - - -
68Y SER* 1.3 82.6 + - - +
70Y GLU* 1.3 56.6 + - - +
71Y ALA 2.6 18.7 + - - -
72Y ASP* 2.9 25.1 + - + +
73Y ALA* 3.0 16.8 + - - +
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Residues in contact with GLU 70 (chain Y).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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2Y ALA* 3.8 27.1 + - - +
31Y SER* 2.5 18.5 + - - -
65Y ALA 3.2 26.1 - - - +
66Y GLU* 4.0 12.5 - - - +
67Y GLY 2.9 20.9 + - - +
68Y SER 3.8 3.1 - - - +
69Y ASP* 1.3 69.1 - - - +
71Y ALA* 1.3 67.8 + - - +
73Y ALA* 3.4 5.2 - - - +
74Y LEU* 3.3 19.2 + - - +
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Residues in contact with ALA 71 (chain Y).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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2Y ALA 4.8 5.8 - - - +
68Y SER 4.6 0.8 + - - -
69Y ASP 2.6 5.3 + - - -
70Y GLU* 1.3 77.0 - - + +
72Y ASP* 1.3 60.8 + - - +
73Y ALA 2.7 4.7 + - - -
74Y LEU* 2.5 31.4 + - - +
75Y ALA* 3.1 10.3 + - - +
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Residues in contact with ASP 72 (chain Y).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
29Y PHE* 3.4 23.1 - - + -
68Y SER 5.5 0.2 - - - +
69Y ASP* 2.9 17.0 + - + +
71Y ALA* 1.3 77.0 - - - +
73Y ALA* 1.3 58.7 + - - +
75Y ALA* 3.9 9.3 - - - +
76Y ALA* 3.3 16.1 + - - +
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Residues in contact with ALA 73 (chain Y).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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29Y PHE* 3.5 26.6 - - + -
33Y ILE* 4.1 13.7 - - + -
65Y ALA* 4.2 5.2 - - + -
69Y ASP* 3.0 26.7 + - - +
70Y GLU 3.4 8.7 - - - +
71Y ALA 2.7 0.6 + - - -
72Y ASP* 1.3 80.9 - - - +
74Y LEU* 1.3 58.8 + - - +
76Y ALA* 3.7 0.5 - - - +
77Y LEU* 3.0 35.7 + - - +
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Residues in contact with LEU 74 (chain Y).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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2Y ALA* 3.4 38.4 - - - +
3Y GLN 3.6 11.9 - - - +
4Y LYS* 3.5 21.5 - - + -
6Y PHE* 5.3 1.6 - - + -
63Y ILE* 3.4 31.6 - - + +
64Y SER* 4.2 0.2 - - - -
65Y ALA* 3.7 19.3 - - + +
70Y GLU 3.3 8.1 + - - +
71Y ALA* 2.5 18.5 + - - +
73Y ALA* 1.3 73.8 - - - +
75Y ALA* 1.3 58.8 + - - +
77Y LEU* 4.7 3.8 - - + -
78Y GLU* 3.0 32.7 + - - +
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Residues in contact with ALA 75 (chain Y).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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71Y ALA 3.1 9.2 + - - +
72Y ASP* 4.2 10.1 - - - +
74Y LEU* 1.3 72.9 - - - +
76Y ALA* 1.3 56.5 + - - +
78Y GLU* 3.0 12.3 + - - +
79Y ASP* 2.7 34.6 + - - +
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Residues in contact with ALA 76 (chain Y).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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25Y ALA* 5.6 2.7 - - + +
29Y PHE* 3.3 36.8 - - + -
72Y ASP 3.3 9.0 + - - +
73Y ALA 3.7 0.7 - - - +
75Y ALA* 1.3 76.8 - - - +
77Y LEU* 1.3 59.2 + - + +
79Y ASP* 2.7 29.4 + - - +
80Y THR* 3.0 18.4 + - + +
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Residues in contact with LEU 77 (chain Y).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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6Y PHE* 5.2 1.8 - - - -
22Y LEU* 4.4 9.9 - - + +
25Y ALA* 3.5 33.2 - - + +
26Y ALA* 3.7 11.7 - - - +
29Y PHE* 5.0 1.3 - - + -
33Y ILE* 4.1 22.9 - - + -
44Y LEU* 4.4 8.3 - - + -
63Y ILE* 3.5 41.7 - - + -
65Y ALA* 5.5 0.9 - - + -
73Y ALA* 3.0 19.1 + - - +
74Y LEU* 4.3 7.4 - - + +
76Y ALA* 1.3 81.1 - - + +
78Y GLU* 1.3 58.6 + - - +
80Y THR* 3.7 6.2 + - - +
81Y MET* 2.8 33.8 + - + +
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Residues in contact with GLU 78 (chain Y).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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4Y LYS* 3.0 40.1 + - - +
6Y PHE* 4.3 17.1 - - + -
74Y LEU* 3.0 25.5 + - - +
75Y ALA* 3.1 12.3 - - - +
76Y ALA 2.9 0.6 - - - -
77Y LEU* 1.3 75.4 - - - +
79Y ASP* 1.3 67.3 + - - +
81Y MET* 3.2 13.4 + - - +
82Y SER* 3.3 10.4 + - - -
87Y GLY 5.4 0.3 - - - +
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Residues in contact with ASP 79 (chain Y).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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75Y ALA 2.7 10.3 + - - +
76Y ALA* 2.7 18.2 + - - +
78Y GLU* 1.3 70.8 - - - +
80Y THR* 1.3 54.3 + - + +
82Y SER* 2.6 33.6 + - - -
83Y LYS* 2.9 37.0 + - + +
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Residues in contact with THR 80 (chain Y).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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21Y THR* 5.0 5.8 - - - +
22Y LEU* 3.4 23.1 - - - +
25Y ALA* 3.9 19.1 - - + +
76Y ALA* 3.0 15.3 + - + +
77Y LEU* 3.7 5.4 - - - -
79Y ASP* 1.3 78.5 - - + +
81Y MET* 1.3 56.1 + - - +
82Y SER 3.1 0.2 - - - -
83Y LYS* 3.3 33.9 - - - +
84Y GLU* 2.7 44.3 + - + +
86Y LEU* 4.4 0.2 - - - +
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Residues in contact with MET 81 (chain Y).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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6Y PHE* 4.0 28.9 - - + -
8Y VAL* 5.1 4.0 - - + -
14Y ILE* 6.4 1.6 - - + -
22Y LEU* 3.6 29.6 - - + -
35Y LEU* 6.5 0.2 - - + -
61Y ILE* 3.8 29.4 - - + -
63Y ILE* 5.7 2.9 - - + -
77Y LEU* 2.8 27.9 + - + +
78Y GLU 3.2 7.2 + - - +
79Y ASP 2.9 1.2 + - - -
80Y THR* 1.3 76.1 + - - +
82Y SER* 1.3 56.0 + - - +
85Y GLY 3.4 0.3 - - - -
86Y LEU* 2.6 57.8 + - + +
87Y GLY* 3.0 25.2 + - - +
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Residues in contact with SER 82 (chain Y).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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78Y GLU 3.3 6.8 + - - -
79Y ASP* 2.6 14.6 + - - -
81Y MET* 1.3 79.1 - - - +
83Y LYS* 1.3 59.3 + - - +
85Y GLY* 2.6 25.2 + - - -
87Y GLY 4.6 5.6 - - - -
88Y GLU* 6.4 0.7 - - - -
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Residues in contact with LYS 83 (chain Y).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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79Y ASP* 2.9 42.3 + - - +
80Y THR* 3.3 31.5 - - - +
82Y SER* 1.3 78.2 - - - +
84Y GLU* 1.3 69.2 + - - +
85Y GLY* 2.8 6.1 + - - -
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Residues in contact with GLU 84 (chain Y).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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10Y ALA* 5.0 1.7 - - - +
17Y ARG* 4.6 4.7 + - - +
18Y PRO* 4.1 20.5 - - + +
21Y THR* 2.6 39.4 + - - +
22Y LEU* 5.3 0.7 - - - +
80Y THR* 2.7 31.6 + - - +
83Y LYS* 1.3 78.0 - - - +
85Y GLY* 1.3 61.6 + - - +
86Y LEU* 3.2 31.7 + - + +
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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