Contacts of the helix formed by residues 69 - 84 (chain T) 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 T).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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29T PHE* 4.2 18.8 - - + -
30T ASP* 2.7 47.2 + - - +
31T SER* 2.8 19.0 + - - +
67T GLY 3.1 0.6 - - - -
68T SER* 1.3 85.8 + - - +
70T GLU* 1.3 54.7 + - - +
71T ALA* 2.6 18.0 + - - -
72T ASP* 3.0 12.3 + - + +
73T ALA 2.9 16.8 + - - -
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Residues in contact with GLU 70 (chain T).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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2T ALA* 3.1 25.6 + - - +
31T SER* 3.3 9.7 + - - -
65T ALA* 3.2 22.6 - - - +
66T GLU* 3.1 12.8 - - - +
67T GLY* 2.7 36.0 + - - +
69T ASP* 1.3 74.0 - - - +
71T ALA* 1.3 66.2 + - - +
73T ALA* 3.2 18.4 - - - +
74T LEU* 3.4 11.8 + - - +
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Residues in contact with ALA 71 (chain T).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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2T ALA 5.4 2.7 - - - +
68T SER 5.1 2.0 + - - +
69T ASP 2.6 5.3 + - - +
70T GLU* 1.3 82.7 - - - +
72T ASP* 1.3 75.0 + - - +
74T LEU* 2.9 16.3 + - - +
75T ALA* 3.7 2.3 + - - +
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Residues in contact with ASP 72 (chain T).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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29T PHE* 4.5 12.6 - - + -
69T ASP* 3.0 11.1 + - + +
71T ALA* 1.3 79.0 - - - +
73T ALA* 1.3 68.2 + - - +
74T LEU 2.9 0.7 + - - -
75T ALA* 2.9 10.5 + - + +
76T ALA* 2.8 26.4 + - + +
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Residues in contact with ALA 73 (chain T).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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29T PHE* 4.1 19.3 - - + -
31T SER* 3.5 25.1 - - - +
33T ILE* 4.4 11.3 - - + +
65T ALA* 3.7 15.0 - - + -
69T ASP 2.9 7.0 + - - +
70T GLU 3.2 13.7 - - - +
72T ASP* 1.3 77.5 - - - +
74T LEU* 1.3 62.4 + - - +
76T ALA* 3.6 2.8 + - - +
77T LEU* 3.2 26.7 + - - +
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Residues in contact with LEU 74 (chain T).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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2T ALA 2.6 45.8 - - - +
3T GLN* 3.1 25.1 - - - +
4T LYS* 4.7 6.3 - - + -
6T PHE* 5.8 0.3 - - - -
63T ILE* 3.8 25.5 - - + +
65T ALA* 3.7 15.9 - - + -
70T GLU 3.8 4.3 - - - +
71T ALA 2.9 9.1 + - - +
72T ASP 2.9 0.4 + - - -
73T ALA* 1.3 78.3 - - - +
75T ALA* 1.3 67.4 + - - +
76T ALA 3.2 0.3 + - - -
77T LEU* 3.2 3.6 + - + +
78T GLU* 2.9 25.7 + - - +
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Residues in contact with ALA 75 (chain T).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
71T ALA 3.7 2.1 + - - +
72T ASP* 2.9 18.4 + - + +
74T LEU* 1.3 74.7 - - - +
76T ALA* 1.3 64.2 + - - +
78T GLU* 3.2 11.7 + - - +
79T ASP* 3.0 27.5 + - - +
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Residues in contact with ALA 76 (chain T).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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25T ALA* 5.1 2.0 - - + +
28T LYS* 4.8 4.9 - - - +
29T PHE* 3.2 41.7 - - + -
72T ASP* 2.8 10.4 + - + +
73T ALA 3.6 0.9 - - - +
75T ALA* 1.3 79.5 - - - +
77T LEU* 1.3 63.3 + - - +
79T ASP* 3.3 6.5 + - - +
80T THR* 3.2 21.1 + - - -
83T LYS* 5.0 0.3 - - - -
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Residues in contact with LEU 77 (chain T).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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6T PHE* 5.2 1.8 - - + -
22T LEU* 3.1 32.8 - - + +
25T ALA* 3.8 8.3 - - + +
26T ALA* 3.2 31.9 - - + +
29T PHE* 5.6 0.9 - - + -
33T ILE* 3.9 16.2 - - + -
44T LEU* 3.4 27.6 - - + -
63T ILE* 4.0 26.7 - - + -
73T ALA 3.2 14.2 + - - +
74T LEU* 3.2 3.9 + - + +
76T ALA* 1.3 78.0 - - + +
78T GLU* 1.3 66.3 + - - +
80T THR* 3.8 3.1 - - - +
81T MET* 2.9 26.1 + - + +
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Residues in contact with GLU 78 (chain T).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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4T LYS* 4.4 22.7 + - + +
6T PHE* 4.0 27.7 - - + -
74T LEU 2.9 18.6 + - - +
75T ALA* 3.5 10.8 - - - +
77T LEU* 1.3 78.0 - - - +
79T ASP* 1.3 68.0 + - - +
81T MET* 3.1 4.3 + - - +
82T SER* 2.9 23.3 + - - -
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Residues in contact with ASP 79 (chain T).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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75T ALA 3.0 13.4 + - - +
76T ALA* 3.4 9.6 - - - +
78T GLU* 1.3 80.3 - - - +
80T THR* 1.3 51.4 + - - +
82T SER* 2.7 12.8 + - - -
83T LYS* 2.5 67.6 + - - +
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Residues in contact with THR 80 (chain T).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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21T THR* 4.0 6.7 + - - +
22T LEU* 3.3 41.7 - - + -
25T ALA* 3.8 15.5 - - + +
76T ALA 3.2 11.6 + - - -
77T LEU* 4.0 2.0 - - - -
79T ASP* 1.3 75.1 - - - +
81T MET* 1.3 59.0 + - - +
83T LYS* 3.5 18.0 - - - +
84T GLU* 2.7 49.6 + - + +
86T LEU* 3.9 1.1 - - + +
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Residues in contact with MET 81 (chain T).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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6T PHE* 3.8 32.8 - - + -
8T VAL* 6.2 0.4 - - - -
22T LEU* 3.8 13.0 - - + -
61T ILE* 3.9 12.8 - - + -
63T ILE* 3.3 34.5 - - + -
77T LEU 2.9 18.1 + - - +
78T GLU 3.2 10.3 - - - +
80T THR* 1.3 77.9 - - - +
82T SER* 1.3 57.6 + - - +
85T GLY 3.0 6.4 + - - -
86T LEU* 3.0 56.5 + - - -
87T GLY* 3.1 33.7 + - - +
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Residues in contact with SER 82 (chain T).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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78T GLU* 2.9 13.6 + - - -
79T ASP* 2.7 11.6 + - - -
81T MET* 1.3 75.3 - - - +
83T LYS* 1.3 62.5 + - - +
85T GLY* 2.8 21.4 + - - -
87T GLY 3.5 9.4 + - - -
88T GLU* 4.6 12.0 + - - +
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Residues in contact with LYS 83 (chain T).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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76T ALA 5.0 0.4 - - - -
79T ASP* 2.5 66.2 + - + +
80T THR* 3.5 20.0 - - - +
82T SER* 1.3 75.4 + - - +
84T GLU* 1.3 64.9 + - + +
85T GLY* 3.0 1.2 - - - -
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Residues in contact with GLU 84 (chain T).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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18T PRO* 5.0 11.1 - - + +
21T THR* 3.3 36.7 + - + +
80T THR* 2.7 42.7 + - + +
83T LYS* 1.3 83.2 - - + +
85T GLY* 1.3 64.3 + - - +
86T LEU* 3.2 21.1 + - + +
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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