Contacts of the helix formed by residues 72 - 89 (chain A) 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 ASN 72 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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69A ASP* 2.9 25.6 + - + +
71A SER* 1.3 74.9 - - - +
73A ILE* 1.3 67.0 + - - +
74A PHE* 3.1 15.9 + - - +
75A TYR* 2.9 46.0 + - + +
76A ALA 2.9 20.1 + - - -
221A TYR* 6.2 2.2 - - - +
249A GLU* 5.6 4.0 + - - -
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Residues in contact with ILE 73 (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 SER 3.3 5.0 + - - -
72A ASN* 1.3 72.2 - - - +
74A PHE* 1.3 67.7 + - - +
76A ALA* 3.2 5.0 + - - +
77A GLU* 3.1 29.2 + - + +
249A GLU* 5.8 2.7 - - - +
277A THR* 3.4 33.4 - - + -
278A ARG* 5.7 10.8 - - + +
279A LEU* 4.5 24.0 - - + -
294A MSE 3.9 8.5 - - + -
71D SER 5.4 4.0 - - - +
73D ILE* 3.5 31.8 - - + +
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Residues in contact with PHE 74 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
72A ASN* 3.1 13.9 + - - +
73A ILE* 1.3 82.9 - - + +
75A TYR* 1.3 92.2 + + - +
77A GLU* 3.5 2.6 + - - +
78A LEU* 3.1 45.2 + - + +
146A ALA* 3.6 23.8 - - + -
161A TYR* 5.3 0.4 - - - -
275A ASP* 4.2 18.8 - - - +
292A GLN* 3.6 28.7 - - + -
294A MSE 3.0 43.6 - - + +
297A ILE* 5.5 0.7 - - + -
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Residues in contact with TYR 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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67A ILE* 3.3 28.0 - - + +
68A PRO* 3.7 35.7 - - + +
69A ASP* 3.2 31.6 - - + +
70A ILE* 4.4 0.7 - - - -
72A ASN* 2.9 32.0 + - + +
74A PHE* 1.3 95.5 - + - +
76A ALA* 1.3 57.7 + - - +
78A LEU* 2.8 4.6 + - + +
79A ALA* 2.5 38.0 + - - +
100A GLN* 4.5 6.4 + - - -
123A MSE 3.9 19.2 + - + -
124A SER 4.8 5.0 + - - -
125A GLY* 5.4 1.2 - - - -
146A ALA* 4.3 15.0 + - + -
191A ILE* 5.5 5.4 - - - +
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Residues in contact with ALA 76 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
70A ILE* 3.8 20.9 + - - +
71A SER 4.4 3.4 - - - +
72A ASN 2.9 11.4 + - - +
73A ILE* 3.2 10.3 + - - +
75A TYR* 1.3 76.5 - - - +
77A GLU* 1.3 57.1 - - - +
79A ALA* 3.1 9.7 - - - +
80A ARG* 3.0 22.5 + - - +
70D ILE* 3.5 26.8 - - - +
71D SER* 3.9 15.0 - - - +
73D ILE* 5.4 1.6 - - + -
76D ALA* 4.2 5.2 - - + -
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Residues in contact with GLU 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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73A ILE* 3.1 16.7 + - + +
74A PHE 3.9 1.1 - - - +
75A TYR 3.1 0.4 - - - -
76A ALA* 1.3 71.4 - - - +
78A LEU* 1.3 70.8 + - - +
79A ALA 2.9 1.6 - - - -
80A ARG* 3.0 15.3 + - - +
81A GLY 3.1 11.3 + - - -
278A ARG* 5.3 10.4 - - - +
294A MSE 3.4 42.0 - - + -
295A TYR* 3.8 24.1 - - + +
71D SER* 2.8 32.7 + - - +
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Residues in contact with LEU 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 PHE* 3.1 43.9 + - + +
75A TYR* 2.8 15.4 + - + +
77A GLU* 1.3 79.4 - - - +
79A ALA* 1.3 62.3 + - - +
81A GLY* 3.6 0.7 + - - -
82A ILE* 3.1 25.6 + - + +
123A MSE 4.3 18.4 - - + -
145A ALA* 4.3 10.8 - - + -
146A ALA* 4.3 3.4 - - + -
294A MSE 3.4 24.0 - - + +
295A TYR* 4.6 0.4 - - - +
297A ILE* 3.7 19.7 - - + -
298A GLY* 3.3 32.3 - - - +
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Residues in contact with ALA 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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65A VAL* 6.4 0.2 - - - -
67A ILE* 4.3 9.8 - - + +
70A ILE* 3.7 28.0 - - + -
75A TYR 2.5 17.0 + - - +
76A ALA 3.1 12.8 - - - +
78A LEU* 1.3 73.8 - - - +
80A ARG* 1.3 58.7 + - - +
82A ILE* 3.1 21.5 + - - +
83A GLU* 3.2 13.5 + - - +
95A LEU* 4.6 10.4 - - + +
70D ILE* 4.2 5.4 - - + -
95D LEU* 6.2 0.2 - - + -
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Residues in contact with ARG 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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76A ALA 3.0 11.9 + - - +
77A GLU* 3.0 10.1 + - - +
79A ALA* 1.3 69.6 - - - +
81A GLY* 1.3 67.2 + - - +
82A ILE 3.0 2.0 + - - -
83A GLU* 3.2 2.7 + - - -
84A ASP* 3.0 37.7 + - - +
295A TYR* 4.1 12.8 - - + -
68D PRO 3.9 1.0 + - - -
69D ASP* 2.9 29.7 + - - +
70D ILE* 3.9 7.8 - - + +
71D SER* 4.1 15.3 - - - -
97D ASN* 3.3 34.7 - - - +
99D ASP* 2.6 33.5 + - - -
17S ARG* 3.0 45.2 - - - +
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Residues in contact with GLY 81 (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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77A GLU 3.1 9.9 + - - -
78A LEU 4.1 0.4 - - - -
80A ARG* 1.3 77.9 - - - +
82A ILE* 1.3 62.8 + - - +
84A ASP* 3.7 1.0 - - - +
85A ILE* 3.4 13.5 + - - +
295A TYR* 3.4 42.9 - - - -
299A ALA* 3.2 23.1 - - - +
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Residues in contact with ILE 82 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
65A VAL* 4.4 13.2 - - + -
67A ILE* 6.3 0.2 - - + -
78A LEU 3.1 17.4 + - - +
79A ALA* 3.3 12.6 - - - +
80A ARG 3.0 0.8 - - - -
81A GLY* 1.3 74.3 - - - +
83A GLU* 1.3 68.7 + - - +
85A ILE* 3.1 3.8 + - - -
86A ALA* 2.8 20.1 + - - +
93A ILE* 3.9 14.8 - - + -
95A LEU* 6.3 0.2 - - + -
121A ILE* 3.8 12.8 - - + -
123A MSE 3.5 31.9 - - + -
298A GLY* 3.8 17.3 - - - +
302A MSE 3.0 41.6 - - + +
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Residues in contact with GLU 83 (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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79A ALA 3.2 8.2 + - - +
80A ARG* 3.2 9.6 + - - +
82A ILE* 1.3 77.7 - - - +
84A ASP* 1.3 60.2 + - - +
86A ALA* 2.9 7.5 + - - +
87A THR* 2.5 73.7 + - - +
91A TYR 4.8 3.1 - - - +
92A ASN* 5.7 0.2 - - - -
93A ILE* 4.8 15.3 + - + +
599A SO4 4.1 2.9 + - - -
70D ILE* 6.1 0.9 - - + -
95D LEU* 4.0 14.2 - - + +
96D SER* 4.0 18.3 + - - -
97D ASN* 3.1 46.8 + - - +
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Residues in contact with ASP 84 (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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80A ARG* 3.0 41.8 + - - +
81A GLY 3.7 3.6 - - - +
83A GLU* 1.3 83.3 - - - +
85A ILE* 1.3 63.1 + - + +
87A THR* 3.5 5.6 + - - +
88A MSE 2.9 28.2 + - - +
295A TYR* 2.7 30.0 + - - +
97D ASN* 5.7 0.5 - - - +
17S ARG* 4.0 11.1 + - - +
20S THR* 4.1 9.5 + - + +
24S GLN* 5.0 0.7 - - - +
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Residues in contact with ILE 85 (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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81A GLY 3.4 4.9 + - - +
82A ILE 3.1 4.6 + - - +
84A ASP* 1.3 74.1 - - + +
86A ALA* 1.3 64.2 + - - +
88A MSE 3.3 18.1 - - + +
89A TYR* 2.9 39.2 + - + +
299A ALA* 3.5 42.8 - - + +
302A MSE 3.9 7.1 - - + +
303A ARG* 3.8 24.0 - - + +
306A THR* 5.1 0.4 - - + +
20S THR* 3.2 35.4 - - + -
47S ILE* 3.7 11.9 - - + -
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Residues in contact with ALA 86 (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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82A ILE 2.8 13.1 + - - +
83A GLU* 3.3 9.4 - - - +
85A ILE* 1.3 73.5 - - - +
87A THR* 1.3 63.8 + - - +
89A TYR* 2.9 10.9 + - - -
90A LYS 3.0 0.2 + - - -
91A TYR* 2.7 47.4 + - + +
93A ILE* 3.4 29.6 - - + -
302A MSE 3.8 12.1 - - - +
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Residues in contact with THR 87 (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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83A GLU* 2.5 52.1 + - - +
84A ASP* 3.7 5.6 - - - +
86A ALA* 1.3 73.0 - - - +
88A MSE 1.3 56.3 + - - +
90A LYS* 2.7 26.5 + - - +
91A TYR 3.9 1.0 + - - -
599A SO4 3.3 30.9 + - - +
108D LEU* 6.2 1.3 - - + -
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Residues in contact with MSE 88 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
84A ASP 2.9 19.5 + - - +
85A ILE* 3.3 20.2 - - + +
87A THR* 1.3 77.7 - - - +
89A TYR* 1.3 76.4 + - + +
90A LYS* 3.3 6.1 + - - +
20S THR* 3.2 38.1 - - + +
23S VAL* 5.1 6.3 - - - +
24S GLN* 3.0 46.7 - - + +
27S SER* 6.5 0.9 - - - -
47S ILE* 4.3 9.2 - - + -
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Residues in contact with TYR 89 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
85A ILE* 2.9 39.3 + - + +
86A ALA 2.9 6.4 + - - +
88A MSE 1.3 103.5 - - + +
90A LYS* 1.3 75.1 + - - +
91A TYR* 3.3 15.6 - + + -
303A ARG* 2.8 46.1 + - - -
306A THR* 3.4 27.8 - - + -
310A ASN* 4.7 6.3 - - - -
45S LYS 5.3 4.5 + - - -
46S SEP 6.0 0.3 - - - -
47S ILE* 5.5 3.7 + - + +
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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
------------------------------------------------------------
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