Contacts of the helix formed by residues 72 - 89 (chain D) 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 D).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
278A ARG* 5.7 4.4 - - - +
69D ASP* 2.9 20.4 + - + +
71D SER* 1.3 76.0 - - - +
73D ILE* 1.3 76.3 + - - +
74D PHE* 2.7 33.2 + - - +
75D TYR* 2.9 35.1 + - + +
76D ALA* 2.9 10.2 + - - +
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Residues in contact with ILE 73 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
71A SER 3.9 19.5 - - - +
73A ILE* 3.5 37.5 - - + +
76A ALA* 5.4 0.7 - - + -
278A ARG* 5.9 4.3 - - - +
282A MSE 6.4 2.0 - - + -
71D SER 3.3 6.1 + - - +
72D ASN* 1.3 88.9 - - - +
74D PHE* 1.3 57.1 + - + +
76D ALA* 3.7 9.0 - - + -
77D GLU* 3.0 34.3 + - + +
249D GLU* 6.0 2.7 - - - +
277D THR* 5.0 18.2 - - + -
279D LEU* 6.0 6.5 - - + -
294D MSE 5.2 0.8 - - - +
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Residues in contact with PHE 74 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
72D ASN* 2.7 20.7 + - - +
73D ILE* 1.3 81.6 - - + +
75D TYR* 1.3 98.1 + + - +
77D GLU 3.6 0.2 + - - -
78D LEU* 3.3 20.7 + - + +
146D ALA* 4.3 18.8 - - + -
161D TYR* 6.5 0.2 - + - -
275D ASP* 4.1 20.4 - - - +
292D GLN* 3.5 24.5 - - - -
294D MSE 3.1 50.9 - - + +
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Residues in contact with TYR 75 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
67D ILE* 3.5 26.0 - - + +
68D PRO* 3.5 37.7 - - + -
69D ASP* 3.9 11.7 - - + +
72D ASN* 2.9 32.0 + - + +
74D PHE* 1.3 105.9 - + - +
76D ALA* 1.3 54.9 + - - +
78D LEU* 3.3 9.5 + - + +
79D ALA* 2.4 36.2 + - - +
100D GLN* 3.7 17.0 + - - -
123D MSE 4.5 18.8 - - + -
124D SER 5.3 2.2 - - - -
125D GLY* 5.3 2.6 + - - -
146D ALA* 5.8 4.0 - - + -
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Residues in contact with ALA 76 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
70A ILE* 3.4 26.2 - - - +
71A SER* 4.4 4.0 - - - +
76A ALA* 4.2 4.7 - - + -
70D ILE* 3.5 26.6 + - + +
72D ASN 2.9 12.5 + - - +
73D ILE* 3.9 10.3 - - - +
75D TYR* 1.3 75.1 - - - +
77D GLU* 1.3 59.8 + - - +
79D ALA* 3.1 10.7 + - - +
80D ARG* 2.8 27.2 + - - +
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Residues in contact with GLU 77 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
71A SER* 4.3 23.4 + - - +
73D ILE* 3.0 21.1 + - + +
74D PHE 3.9 3.6 - - - +
76D ALA* 1.3 71.5 - - - +
78D LEU* 1.3 60.7 + - - +
80D ARG* 2.7 28.2 + - - +
81D GLY* 2.8 10.4 + - - -
278D ARG* 3.8 31.8 + - + -
294D MSE 4.1 24.1 - - + +
295D TYR* 3.3 41.3 + - - +
16Y ALA* 5.0 0.3 - - - +
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Residues in contact with LEU 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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74D PHE* 3.3 16.8 + - + +
75D TYR* 3.5 17.3 - - + +
77D GLU* 1.3 80.0 - - - +
79D ALA* 1.3 53.7 + - - +
81D GLY* 2.6 24.9 + - - +
82D ILE* 3.2 4.8 + - + +
123D MSE 3.2 44.4 - - + -
145D ALA* 4.4 6.3 - - + -
146D ALA* 3.6 30.5 - - + -
294D MSE 3.5 22.8 + - + +
295D TYR* 4.3 0.7 - - - +
297D ILE* 4.7 1.1 - - + -
298D GLY* 3.3 25.8 - - - +
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Residues in contact with ALA 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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70A ILE* 4.7 6.1 - - + -
67D ILE* 4.0 10.8 - - + -
70D ILE* 3.8 18.2 - - + -
75D TYR 2.4 32.0 + - - +
76D ALA* 3.1 13.2 - - - +
78D LEU* 1.3 69.2 - - - +
80D ARG* 1.3 62.1 + - - +
82D ILE* 3.5 15.7 + - - +
83D GLU* 3.3 20.3 + - - +
93D ILE* 5.0 5.0 - - - +
95D LEU* 4.9 10.7 - - + +
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Residues in contact with ARG 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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69A ASP* 3.1 33.6 + - - +
70A ILE* 4.1 7.9 - - + -
71A SER* 3.7 15.9 - - - +
97A ASN* 3.1 43.3 + - - +
99A ASP* 2.8 26.5 + - - -
104A LYS* 5.3 2.2 - - - +
76D ALA 2.8 12.5 + - - +
77D GLU* 2.7 12.2 + - - +
79D ALA* 1.3 73.8 - - - +
81D GLY* 1.3 63.8 + - - +
82D ILE 3.4 0.2 - - - -
83D GLU* 3.9 3.6 - - - -
84D ASP* 3.2 55.6 + - - +
295D TYR* 4.0 12.3 - - + -
17Y ARG* 3.6 22.4 - - + +
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Residues in contact with GLY 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 GLU 2.8 7.1 + - - -
78D LEU 2.6 17.7 + - - -
80D ARG* 1.3 71.7 - - - +
82D ILE* 1.3 64.3 + - - +
84D ASP* 3.7 1.9 + - - +
85D ILE* 3.5 13.5 + - - +
295D TYR* 3.7 33.0 - - - -
298D GLY 3.6 6.7 - - - -
299D ALA* 3.6 13.9 - - - +
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Residues in contact with ILE 82 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
63D VAL* 4.4 4.7 - - + -
65D VAL* 4.0 23.1 - - + -
78D LEU* 3.2 10.8 + - + +
79D ALA* 3.7 11.0 - - - +
80D ARG 3.4 0.2 - - - -
81D GLY* 1.3 77.6 - - - +
83D GLU* 1.3 53.9 + - - +
86D ALA* 2.6 37.9 + - - +
93D ILE* 4.1 18.4 - - + -
95D LEU* 5.9 0.4 - - + -
121D ILE* 3.7 22.0 - - + -
123D MSE 3.1 35.2 - - + -
298D GLY* 3.7 9.0 - - - +
302D MSE 2.9 33.4 - - + +
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Residues in contact with GLU 83 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
70A ILE* 5.9 0.9 - - + -
95A LEU* 3.9 9.8 - - + +
96A SER* 2.7 30.0 + - - -
97A ASN* 3.1 33.8 + - - +
104A LYS* 4.7 2.9 + - - -
946A SO4 4.2 1.4 + - - -
79D ALA 3.3 13.8 + - - +
80D ARG* 3.9 6.3 - - - +
81D GLY 3.3 0.4 - - - -
82D ILE* 1.3 81.0 - - - +
84D ASP* 1.3 60.5 + - - +
86D ALA* 4.4 4.3 - - - -
87D THR* 2.6 67.3 + - - -
91D TYR 5.3 1.0 - - - +
93D ILE* 3.8 25.7 + - + +
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Residues in contact with ASP 84 (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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104A LYS* 5.0 6.1 + - - -
80D ARG* 3.2 45.3 + - - +
81D GLY 4.1 3.1 - - - +
82D ILE 3.4 0.2 - - - -
83D GLU* 1.3 83.6 - - - +
85D ILE* 1.3 59.3 + - - +
87D THR* 3.9 3.6 - - - +
88D MSE 3.0 27.4 + - - +
295D TYR* 2.6 33.5 + - - +
17Y ARG* 3.2 22.8 + - - -
20Y THR* 4.2 10.7 - - + +
24Y GLN* 4.9 0.5 - - - +
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Residues in contact with ILE 85 (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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81D GLY 3.5 5.0 + - - +
82D ILE 3.3 1.9 + - - +
84D ASP* 1.3 76.5 - - - +
86D ALA* 1.3 72.5 + - - +
87D THR 3.2 0.2 - - - -
88D MSE 3.0 7.1 + - - +
89D TYR* 2.8 32.5 + - + +
299D ALA* 3.5 27.8 - - + +
302D MSE 3.1 30.7 - - + +
303D ARG* 3.5 14.6 - - - +
306D THR* 4.8 1.8 - - + +
20Y THR* 3.4 34.1 - - + -
47Y ILE* 3.2 30.7 - - + -
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Residues in contact with ALA 86 (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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82D ILE 2.6 23.4 + - - +
83D GLU 4.0 1.6 - - - +
85D ILE* 1.3 76.2 - - - +
87D THR* 1.3 64.6 + - - +
89D TYR* 3.0 9.9 + - - +
91D TYR* 2.8 40.8 + - + +
93D ILE* 3.9 18.8 - - + -
302D MSE 3.3 27.1 - - - -
306D THR* 6.4 0.4 - - - -
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Residues in contact with THR 87 (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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104A LYS* 4.3 26.0 - - - +
946A SO4 3.0 33.9 + - - +
83D GLU* 2.6 50.4 + - - -
84D ASP* 3.9 4.3 - - - +
86D ALA* 1.3 74.6 - - - +
88D MSE 1.3 63.0 + - - +
90D LYS* 3.0 14.2 + - - -
91D TYR 3.8 5.4 + - - +
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Residues in contact with MSE 88 (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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84D ASP 3.0 21.2 + - - +
85D ILE* 3.3 7.4 - - + +
87D THR* 1.3 78.8 - - - +
89D TYR* 1.3 83.0 + - + +
90D LYS* 3.3 3.8 + - - +
20Y THR* 3.3 29.8 - - - +
23Y VAL* 5.0 4.5 - - + -
24Y GLN* 3.1 60.5 - - + +
27Y SER* 5.9 2.0 - - - -
47Y ILE* 3.7 20.4 - - + -
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Residues in contact with TYR 89 (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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85D ILE* 2.8 28.7 + - + +
86D ALA* 3.2 4.7 - - - +
88D MSE 1.3 98.0 - - + +
90D LYS* 1.3 78.7 + - - +
91D TYR* 2.8 13.7 - + + -
303D ARG* 2.7 54.3 + - - -
306D THR* 3.5 27.1 - - + -
45Y LYS 4.9 8.1 + - - -
46Y SEP 5.4 1.2 + - - -
47Y ILE* 4.0 9.8 - - + +
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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