Contacts of the helix formed by residues 72 - 86 (chain D) in PDB entry 2AAZ
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 PHE 72 (chain D).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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70D ARG* 4.1 2.7 + - - +
71D VAL* 1.3 72.6 - - - +
73D LEU* 1.3 66.4 + - - +
74D ARG* 3.7 35.2 - - + -
75D GLY* 3.0 37.6 + - - -
76D VAL* 3.1 13.9 + - - +
97D GLY 3.8 23.1 - - - -
98D VAL* 4.1 12.1 - - + -
100D ILE* 5.0 2.2 - - + -
226D PHE* 3.9 16.8 - + + -
2501D CB3 3.5 45.1 + - + +
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Residues in contact with LEU 73 (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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63D LEU* 4.5 7.9 - - + -
65D LEU* 4.1 30.7 - - + -
71D VAL 2.7 13.5 + - - +
72D PHE* 1.3 71.1 - - - +
74D ARG* 1.3 65.7 + - - +
76D VAL* 3.0 20.2 + - + +
77D ILE* 3.0 35.9 + - + +
233D LEU* 4.7 8.3 - - + -
300D PHE 5.9 0.4 - - - +
302D VAL* 3.5 40.6 - - + -
305D TYR* 5.4 6.5 - - + -
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Residues in contact with ARG 74 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
72D PHE* 3.3 28.9 - - + -
73D LEU* 1.3 79.1 - - - +
75D GLY* 1.3 56.1 - - - +
77D ILE* 3.5 9.6 + - - +
78D ALA* 2.9 31.1 + - + +
96D GLN* 2.8 32.4 + - - +
97D GLY* 4.2 7.7 + - - -
98D VAL* 4.1 11.5 - - + +
297D VAL* 4.5 21.0 - - + +
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Residues in contact with GLY 75 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
72D PHE* 3.0 35.1 + - - -
74D ARG* 1.3 76.2 - - - +
76D VAL* 1.3 65.4 + - - +
78D ALA* 3.9 0.9 - - - +
79D GLU* 3.0 26.3 + - - +
98D VAL* 3.9 17.8 - - - +
100D ILE* 4.5 0.2 - - - +
226D PHE* 3.9 8.9 - - - -
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Residues in contact with VAL 76 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
65D LEU* 5.2 0.4 - - + -
71D VAL* 4.3 8.7 - - + -
72D PHE 3.1 16.5 + - - +
73D LEU* 3.0 10.9 + - + +
75D GLY* 1.3 77.9 - - - +
77D ILE* 1.3 62.8 + - - +
79D GLU* 3.7 4.7 - - - +
80D LEU* 3.0 22.9 + - - +
226D PHE* 3.5 41.3 - - + +
229D ALA* 4.0 8.5 - - + -
230D SER* 3.6 36.6 + - - +
233D LEU* 3.9 14.4 - - + -
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Residues in contact with ILE 77 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
73D LEU* 3.0 43.3 + - + +
74D ARG* 3.8 7.4 - - - +
76D VAL* 1.3 77.2 - - - +
78D ALA* 1.3 64.4 + - - +
80D LEU* 3.2 6.8 + - - +
81D LEU* 3.0 33.6 + - + +
233D LEU* 4.0 15.0 - - + -
297D VAL* 4.1 18.8 - - + +
300D PHE* 3.6 58.6 - - + +
302D VAL* 5.2 0.4 - - + -
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Residues in contact with ALA 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 ARG* 2.9 23.9 + - + +
75D GLY 3.9 1.1 - - - +
77D ILE* 1.3 75.6 - - - +
79D GLU* 1.3 63.6 + - - +
81D LEU* 3.4 3.7 + - - +
82D TRP* 3.0 23.6 + - - +
93D LEU* 3.7 7.2 - - + +
96D GLN* 3.7 31.0 - - - +
98D VAL* 3.9 20.0 - - + -
297D VAL* 4.7 8.9 - - + +
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Residues in contact with GLU 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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75D GLY 3.0 19.7 + - - +
76D VAL* 3.7 5.1 - - - +
78D ALA* 1.3 75.2 - - - +
80D LEU* 1.3 56.6 + - - +
82D TRP* 3.1 15.4 - - + +
83D PHE* 2.9 60.1 + - + -
93D LEU* 4.0 7.1 - - + +
100D ILE* 3.6 18.9 - - + +
101D TRP* 2.8 25.9 + - + +
188D HIS* 5.3 1.2 + - - -
226D PHE* 4.2 9.5 - - - +
230D SER* 4.7 8.0 + - - -
2501D CB3 3.1 24.7 - - - +
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Residues in contact with LEU 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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76D VAL 3.0 16.6 + - - +
77D ILE* 3.2 6.3 + - - +
79D GLU* 1.3 75.3 + - - +
81D LEU* 1.3 59.5 - - + +
83D PHE* 3.1 18.3 + - + +
84D VAL* 3.0 35.7 + - + +
131D TRP* 4.5 7.0 - - + -
230D SER* 3.7 24.9 - - - +
233D LEU* 3.6 29.8 - - + -
234D LEU* 3.7 26.5 - - + +
237D MET* 3.5 30.7 - - - -
300D PHE* 5.0 3.6 - - + -
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Residues in contact with LEU 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 ILE* 3.0 21.5 + - + +
78D ALA* 4.0 3.8 - - - +
80D LEU* 1.3 77.0 - - + +
82D TRP* 1.3 57.3 + - - +
84D VAL* 3.7 6.9 - - + +
85D SER* 3.0 28.2 + - - -
237D MET* 3.8 20.0 - - + -
292D ILE 5.9 0.2 - - - +
295D PHE* 3.8 28.9 - - + +
296D LYS* 3.6 12.1 - - - +
297D VAL* 3.5 44.4 - - + +
300D PHE* 4.1 9.0 - - + -
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Residues in contact with TRP 82 (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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78D ALA 3.0 14.3 + - - +
79D GLU* 3.1 14.6 - - + +
81D LEU* 1.3 75.1 - - - +
83D PHE* 1.3 98.0 - + - +
85D SER* 2.5 22.9 + - - -
86D GLY 3.4 3.3 + - - -
87D CYS* 3.4 41.3 + - + +
88D THR* 3.7 22.9 - - - -
89D ASP 3.1 25.4 + - - -
90D ALA* 4.0 5.2 - - - -
92D MET* 4.1 13.2 - - + +
93D LEU* 3.7 24.4 - - + +
96D GLN* 5.8 0.7 - - - +
101D TRP* 3.7 22.7 - + - -
123D LEU* 3.5 24.9 - - + -
126D VAL* 4.7 8.3 - - + -
127D TYR* 5.3 0.4 - + - -
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Residues in contact with PHE 83 (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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79D GLU* 2.9 49.4 + - + -
80D LEU* 3.4 15.9 - - + +
82D TRP* 1.3 104.4 - + - +
84D VAL* 1.3 58.5 + - - +
86D GLY* 2.8 19.1 + - - -
87D CYS 5.1 0.2 - - - -
101D TRP* 4.7 0.2 - - - -
127D TYR* 3.5 43.1 - + + -
128D GLY* 3.1 21.8 - - - +
131D TRP* 3.5 35.3 - + + -
132D ARG* 4.5 0.9 - - - +
188D HIS* 3.7 22.7 - + - -
230D SER* 4.4 10.1 - - - -
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Residues in contact with VAL 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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80D LEU* 3.0 27.8 + - + +
81D LEU* 3.7 8.5 - - + +
82D TRP 3.3 0.2 - - - -
83D PHE* 1.3 80.6 - - - +
85D SER* 1.3 59.7 + - - +
86D GLY 3.1 1.2 + - - -
131D TRP* 4.6 8.1 - - + -
132D ARG* 2.7 32.3 + - - +
153D LEU* 3.8 28.7 - - + -
234D LEU* 4.6 5.4 - - + -
237D MET* 4.3 18.6 - - + -
292D ILE* 3.4 26.2 - - + +
293D ASP* 3.8 11.2 - - - +
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Residues in contact with SER 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 LEU 3.0 14.6 + - - -
82D TRP* 2.5 24.5 + - - -
84D VAL* 1.3 76.6 - - - +
86D GLY* 1.3 58.6 + - - +
87D CYS* 3.1 19.5 + - - +
132D ARG* 4.6 3.3 - - - +
133D HIS* 5.3 3.1 + - - -
293D ASP* 4.7 5.8 - - - -
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Residues in contact with GLY 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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83D PHE 2.8 10.9 + - - -
84D VAL 3.1 1.4 - - - -
85D SER* 1.3 77.7 + - - +
87D CYS* 1.3 63.1 + - - +
88D THR* 3.8 3.6 + - - +
128D GLY 3.3 25.5 - - - -
129D PHE* 3.7 17.8 + - - +
132D ARG* 4.0 9.9 - - - -
133D HIS* 4.7 8.6 - - - -
145D TYR* 5.9 1.7 - - - -
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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