Contacts of the helix formed by residues 75 - 97 (chain P) in PDB entry 2AIZ
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 THR 75 (chain P).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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74P GLY* 1.3 82.0 - - - +
76P PRO* 1.4 65.1 - - + -
77P GLU* 4.4 7.6 - - - +
78P TYR* 2.7 23.0 + - - +
79P ASN* 2.6 43.5 + - - +
111P GLU* 3.1 5.7 + - - +
102U UDP 5.6 1.2 + - - -
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Residues in contact with PRO 76 (chain P).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
75P THR* 1.4 88.3 - - + +
77P GLU* 1.3 57.5 + - + +
79P ASN* 3.2 6.9 - - + +
80P ILE* 2.5 50.2 + - + +
109P TYR 6.3 0.2 - - - -
110P GLY* 5.3 0.7 - - - +
111P GLU* 3.4 29.8 - - + +
112P GLU* 4.4 13.5 - - + +
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Residues in contact with GLU 77 (chain P).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
75P THR* 3.0 6.6 + - - +
76P PRO* 1.3 80.3 - - + +
78P TYR* 1.3 58.2 + - - +
80P ILE* 3.8 9.9 - - - +
81P ALA* 3.0 29.5 + - - +
102U UDP 5.5 12.3 + - - +
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Residues in contact with TYR 78 (chain P).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
37P ASP* 3.6 12.3 + - - -
74P GLY* 5.4 3.1 - - - -
75P THR* 2.7 31.9 + - - +
77P GLU* 1.3 73.5 - - - +
79P ASN* 1.3 69.2 - - - +
81P ALA* 3.7 2.9 - - - +
82P LEU* 3.1 30.2 + - + +
4U DGL 2.9 41.5 - - - +
5U 6CL 2.7 52.8 + - + +
102U UDP 2.9 47.1 - - - +
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Residues in contact with ASN 79 (chain P).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
70P THR* 3.8 14.1 + - - +
71P ASP 3.1 25.6 + - - -
73P ARG 3.2 17.8 + - - -
74P GLY* 4.7 0.2 - - - -
75P THR 2.6 38.1 + - - +
76P PRO* 3.2 1.6 - - + +
78P TYR* 1.3 68.1 - - - +
80P ILE* 1.3 70.1 + - - +
81P ALA 2.9 1.1 - - - -
82P LEU* 2.6 21.0 + - - -
83P GLY* 2.8 11.0 + - - -
108P SER* 4.3 1.3 - - - -
110P GLY* 3.7 18.4 - - - -
111P GLU* 3.0 19.9 + - - +
5U 6CL 4.2 9.9 + - - +
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Residues in contact with ILE 80 (chain P).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
76P PRO* 2.5 34.9 + - + +
77P GLU* 3.8 14.6 - - + +
79P ASN* 1.3 71.8 - - - +
81P ALA* 1.3 58.5 + - + +
84P GLN* 2.6 44.5 + - + +
108P SER* 2.7 48.7 + - - +
109P TYR* 4.8 2.5 - - - -
110P GLY* 4.8 2.0 - - - +
112P GLU* 5.8 5.2 - - + +
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Residues in contact with ALA 81 (chain P).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
77P GLU 3.0 19.0 + - - +
78P TYR* 3.7 4.5 - - - +
79P ASN 2.6 4.6 + - - -
80P ILE* 1.3 79.2 - - + +
82P LEU* 1.3 68.6 + - + +
83P GLY 3.1 0.2 + - - -
84P GLN* 3.8 3.8 - - - -
85P ARG* 2.9 38.1 + - - +
102U UDP 5.3 8.3 - - - +
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Residues in contact with LEU 82 (chain P).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
37P ASP* 3.5 49.1 - - - +
38P LYS 4.7 2.0 - - - +
39P TYR* 5.1 8.3 - - + -
70P THR* 5.6 4.9 - - + +
78P TYR* 3.1 30.4 + - + +
79P ASN* 2.6 15.2 + - - +
81P ALA* 1.3 76.3 - - + +
83P GLY* 1.3 58.4 + - - +
85P ARG* 3.6 28.0 + - - +
86P ARG* 3.0 42.6 + - + +
5U 6CL 5.4 2.5 - - + -
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Residues in contact with GLY 83 (chain P).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
68P GLY* 5.6 7.1 - - - -
70P THR* 4.8 9.5 - - - +
79P ASN 2.8 17.7 + - - -
80P ILE 3.8 0.9 - - - -
82P LEU* 1.3 69.9 - - - +
84P GLN* 1.3 64.9 + - - +
85P ARG 2.9 1.8 - - - -
86P ARG* 2.7 17.8 + - - +
87P ALA* 2.7 24.4 + - - +
107P VAL 5.4 0.4 - - - -
108P SER* 4.7 10.1 - - - -
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Residues in contact with GLN 84 (chain P).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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80P ILE* 2.6 29.0 + - + +
81P ALA* 3.8 4.5 - - - +
83P GLY* 1.3 70.1 - - - +
85P ARG* 1.3 62.0 + - + +
87P ALA* 3.3 9.8 - - - +
88P ASP* 2.9 38.9 + - - +
106P THR* 4.4 18.3 + - - +
107P VAL* 5.2 8.3 - - - +
108P SER* 4.2 9.0 - - - -
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Residues in contact with ARG 85 (chain P).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
39P TYR* 2.8 47.4 + - + +
81P ALA* 2.9 33.8 - - - +
82P LEU* 3.7 27.5 - - - +
83P GLY 2.8 1.2 + - - -
84P GLN* 1.3 78.6 - - - +
86P ARG* 1.3 58.4 + - - +
87P ALA 3.0 1.1 - - - -
88P ASP* 2.6 30.1 + - - +
89P ALA 2.9 3.1 + - - -
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Residues in contact with ARG 86 (chain P).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
34P PHE* 3.1 52.5 - - + +
35P GLY 3.1 25.7 + - - -
37P ASP* 4.4 3.0 - - - +
38P LYS 2.5 31.9 + - - +
39P TYR* 3.7 24.7 - - + -
69P ASN 5.4 1.0 - - - +
70P THR* 2.8 32.1 - - - +
82P LEU* 3.0 28.6 - - + +
83P GLY* 2.7 17.0 + - - +
85P ARG* 1.3 72.5 - - - +
87P ALA* 1.3 57.9 + - - +
89P ALA* 2.8 25.4 + - - +
90P VAL* 3.2 11.1 + - - +
128P ARG* 4.7 2.0 - - - +
129P ARG 5.0 4.9 - - - +
130P ALA* 6.0 1.2 - - - +
5U 6CL 5.7 0.2 + - - -
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Residues in contact with ALA 87 (chain P).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
66P VAL* 4.7 17.2 - - + +
68P GLY* 5.7 4.0 - - - +
83P GLY 2.7 15.7 + - - +
84P GLN* 3.3 15.0 - - - +
86P ARG* 1.3 72.6 - - - +
88P ASP* 1.3 56.7 + - - +
89P ALA 3.3 0.2 + - - -
90P VAL* 3.3 5.2 + - - +
91P LYS* 2.8 31.2 + - - +
106P THR* 3.6 27.0 - - + +
107P VAL 4.7 8.7 - - - +
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Residues in contact with ASP 88 (chain P).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
39P TYR* 4.2 5.6 - - - +
84P GLN* 2.9 32.1 + - - +
85P ARG* 2.6 22.1 + - - +
87P ALA* 1.3 72.5 - - - +
89P ALA* 1.3 54.5 + - - +
91P LYS* 3.1 34.9 + - - +
92P GLY* 2.9 25.8 + - - -
106P THR* 4.9 3.1 - - - -
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Residues in contact with ALA 89 (chain P).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
34P PHE* 6.3 1.1 - - + -
39P TYR* 3.8 26.9 + - + +
40P ASP* 6.2 1.6 - - - -
41P ILE* 4.6 15.2 - - + +
85P ARG 2.9 4.2 + - - -
86P ARG* 2.8 17.0 + - - +
88P ASP* 1.3 79.2 - - - +
90P VAL* 1.3 54.7 + - - +
92P GLY* 3.9 1.2 - - - -
93P TYR* 3.0 25.8 + - - +
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Residues in contact with VAL 90 (chain P).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
32P VAL* 5.6 4.7 - - + -
34P PHE* 4.8 8.5 - - + -
41P ILE* 3.6 26.5 - - + -
49P LEU* 3.8 31.4 - - + -
66P VAL* 4.5 22.0 - - + -
86P ARG 3.2 12.0 + - - +
87P ALA* 3.3 4.5 + - - +
89P ALA* 1.3 73.2 - - - +
91P LYS* 1.3 66.1 + - - +
93P TYR* 3.0 21.2 + - - +
94P LEU* 3.2 19.7 + - + +
130P ALA* 6.1 2.2 - - + -
132P LEU* 4.7 8.7 - - + -
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Residues in contact with LYS 91 (chain P).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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66P VAL* 4.8 4.8 - - + +
87P ALA 2.8 13.2 + - - +
88P ASP* 3.1 42.0 + - - +
90P VAL* 1.3 76.9 - - - +
92P GLY* 1.3 72.7 + - - +
95P ALA* 3.1 22.4 + - + +
101P ALA* 5.2 9.6 - - - -
104P LEU* 3.2 47.6 - - + +
106P THR* 3.6 22.4 - - + -
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Residues in contact with GLY 92 (chain P).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
88P ASP 2.9 18.5 + - - -
89P ALA 3.9 1.1 - - - -
91P LYS* 1.3 80.5 - - - +
93P TYR* 1.3 59.3 + - - +
95P ALA* 3.2 10.4 - - - +
96P GLY* 2.8 26.2 + - - -
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Residues in contact with TYR 93 (chain P).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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41P ILE* 4.9 7.4 - - + -
46P VAL* 3.8 22.9 - - + +
49P LEU* 3.6 39.9 - - + +
50P ASP* 5.3 3.3 + - - +
89P ALA 3.0 14.6 + - - +
90P VAL* 3.0 15.2 + - + +
92P GLY* 1.3 76.2 - - - +
94P LEU* 1.3 66.8 + - + +
96P GLY* 2.9 13.4 + - - -
97P LYS* 3.2 45.1 + - + +
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Residues in contact with LEU 94 (chain P).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
49P LEU* 3.3 34.5 - - + +
52P HIS* 4.9 4.5 - - + -
53P ALA* 3.5 20.4 - - + +
56P LEU* 4.3 6.7 - - + -
64P VAL* 3.5 34.5 - - + -
66P VAL* 5.8 0.4 - - + -
90P VAL* 3.2 18.8 + - + +
93P TYR* 1.3 81.6 - - + +
95P ALA* 1.3 59.2 - - - +
97P LYS* 3.1 15.0 + - + +
99P VAL* 3.0 39.1 + - + +
104P LEU* 3.8 16.6 - - + -
132P LEU* 5.0 5.6 - - + -
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Residues in contact with ALA 95 (chain P).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
91P LYS* 3.1 19.1 + - + +
92P GLY* 3.2 18.4 - - - +
93P TYR 3.0 0.4 - - - -
94P LEU* 1.3 77.2 - - - +
96P GLY* 1.3 59.3 + - - +
98P GLY* 3.1 13.9 + - - -
99P VAL 3.3 16.1 + - - +
101P ALA* 5.8 2.2 - - + +
104P LEU* 3.9 11.4 - - + +
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Residues in contact with GLY 96 (chain P).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
92P GLY 2.8 14.9 + - - -
93P TYR 2.9 4.2 + - - -
95P ALA* 1.3 76.7 - - - +
97P LYS* 1.3 61.2 + - - +
98P GLY* 3.1 1.5 + - - -
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Residues in contact with LYS 97 (chain P).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
50P ASP* 3.9 22.7 + - - +
53P ALA* 3.1 35.8 - - + +
54P ALA* 4.7 1.4 - - - +
57P ASN* 4.5 8.3 + - - -
93P TYR* 3.3 44.9 - - + +
94P LEU* 3.1 13.3 + - + +
96P GLY* 1.3 76.2 - - - +
98P GLY* 1.3 57.4 + - - +
99P VAL* 3.6 6.1 - - + -
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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
------------------------------------------------------------
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) + - + + + + + -
------------------------------------------------------------
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