Contacts of the helix formed by residues 70 - 90 (chain I) in PDB entry 4ADV
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 GLY 70 (chain I).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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1249A C 3.4 19.1 - - - -
1250A A 5.2 0.4 - - - -
1287A A 5.8 0.2 - - - -
1371A G 3.1 35.9 + - - -
1372A U 3.2 5.2 + - - -
69I GLY* 1.3 71.9 - - - -
71I ILE* 1.3 56.8 + - - +
73I GLY* 3.3 1.5 + - - +
74I GLN* 2.6 37.1 + - - +
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Residues in contact with ILE 71 (chain I).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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1248A A 3.7 17.5 - - + +
1249A C 3.8 9.7 + - + +
1289A A 3.4 35.4 - - + +
1290A G 5.3 4.0 - - - +
1371A G 4.2 0.2 + - - -
1372A U 3.5 5.2 + - - -
38I PHE* 3.7 28.0 - - + -
41I GLU* 4.1 29.8 - - + -
42I THR* 4.2 19.7 - - + +
44I ARG* 5.3 3.4 - - + -
70I GLY* 1.3 73.4 - - - +
72I SER* 1.3 72.4 + - - +
74I GLN* 3.5 1.2 - - - -
75I ALA* 2.7 25.3 + - + +
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Residues in contact with SER 72 (chain I).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
1347A G 5.2 2.7 - - - -
1372A U 2.9 33.6 + - - -
1373A G 2.6 31.8 + - - -
11I ARG* 4.9 3.1 - - - -
12I LYS* 4.8 3.6 - - - -
42I THR* 4.8 6.2 + - - +
71I ILE* 1.3 77.6 - - - +
73I GLY* 1.3 55.6 + - - -
75I ALA* 3.3 6.5 + - - +
76I GLY* 2.9 24.6 + - - -
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Residues in contact with GLY 73 (chain I).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
1372A U 2.8 16.2 + - - -
11I ARG* 3.7 20.5 - - - +
12I LYS* 4.7 10.5 - - - +
14I SER* 3.3 15.1 + - - -
70I GLY 3.7 3.1 - - - -
71I ILE 2.9 1.4 + - - -
72I SER* 1.3 68.5 - - - +
74I GLN* 1.3 52.4 + - - +
75I ALA 2.9 4.7 - - - -
76I GLY* 2.6 22.1 + - - -
77I ALA 2.7 15.6 + - - -
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Residues in contact with GLN 74 (chain I).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
1249A C 3.1 23.4 + - - -
1250A A 4.3 0.4 + - - -
14I SER* 3.4 7.2 + - - -
30I ASN* 4.3 0.2 - - - +
37I TYR* 2.6 27.3 + - + -
38I PHE* 3.9 9.9 - - + -
66I VAL* 3.2 46.8 - - + +
67I LYS* 4.1 1.6 + - - -
68I GLY 3.7 20.4 + - - +
69I GLY 2.8 19.8 + - - -
70I GLY 2.6 21.0 + - - +
71I ILE* 3.6 1.8 - - - +
73I GLY* 1.3 70.4 - - - -
75I ALA* 1.3 56.0 + - - +
77I ALA 4.0 0.8 + - - -
78I ILE* 3.2 26.2 + - - +
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Residues in contact with ALA 75 (chain I).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
38I PHE* 3.4 28.0 - - + -
44I ARG* 5.0 5.6 - - - -
46I VAL* 3.8 21.2 - - + +
47I VAL* 3.7 11.0 - - + +
71I ILE* 2.7 19.3 + - + +
72I SER* 3.5 6.7 - - - +
74I GLN* 1.3 77.0 - - - +
76I GLY* 1.3 64.0 + - - +
77I ALA 3.3 0.7 - - - -
78I ILE 3.7 0.2 + - - -
79I ARG* 3.3 19.8 + - - +
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Residues in contact with GLY 76 (chain I).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
11I ARG* 3.6 19.9 - - - +
46I VAL* 5.1 3.4 - - - -
72I SER 2.9 11.8 + - - -
73I GLY 2.6 14.0 + - - -
75I ALA* 1.3 69.2 - - - +
77I ALA* 1.3 61.9 + - - -
79I ARG* 3.4 12.2 + - - +
80I HIS* 3.1 21.0 + - - +
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Residues in contact with ALA 77 (chain I).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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9I GLY 3.6 0.9 - - - -
10I ARG* 3.4 24.9 - - - +
11I ARG* 3.5 1.2 - - - +
14I SER* 3.4 32.1 - - - -
15I ALA 4.3 0.7 - - - +
16I ALA* 3.2 19.7 - - + +
66I VAL* 4.6 0.7 - - + -
73I GLY 2.7 10.5 + - - +
74I GLN* 4.0 5.8 - - - +
76I GLY* 1.3 69.9 - - - +
78I ILE* 1.3 66.4 + - - +
80I HIS* 2.8 14.9 + - - +
81I GLY 2.9 10.9 + - - -
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Residues in contact with ILE 78 (chain I).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
16I ALA* 3.3 8.9 - - + +
18I VAL* 3.6 6.0 - - + +
29I ILE* 4.1 18.8 - - + -
38I PHE* 4.1 9.9 - - + -
47I VAL* 3.8 25.6 - - + -
64I ILE* 3.4 29.8 - - + -
66I VAL* 3.9 29.6 - - + -
74I GLN 3.2 19.1 - - - +
75I ALA 3.7 0.9 + - - +
77I ALA* 1.3 75.4 - - - +
79I ARG* 1.3 56.0 + - - +
81I GLY* 2.9 2.1 + - - -
82I ILE* 2.7 52.2 + - + +
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Residues in contact with ARG 79 (chain I).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
12G LEU* 6.2 2.0 - - - +
46I VAL* 3.1 44.2 - - - +
47I VAL* 4.8 2.2 - - - +
49I GLN* 3.1 25.2 - - - +
50I PRO* 3.7 13.9 - - + +
75I ALA 3.3 12.7 + - - +
76I GLY* 3.5 12.9 - - - +
77I ALA 3.2 0.2 - - - -
78I ILE* 1.3 79.4 - - - +
80I HIS* 1.3 57.3 + - - +
82I ILE* 4.0 5.0 - - - +
83I THR* 2.9 31.6 + - - +
100I ALA 5.6 0.2 + - - -
101I GLY 3.9 10.7 + - - -
102I PHE* 3.1 40.4 - - + +
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Residues in contact with HIS 80 (chain I).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
1118A U 5.6 0.2 - - - -
1179A A 5.3 1.5 + - - -
9I GLY* 3.4 21.1 - - - -
10I ARG* 3.5 21.8 - - + +
11I ARG* 5.8 0.4 - - + -
76I GLY 3.1 11.4 + - - +
77I ALA 2.8 10.2 + - - +
79I ARG* 1.3 75.5 - - - +
81I GLY* 1.3 60.0 + - - +
83I THR* 2.9 20.8 - - - +
84I ARG* 3.0 46.6 + - - +
102I PHE 2.9 18.3 + - - -
103I VAL 3.0 28.5 - - - -
104I THR 3.3 19.8 + - - -
105I ARG* 3.4 16.2 - - + +
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Residues in contact with GLY 81 (chain I).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
7I GLY* 3.3 26.6 - - - -
8I THR 3.3 11.9 - - - -
9I GLY* 3.3 4.4 - - - -
16I ALA* 4.6 1.8 - - - -
18I VAL* 4.5 3.4 - - - -
77I ALA 2.9 11.5 + - - -
78I ILE 3.4 2.2 - - - -
80I HIS* 1.3 77.6 - - - +
82I ILE* 1.3 50.8 + - - +
84I ARG* 3.2 4.0 - - - +
85I ALA* 2.7 35.5 + - - +
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Residues in contact with ILE 82 (chain I).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
18I VAL* 3.3 27.3 - - + +
20I ILE* 4.7 4.5 - - + -
27I ILE* 6.3 0.2 - - + -
47I VAL* 3.3 24.9 - - + +
50I PRO* 4.0 3.4 - - + -
51I LEU* 3.4 30.5 - - + -
62I LEU* 4.7 4.5 - - + -
64I ILE* 4.4 5.8 - - + -
78I ILE* 2.7 39.6 + - + +
79I ARG 4.0 3.1 - - - +
81I GLY* 1.3 67.5 - - - +
83I THR* 1.3 60.4 + - - +
85I ALA* 2.7 27.6 + - - +
86I LEU* 2.9 35.8 + - + +
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Residues in contact with THR 83 (chain I).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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50I PRO* 4.4 5.6 - - - +
79I ARG 2.9 17.1 + - - +
80I HIS* 2.9 32.5 - - - +
82I ILE* 1.3 79.9 - - - +
84I ARG* 1.3 65.7 + - - +
86I LEU* 3.3 15.2 + - - +
87I MET* 3.6 21.6 + - - +
97I LEU* 3.2 34.3 - - - +
102I PHE* 3.3 34.2 - - + +
103I VAL* 4.0 5.6 + - - +
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Residues in contact with ARG 84 (chain I).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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1118A U 3.0 38.2 + - - -
1119A C 3.0 15.4 + - - -
1179A A 5.1 7.7 + - - -
6I TYR 5.0 0.9 - - - +
7I GLY* 4.5 7.4 - - - -
8I THR* 4.1 4.2 - - - +
9I GLY* 3.1 33.1 - - - +
10I ARG* 5.9 0.2 - - - +
80I HIS* 3.0 48.8 + - - +
81I GLY* 3.2 6.3 - - - +
83I THR* 1.3 82.8 - - - +
85I ALA* 1.3 64.3 + - - +
87I MET* 3.2 31.0 - - + +
88I GLU* 3.9 4.5 + - - +
103I VAL* 4.1 11.3 + - - +
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Residues in contact with ALA 85 (chain I).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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5I TYR* 3.9 15.8 - - - +
6I TYR 4.0 11.0 - - - -
7I GLY* 4.1 8.3 - - - +
18I VAL 4.5 0.9 - - - +
20I ILE* 3.4 28.9 - - + -
81I GLY 2.7 17.5 + - - +
82I ILE* 2.7 12.1 + - - +
84I ARG* 1.3 67.5 - - - +
86I LEU* 1.3 56.0 + - - +
87I MET 3.0 1.3 - - - -
88I GLU* 2.7 36.1 + - - +
89I TYR 3.6 1.6 + - - -
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Residues in contact with LEU 86 (chain I).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
20I ILE* 3.6 30.7 - - + -
50I PRO* 4.5 17.3 - - + +
51I LEU* 5.3 3.6 - - + +
54I VAL* 5.5 9.4 - - + -
59I LYS* 6.5 1.1 - - - -
60I LEU* 4.7 13.7 - - + -
62I LEU* 5.3 0.2 - - + -
82I ILE* 2.9 45.5 + - + +
83I THR* 3.3 19.3 - - - +
84I ARG 3.5 0.2 - - - -
85I ALA* 1.3 70.9 - - - +
87I MET* 1.3 64.0 + - - +
88I GLU 2.9 1.4 + - - -
89I TYR* 3.0 21.6 + - + +
90I ASP 3.1 10.2 + - - +
93I LEU* 4.0 19.8 - - + +
97I LEU* 5.1 6.1 - - + -
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Residues in contact with MET 87 (chain I).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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1179A A 4.6 11.2 - - - +
83I THR 3.6 12.7 + - - +
84I ARG* 3.2 27.5 + - + +
85I ALA 2.9 0.4 + - - -
86I LEU* 1.3 78.3 - - - +
88I GLU* 1.3 55.2 + - - +
90I ASP 2.8 26.7 - - - +
91I GLU* 2.8 33.5 + - - +
93I LEU* 3.7 13.6 - - + +
94I ARG* 3.2 57.9 - - + +
97I LEU* 5.0 1.1 - - - -
103I VAL* 4.0 21.8 - - + -
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Residues in contact with GLU 88 (chain I).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
5I TYR* 3.0 22.9 - - + +
6I TYR* 2.6 48.0 + - - +
84I ARG 3.9 3.3 + - - +
85I ALA 2.7 16.9 + - - +
87I MET* 1.3 71.7 - - - +
89I TYR* 1.3 61.6 + - - +
90I ASP* 3.0 6.9 + - - -
91I GLU* 4.2 11.1 + - + +
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Residues in contact with TYR 89 (chain I).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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5I TYR* 3.2 49.1 - + + -
20I ILE* 5.2 3.4 - - + -
22I PRO* 5.5 11.8 - - + +
59I LYS* 5.1 7.6 - - + -
60I LEU* 4.3 25.4 - - + -
85I ALA 3.6 1.4 + - - -
86I LEU* 3.0 15.3 + - + +
88I GLU* 1.3 78.3 - - - +
90I ASP* 1.3 63.6 + - + +
93I LEU* 6.3 0.4 - - + -
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Residues in contact with ASP 90 (chain I).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
86I LEU 3.1 3.4 + - - +
87I MET* 2.8 10.7 - - - +
88I GLU 3.0 0.6 - - - -
89I TYR* 1.3 87.2 - - + +
91I GLU* 1.3 58.7 + - - +
92I SER* 3.0 30.8 + - - +
93I LEU* 3.0 42.9 - - + +
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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) + - + + + + + -
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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