Contacts of the helix formed by residues 50 - 71 (chain Y) in PDB entry 5M32
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 ALA 50 (chain Y).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
48Y GLY 3.2 0.6 - - - -
49Y ALA* 1.3 76.3 - - - +
51Y ASP* 1.3 61.8 + - - +
52Y CYS 3.5 0.2 - - - -
53Y SER* 4.2 1.7 - - - -
54Y PHE* 2.9 32.0 + - - +
97Z TYR* 3.8 6.1 - - + -
125Z ASP* 4.2 1.4 + - - -
127Z VAL* 3.5 45.1 - - + +
128Z GLY 3.3 22.5 - - - +
129Z SER* 3.2 5.5 + - - +
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Residues in contact with ASP 51 (chain Y).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
48Y GLY* 2.7 21.3 + - - +
50Y ALA* 1.3 72.3 - - - +
52Y CYS* 1.3 57.7 + - - +
54Y PHE* 3.2 2.3 + - - +
55Y TRP* 2.9 38.3 + - - -
95Y LEU* 3.6 21.3 - - + -
96Y SER* 3.9 25.6 + - - +
97Y MET* 4.9 1.6 - - + -
97Z TYR* 3.4 10.3 + - - -
100Z ARG* 2.6 50.8 + - - -
127Z VAL* 5.9 0.2 - - - -
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Residues in contact with CYS 52 (chain Y).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
45Y MET* 3.6 26.0 - - + -
46Y ALA 4.5 1.1 - - - +
47Y GLY 3.8 14.6 + - - +
48Y GLY 3.0 19.9 + - - -
49Y ALA* 3.7 5.4 - - - -
51Y ASP* 1.3 76.9 - - - +
53Y SER* 1.3 65.7 + - - +
56Y GLU* 2.8 42.1 + - - +
97Y MET* 4.2 21.5 - - + +
98Y GLY 5.4 0.2 - - - +
4u 6VA 3.5 31.2 - - - -
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Residues in contact with SER 53 (chain Y).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
35Y ILE* 5.4 6.9 - - - +
45Y MET* 3.6 18.4 - - - +
49Y ALA 3.3 19.9 + - - -
50Y ALA* 3.7 3.8 + - - -
51Y ASP 3.3 0.4 - - - -
52Y CYS* 1.3 81.2 - - - +
54Y PHE* 1.3 58.3 + - - +
56Y GLU* 4.8 1.0 - - - +
57Y ARG* 2.9 30.1 + - - +
128Z GLY 5.3 2.9 - - - -
129Z SER* 5.0 6.5 - - - -
130Z TYR* 5.6 5.7 - - - -
4u 6VA 5.3 1.6 - - - -
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Residues in contact with PHE 54 (chain Y).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
101R PHE* 3.4 32.9 - + - -
50Y ALA 2.9 20.8 + - - +
51Y ASP 3.6 2.5 - - - +
53Y SER* 1.3 79.4 - - - +
55Y TRP* 1.3 76.6 + + - +
57Y ARG* 3.4 5.1 - - + +
58Y LEU* 2.8 47.4 + - + +
93Z SER* 6.1 0.7 - - - -
94Z THR* 4.1 18.4 - - - -
97Z TYR* 3.4 49.6 - + + -
98Z SER* 6.3 0.4 - - - -
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Residues in contact with TRP 55 (chain Y).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
51Y ASP 2.9 32.4 + - - +
52Y CYS 4.3 0.2 - - - +
54Y PHE* 1.3 86.8 - + - +
56Y GLU* 1.3 62.5 + - - +
58Y LEU* 3.5 28.1 - - + +
59Y LEU* 2.9 26.0 + - - +
83Y LEU* 3.9 14.0 - - + +
86Y MET* 3.6 35.6 - - + +
87Y VAL* 3.9 9.9 - - + -
90Y TYR* 3.5 43.5 - + - -
95Y LEU* 3.5 18.7 - - + +
97Y MET* 3.9 26.9 - - + -
97Z TYR* 3.2 25.6 + + - -
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Residues in contact with GLU 56 (chain Y).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
35Y ILE* 4.1 23.7 - - + +
37Y ILE* 4.1 8.2 - - + +
43Y GLY* 4.7 13.0 - - - -
44Y THR 3.0 23.6 - - - +
45Y MET* 3.3 8.5 - - - +
52Y CYS* 2.8 33.5 + - - +
55Y TRP* 1.3 75.6 - - - +
57Y ARG* 1.3 61.4 + - - +
59Y LEU* 3.7 16.5 - - + +
60Y ALA* 3.0 26.7 + - - +
83Y LEU* 4.0 2.9 - - - +
97Y MET* 3.4 13.7 - - - +
99Y THR* 3.2 31.7 - - - +
101Y ILE* 4.8 2.5 - - + -
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Residues in contact with ARG 57 (chain Y).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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100R TRP* 2.8 61.8 + - - -
101R PHE* 3.5 36.8 + - + +
104R ASN* 3.1 38.7 + - - +
35Y ILE* 5.0 4.3 - - - +
53Y SER* 2.9 23.9 + - - +
54Y PHE* 3.4 8.3 - - + +
56Y GLU* 1.3 76.6 - - - +
58Y LEU* 1.3 58.3 + - - +
60Y ALA* 3.0 20.6 + - - +
61Y ARG 3.1 9.5 + - - -
90Z ALA* 5.6 0.2 - - - +
130Z TYR* 4.6 7.6 + - - -
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Residues in contact with LEU 58 (chain Y).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
101R PHE* 3.7 22.6 - - + -
54Y PHE* 2.8 31.6 + - + +
55Y TRP* 3.5 36.1 - - + +
57Y ARG* 1.3 70.4 - - - +
59Y LEU* 1.3 61.1 + - - +
61Y ARG* 3.2 43.3 + - - +
62Y GLN* 2.9 31.3 + - + +
86Y MET* 4.2 11.9 - - + -
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Residues in contact with LEU 59 (chain Y).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
37Y ILE* 3.7 32.3 - - + -
55Y TRP 2.9 17.8 + - - +
56Y GLU* 3.7 11.2 - - + +
57Y ARG 3.3 0.2 - - - -
58Y LEU* 1.3 75.9 - - - +
60Y ALA* 1.3 58.4 + - - +
62Y GLN* 4.0 5.9 - - - +
63Y CYS* 2.9 32.0 + - + +
79Y ALA* 4.0 26.2 - - + +
82Y LEU* 4.6 9.6 - - + -
83Y LEU* 3.6 43.3 - - + -
86Y MET* 5.4 2.6 - - - -
101Y ILE* 3.9 17.7 - - + -
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Residues in contact with ALA 60 (chain Y).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
97R GLN* 4.8 0.5 + - - -
100R TRP* 4.2 22.5 - - + -
35Y ILE* 5.4 2.2 - - + -
37Y ILE* 4.0 27.7 - - + +
56Y GLU 3.0 15.7 + - - +
57Y ARG* 3.0 11.9 + - - +
59Y LEU* 1.3 78.3 - - - +
61Y ARG* 1.3 61.0 + - - +
63Y CYS* 3.3 11.6 - - - -
64Y ARG* 3.0 24.9 + - - +
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Residues in contact with ARG 61 (chain Y).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
94R VAL* 4.7 10.9 + - - +
97R GLN* 3.3 45.0 - - + +
98R ASN* 3.4 29.6 + - - +
100R TRP* 4.5 3.7 - - + -
101R PHE* 3.7 17.1 - - + -
57Y ARG 3.1 12.2 + - - +
58Y LEU* 3.2 33.0 + - - +
60Y ALA* 1.3 76.6 - - - +
62Y GLN* 1.3 84.8 + - - +
64Y ARG* 3.2 3.8 + - - +
65Y ILE* 3.0 41.2 + - + +
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Residues in contact with GLN 62 (chain Y).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
58Y LEU* 2.9 22.4 + - + +
59Y LEU 4.0 1.3 - - - +
61Y ARG* 1.3 112.4 - - - +
63Y CYS* 1.3 58.5 - - - +
65Y ILE* 3.3 14.1 + - - +
66Y TYR* 3.0 25.5 + - - +
82Y LEU* 4.0 25.2 - - + +
86Y MET* 4.2 23.0 - - + +
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Residues in contact with CYS 63 (chain Y).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
37Y ILE* 4.1 29.6 - - + -
38Y ASN* 5.0 6.3 - - - -
59Y LEU* 2.9 25.4 + - + +
60Y ALA* 3.3 20.9 - - - -
62Y GLN* 1.3 77.2 - - - +
64Y ARG* 1.3 62.7 + - - +
66Y TYR* 3.2 3.6 + - - +
67Y GLU* 2.9 32.0 + - - +
74Y ILE* 3.8 36.0 - - + +
79Y ALA* 5.1 1.1 - - + -
82Y LEU* 5.5 1.5 - - + +
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Residues in contact with ARG 64 (chain Y).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
71R ASP* 4.6 6.3 + - - -
72R ALA* 3.8 34.4 - - - +
97R GLN* 3.4 34.1 - - + +
100R TRP* 6.1 0.2 - - + -
226R PHE* 5.9 1.8 - - - -
37Y ILE 5.9 3.6 - - - +
38Y ASN* 6.2 3.8 - - - -
60Y ALA 3.0 19.9 + - - +
61Y ARG 3.2 1.1 + - - +
63Y CYS* 1.3 77.7 - - - +
65Y ILE* 1.3 59.5 + - - +
67Y GLU* 3.2 34.2 + - - +
68Y LEU* 3.0 59.0 + - + +
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Residues in contact with ILE 65 (chain Y).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
93R ARG* 3.6 35.6 - - + +
94R VAL* 4.2 12.6 - - + +
97R GLN* 3.7 19.5 - - + -
61Y ARG* 3.0 30.8 + - + +
62Y GLN* 3.5 17.7 - - - +
64Y ARG* 1.3 74.3 - - - +
66Y TYR* 1.3 59.1 + - - +
68Y LEU* 3.8 8.8 - - + +
69Y ARG* 2.9 68.3 + - - +
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Residues in contact with TYR 66 (chain Y).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
94Q HIS* 4.5 14.2 + + - -
98Q VAL* 3.8 27.2 - - + +
100Q ASP* 5.2 1.2 + - - -
62Y GLN 3.0 14.0 + - - +
63Y CYS 3.2 8.0 + - - +
65Y ILE* 1.3 79.0 - - - +
67Y GLU* 1.3 56.4 + - - +
69Y ARG* 4.4 4.7 - - - +
70Y ASN* 3.0 61.8 + - + +
71Y LYS 4.1 0.7 + - - -
72Y GLU* 4.3 9.5 - - + +
73Y ARG 4.3 5.4 - - - -
74Y ILE* 3.6 51.1 - - + -
75Y SER 4.7 1.6 - - - -
78Y ALA* 5.6 2.0 - - + -
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Residues in contact with GLU 67 (chain Y).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
38Y ASN* 4.0 15.8 + - + +
40Y TYR* 6.5 0.2 - - - -
63Y CYS* 2.9 19.4 + - - +
64Y ARG* 3.2 31.6 + - - +
66Y TYR* 1.3 77.5 - - - +
68Y LEU* 1.3 61.8 + - - +
71Y LYS* 3.3 22.3 + - - -
72Y GLU 2.9 22.8 + - - +
73Y ARG* 3.3 14.2 - - - +
74Y ILE* 2.7 36.9 + - - +
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Residues in contact with LEU 68 (chain Y).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
69R GLU* 4.1 12.5 - - + +
70R ILE 3.3 28.0 - - - +
71R ASP* 4.4 10.8 - - - +
93R ARG* 2.9 41.1 + - + +
96R THR* 6.1 0.2 - - - -
97R GLN* 4.5 11.4 - - + -
64Y ARG* 3.0 47.7 + - - +
65Y ILE* 3.9 13.2 - - + +
67Y GLU* 1.3 77.7 - - - +
69Y ARG* 1.3 63.4 + - - +
70Y ASN 3.5 0.2 - - - -
71Y LYS* 4.0 6.4 + - - +
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Residues in contact with ARG 69 (chain Y).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
106Q TYR* 4.9 14.9 + - - -
109Q ARG* 3.6 30.1 + - - +
90R ASP* 3.3 31.4 + - - -
93R ARG* 3.5 16.4 + - - +
94R VAL* 4.1 7.5 - - - +
65Y ILE* 2.9 43.5 + - + +
66Y TYR* 3.3 4.9 + - - +
68Y LEU* 1.3 80.1 - - - +
70Y ASN* 1.3 76.7 + - - +
71Y LYS* 4.0 0.9 + - - +
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Residues in contact with ASN 70 (chain Y).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
94Q HIS* 4.7 4.6 + - - -
103Q THR* 6.3 1.3 - - + -
106Q TYR* 3.1 45.7 - - - +
109Q ARG* 3.4 4.5 + - - -
66Y TYR* 3.0 52.6 + - + +
69Y ARG* 1.3 89.3 - - - +
71Y LYS* 1.3 66.1 + - - +
72Y GLU* 2.9 33.6 + - + +
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Residues in contact with LYS 71 (chain Y).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
105Q GLU* 3.8 33.5 + - - +
109Q ARG* 5.5 2.4 - - - +
143Q ARG* 5.9 1.5 - - - +
65R GLU* 5.1 16.4 - - - +
67Y GLU 3.3 17.1 + - - -
68Y LEU 4.0 5.3 + - - +
69Y ARG 3.6 2.3 - - - +
70Y ASN* 1.3 81.0 + - - +
72Y GLU* 1.3 61.2 + - - +
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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