Contacts of the helix formed by residues 57 - 76 (chain b) in PDB entry 5A0Q
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 TYR 57 (chain b).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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119V MET* 1.9 53.6 - - + -
121V VAL* 5.1 6.1 - - + -
6b VAL 2.9 13.9 + - - +
8b GLY 5.1 1.8 - - - +
39b ILE* 3.4 45.6 - - + +
40b SER 3.3 18.4 + - - -
41b ARG* 4.1 15.5 - - + -
53b ALA* 5.9 0.4 - - + -
55b GLY 3.2 6.0 + - - +
56b ASP* 1.3 72.1 - - - +
58b ALA* 1.3 58.9 + - - +
59b ASP 3.2 0.4 - - - -
60b PHE* 3.1 36.5 + + + +
61b GLN* 3.0 50.1 + - + +
64b LYS* 5.8 0.5 + - - -
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Residues in contact with ALA 58 (chain b).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
88V TYR* 3.3 21.9 + - + -
91V ARG* 6.3 1.3 - - - -
117V GLY* 4.3 12.8 - - - +
118V GLY 3.3 29.4 - - - +
119V MET* 3.9 12.7 - - + -
5b MET* 5.7 4.5 - - + -
56b ASP* 4.6 3.8 - - + +
57b TYR* 1.3 76.2 - - - +
59b ASP* 1.3 59.8 + - - +
61b GLN* 3.2 5.4 + - - +
62b TYR 3.0 22.2 + - - -
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Residues in contact with ASP 59 (chain b).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
88V TYR* 3.7 15.8 + - - -
56b ASP* 3.4 18.1 - - - +
57b TYR 3.2 0.2 - - - -
58b ALA* 1.3 76.1 - - - +
60b PHE* 1.4 55.5 + - - +
62b TYR* 3.4 2.3 + - - +
63b LEU* 2.9 29.5 + - - +
99b ARG* 4.0 10.9 + - - -
105b PRO 4.4 0.7 - - - +
106b LEU* 3.6 30.0 - - + +
107b TRP* 3.1 16.1 + - - +
108b ASN* 2.3 46.0 + - - +
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Residues in contact with PHE 60 (chain b).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
40b SER 3.9 8.5 - - - -
41b ARG* 3.1 31.4 - - - -
43b MET* 3.6 45.5 - - + -
51b LEU 4.5 0.7 - - - -
52b GLY 4.7 0.4 - - - -
53b ALA* 3.2 30.1 - - + -
55b GLY 5.5 0.4 - - - +
57b TYR* 3.1 57.2 + + + +
59b ASP* 1.4 72.2 - - - +
61b GLN* 1.3 64.6 + - - +
63b LEU* 5.0 1.8 - - - -
64b LYS* 2.8 43.6 + - + +
108b ASN* 2.6 13.0 + - - +
110b MET* 4.3 2.9 - - - -
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Residues in contact with GLN 61 (chain b).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
84V LYS* 4.2 24.7 + - + +
88V TYR* 6.1 0.2 - - + -
118V GLY 5.4 0.4 - - - +
119V MET* 3.8 20.2 - - + -
120V MET* 3.2 25.5 + - - +
57b TYR* 3.0 41.3 + - + +
58b ALA* 3.2 8.5 + - - +
60b PHE* 1.3 83.5 - - - +
62b TYR* 1.3 65.6 + - - +
64b LYS* 3.4 10.7 + - - +
65b GLN* 3.1 26.6 + - - +
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Residues in contact with TYR 62 (chain b).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
84V LYS* 5.5 0.2 - - - +
88V TYR* 1.9 59.1 - + + +
58b ALA 3.0 4.4 + - - -
59b ASP* 3.5 4.7 - - - +
61b GLN* 1.3 76.9 - - - +
63b LEU* 1.3 65.9 + - + +
65b GLN* 3.4 9.2 - - + +
66b VAL* 3.0 53.8 + - + +
95b ALA* 6.0 1.6 - - - +
99b ARG* 3.8 41.2 + - + +
106b LEU* 3.4 33.4 - - + -
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Residues in contact with LEU 63 (chain b).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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43b MET* 4.0 4.5 - - + +
59b ASP 2.9 11.3 + - - +
60b PHE 4.6 1.3 - - - +
62b TYR* 1.3 100.6 - - + +
64b LYS* 1.3 59.3 + - - +
66b VAL* 3.8 13.9 - - + +
67b LEU* 3.0 30.5 + - + +
92b LEU* 4.0 15.0 - - + -
95b ALA* 4.4 17.0 - - + -
96b MET* 3.5 25.6 - - - -
106b LEU* 3.4 28.3 - - + -
110b MET* 3.6 24.7 - - + -
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Residues in contact with LYS 64 (chain b).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
40b SER* 5.0 5.7 + - - -
42b ILE 5.2 1.2 + - - -
43b MET* 3.8 46.4 - - + +
44b ARG 5.5 0.4 - - - +
57b TYR* 5.8 0.6 + - - -
60b PHE* 2.8 42.9 + - + +
61b GLN* 3.8 13.2 + - - +
63b LEU* 1.3 77.0 - - - +
65b GLN* 1.4 57.9 + - - +
67b LEU* 4.2 1.0 - - - +
68b GLY* 3.1 24.3 + - - -
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Residues in contact with GLN 65 (chain b).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
99U ARG 4.9 0.5 - - - +
100U SER* 3.5 35.1 - - - +
84V LYS* 3.5 29.6 + - - +
85V GLU* 3.9 15.4 + - - -
88V TYR* 5.3 5.5 - - - -
61b GLN 3.1 15.5 + - - +
62b TYR* 3.4 18.7 + - - +
64b LYS* 1.4 78.1 - - - +
66b VAL* 1.4 61.8 + - + +
68b GLY* 3.8 1.4 + - - -
69b GLN* 3.2 22.3 + - - +
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Residues in contact with VAL 66 (chain b).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
62b TYR* 3.0 40.9 + - + +
63b LEU* 4.3 15.9 - - + -
65b GLN* 1.4 83.2 - - + +
67b LEU* 1.3 64.5 + - - +
68b GLY 3.2 1.6 - - - -
69b GLN* 3.0 17.6 + - + +
70b MET* 3.0 28.8 + - + +
91b TRP* 5.6 3.4 - - - +
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Residues in contact with LEU 67 (chain b).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
43b MET* 4.1 9.6 - - + -
45b VAL* 3.4 41.1 - - + -
51b LEU* 3.5 38.1 - - + -
63b LEU* 3.0 18.0 + - + +
64b LYS 4.2 1.6 - - - +
66b VAL* 1.3 76.9 - - - +
68b GLY* 1.3 62.2 + - - +
70b MET* 3.3 9.3 + - + +
71b VAL* 3.1 34.4 + - + +
88b ILE* 3.7 22.2 - - + -
92b LEU* 4.0 15.7 - - + -
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Residues in contact with GLY 68 (chain b).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
64b LYS 3.1 18.1 + - - -
65b GLN* 3.9 3.4 - - - -
67b LEU* 1.3 77.1 - - - +
69b GLN* 1.3 57.3 + - - +
71b VAL* 4.1 4.7 - - - +
72b ILE* 2.9 45.4 + - - +
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Residues in contact with GLN 69 (chain b).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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96U SER* 3.3 40.5 + - - -
97U ASN* 5.3 2.0 + - - -
100U SER* 5.8 2.0 + - - -
65b GLN 3.2 15.0 + - - +
66b VAL* 3.0 15.5 + - + +
68b GLY* 1.3 76.4 - - - +
70b MET* 1.4 70.2 + - + +
72b ILE* 3.9 6.0 - - - +
73b ASP* 2.9 55.8 + - - +
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Residues in contact with MET 70 (chain b).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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99T PHE* 5.1 13.7 - - + -
66b VAL* 3.0 24.2 + - + +
67b LEU* 3.3 11.4 + - + +
69b GLN* 1.4 94.3 - - + +
71b VAL* 1.3 64.7 + - + +
73b ASP* 3.8 8.5 - - - +
74b GLU* 3.1 26.7 + - - +
88b ILE* 5.5 6.5 - - + -
91b TRP* 3.2 42.4 - - + +
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Residues in contact with VAL 71 (chain b).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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45b VAL* 3.7 23.1 - - + +
46b ASN* 3.2 39.9 - - - +
67b LEU* 3.1 18.1 + - + +
68b GLY* 4.1 4.7 - - - +
70b MET* 1.3 73.5 - - - +
72b ILE* 1.3 68.9 + - + +
74b GLU* 3.4 8.6 + - - +
75b GLU* 3.0 31.3 + - + +
88b ILE* 3.8 20.2 - - + -
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Residues in contact with ILE 72 (chain b).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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70U ASP* 4.4 13.2 - - - +
71U ARG* 4.7 19.5 - - + +
96U SER* 6.4 1.1 - - - -
99U ARG* 4.1 32.3 - - - +
68b GLY* 2.9 28.4 + - - +
69b GLN* 4.0 8.1 - - - +
71b VAL* 1.3 79.5 - - + +
73b ASP* 1.4 62.3 + - - +
75b GLU* 3.7 8.8 + - - +
76b LEU* 3.1 31.3 + - + +
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Residues in contact with ASP 73 (chain b).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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92U ARG* 5.1 7.1 - - - +
96U SER* 4.8 6.2 + - - -
69b GLN* 2.9 49.4 + - - +
70b MET* 3.8 11.4 - - - +
72b ILE* 1.4 76.6 - - - +
74b GLU* 1.3 63.6 + - + +
75b GLU 3.3 0.2 + - - -
76b LEU* 3.2 19.4 - - + +
77b LEU* 3.2 29.8 + - + +
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Residues in contact with GLU 74 (chain b).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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101T ARG* 4.8 11.0 - - - +
107T ARG* 3.0 34.1 + - - +
46b ASN* 5.6 1.0 + - - -
70b MET 3.1 16.6 + - - +
71b VAL* 4.0 7.5 - - - +
73b ASP* 1.3 80.1 - - - +
75b GLU* 1.3 75.0 + - - +
76b LEU 3.3 1.0 + - - -
77b LEU* 3.4 24.4 + - + +
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Residues in contact with GLU 75 (chain b).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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223U ARG* 5.4 10.5 - - - +
46b ASN* 3.8 22.8 + - - -
47b ASN* 5.0 8.3 + - - -
71b VAL* 3.0 22.1 + - + +
72b ILE* 3.9 8.5 - - - +
73b ASP 3.2 0.2 - - - -
74b GLU* 1.3 89.4 - - - +
76b LEU* 1.3 58.0 - - + +
77b LEU 5.1 1.3 - - - -
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Residues in contact with LEU 76 (chain b).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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68U ASN* 3.5 36.9 - - + +
69U VAL 4.4 1.3 - - - +
70U ASP* 3.9 26.2 - - - +
71U ARG* 4.2 3.4 - - + +
92U ARG* 3.3 54.7 + - + -
72b ILE* 3.1 31.0 - - + +
73b ASP* 3.2 22.2 - - - +
75b GLU* 1.3 76.4 - - + +
77b LEU* 1.4 67.9 + - + +
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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