Contacts of the helix formed by residues 60 - 79 (chain N) in PDB entry 1S5E
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 SER 60 (chain N).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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34J LYS* 4.5 3.2 + - - +
36J GLU* 2.5 43.8 + - - +
52J VAL* 6.0 1.6 - - - -
53J PRO* 6.4 1.3 - - - -
58N ILE* 3.3 18.9 - - - +
59N ASP* 1.3 77.5 - - - +
61N GLN* 1.3 57.8 + - - +
62N LYS 3.6 0.2 + - - -
63N LYS* 4.4 4.0 + - - +
64N ALA* 4.4 6.2 + - - +
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Residues in contact with GLN 61 (chain N).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
31J LEU* 2.8 33.5 + - - +
32J ALA* 3.9 2.2 - - - +
33J GLY* 3.3 19.5 - - - +
36J GLU* 3.5 19.1 - - - +
56N GLN 4.0 4.3 + - - +
57N HIS* 3.3 28.4 - - + -
58N ILE* 2.8 42.1 + - + +
60N SER* 1.3 78.9 - - - +
62N LYS* 1.3 62.9 + - - -
63N LYS 3.4 0.4 - - - -
64N ALA* 3.1 4.0 + - - +
65N ILE* 2.9 28.9 + - + +
88N TRP* 4.4 6.9 - - - -
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Residues in contact with LYS 62 (chain N).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
53N PRO* 4.3 24.6 - - + +
54N GLY 5.8 0.9 - - - +
57N HIS* 4.8 12.3 - - + +
58N ILE 4.6 5.4 - - - +
59N ASP* 3.0 29.8 + - - +
61N GLN* 1.3 79.9 - - - +
63N LYS* 1.3 63.2 + - - +
65N ILE* 3.3 7.9 + - + +
66N GLU* 3.3 23.9 + - - +
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Residues in contact with LYS 63 (chain N).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
66J GLU* 4.6 18.7 - - + +
59N ASP 4.6 1.0 + - - -
60N SER 4.4 4.6 + - - +
61N GLN 3.4 0.4 - - - -
62N LYS* 1.3 78.7 - - - +
64N ALA* 1.3 57.7 + - - +
66N GLU* 3.3 9.4 + - - +
67N ARG* 2.9 28.3 + - - +
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Residues in contact with ALA 64 (chain N).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
29J GLU* 5.0 1.0 - - - +
30J SER 4.1 7.8 - - - +
31J LEU* 3.7 28.7 - - + +
36J GLU* 4.1 19.7 - - + -
69J LYS* 6.4 0.2 - - - +
60N SER 4.4 1.7 + - - +
61N GLN* 3.1 9.6 + - - +
63N LYS* 1.3 78.0 - - - +
65N ILE* 1.3 59.1 + - - +
67N ARG* 3.6 10.6 - - - +
68N MET* 2.9 30.1 + - - +
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Residues in contact with ILE 65 (chain N).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
31J LEU* 4.1 22.4 - - + -
50N VAL* 3.9 17.8 - - + +
51N GLU 4.1 9.2 - - - +
53N PRO* 4.3 17.5 - - + -
57N HIS* 3.4 49.8 - - + +
61N GLN* 2.9 21.4 + - + +
62N LYS* 3.5 9.9 - - + +
63N LYS 3.3 0.2 - - - -
64N ALA* 1.3 76.3 - - - +
66N GLU* 1.3 77.1 + - - +
68N MET* 3.2 4.0 + - - +
69N LYS* 3.2 29.5 + - - +
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Residues in contact with GLU 66 (chain N).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
63M LYS* 4.5 19.6 - - + +
67M ARG* 2.8 44.5 + - - +
53N PRO* 4.5 8.0 - - - +
62N LYS 3.3 13.1 + - - +
63N LYS* 3.3 11.1 + - - +
65N ILE* 1.3 84.8 - - - +
67N ARG* 1.3 62.3 + - - +
69N LYS* 3.0 26.3 + - - +
70N ASP* 3.1 15.6 + - - +
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Residues in contact with ARG 67 (chain N).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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29J GLU* 3.2 34.4 + - - +
66J GLU* 3.0 51.1 + - - +
69J LYS* 3.5 30.2 + - - +
70J ASP* 2.8 37.2 + - - +
73J ARG* 4.0 13.3 - - - +
63N LYS 2.9 16.6 + - - +
64N ALA* 3.6 10.0 - - - +
66N GLU* 1.3 75.0 - - - +
68N MET* 1.3 55.5 + - - +
70N ASP* 3.1 14.0 + - - +
71N THR* 2.9 30.1 + - - -
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Residues in contact with MET 68 (chain N).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
29J GLU* 3.4 41.2 + - + +
30J SER 4.8 0.2 - - - -
31J LEU* 3.7 20.0 - - + +
50N VAL* 3.9 21.5 - - + -
64N ALA 2.9 16.0 + - - +
65N ILE 3.2 5.6 + - - +
67N ARG* 1.3 76.5 - - - +
69N LYS* 1.3 57.2 + - - +
71N THR* 3.2 2.2 + - - -
72N LEU* 2.9 37.5 + - + +
96N ILE* 4.1 16.4 - - + -
97N ALA 4.1 6.1 - - - +
98N ALA* 3.9 17.7 - - - -
99N ILE* 3.7 23.1 - - + -
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Residues in contact with LYS 69 (chain N).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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64M ALA* 6.3 1.2 - - - +
67M ARG* 3.6 30.2 - - - +
27N TYR* 3.6 9.4 + - - +
36N GLU* 3.9 22.4 + - - +
37N MET* 4.6 4.0 - - - +
38N ALA* 4.1 24.5 - - + +
50N VAL* 3.9 21.3 - - + -
51N GLU 5.3 0.6 + - - -
53N PRO* 5.0 3.8 - - - +
65N ILE* 3.2 23.9 + - - +
66N GLU* 3.0 38.9 + - - +
67N ARG 3.3 0.2 - - - -
68N MET* 1.3 78.0 - - - +
70N ASP* 1.3 61.8 + - - +
72N LEU* 3.5 6.0 + - - +
73N ARG* 3.0 25.1 + - - +
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Residues in contact with ASP 70 (chain N).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
229B ASP* 4.8 4.4 - - - +
73J ARG* 3.7 19.8 + - - +
67M ARG* 2.5 36.8 + - - +
66N GLU* 3.1 12.8 + - - +
67N ARG* 3.1 13.7 + - - +
69N LYS* 1.3 75.1 - - - +
71N THR* 1.3 62.8 + - - +
73N ARG* 3.3 23.9 + - - +
74N ILE* 3.1 26.2 + - - +
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Residues in contact with THR 71 (chain N).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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27J TYR* 4.8 1.1 - - + -
29J GLU* 2.8 34.1 + - - +
73J ARG* 2.8 33.1 + - - +
67N ARG 2.9 4.9 + - - -
68N MET* 3.2 6.9 + - - -
70N ASP* 1.3 78.6 - - - +
72N LEU* 1.3 57.7 + - - +
74N ILE* 3.5 6.9 - - - +
75N ALA* 2.9 28.4 + - - +
99N ILE* 4.1 26.0 - - + -
101N MET* 4.2 16.8 - - + +
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Residues in contact with LEU 72 (chain N).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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24N ILE* 3.8 7.9 - - + +
27N TYR* 4.1 11.3 - - + -
38N ALA* 5.2 5.4 - - + -
40N ILE* 4.0 33.0 - - + -
50N VAL* 3.5 32.3 - - + +
68N MET* 2.9 26.9 + - + +
69N LYS* 3.9 4.5 - - - +
71N THR* 1.3 76.7 - - - +
73N ARG* 1.3 63.2 + - - +
75N ALA* 4.3 2.7 - - - -
76N TYR* 2.9 25.3 + - - +
85N LEU* 4.9 0.4 - - + -
96N ILE* 3.7 19.3 - - + -
99N ILE* 3.6 29.4 - - + -
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Residues in contact with ARG 73 (chain N).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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229B ASP* 3.6 39.4 + - - +
67M ARG* 3.5 29.9 + - - +
70M ASP* 3.6 12.6 + - - +
71M THR* 2.9 41.1 + - + +
74M ILE* 4.3 7.6 - - + +
101M MET* 5.0 1.3 - - + -
27N TYR* 3.6 27.9 - - + +
29N GLU* 4.4 2.2 - - - -
69N LYS 3.0 18.3 + - - +
70N ASP* 3.3 31.4 + - - +
72N LEU* 1.3 77.8 - - - +
74N ILE* 1.3 57.7 + - - +
76N TYR* 3.3 3.1 + - - +
77N LEU* 3.0 44.6 + - + +
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Residues in contact with ILE 74 (chain N).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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226B TYR* 3.4 31.6 - - + +
229B ASP* 4.0 13.2 - - - +
73J ARG* 4.2 13.5 - - - +
74J ILE* 5.7 1.8 - - + -
77J LEU* 3.8 28.7 - - + -
74M ILE* 3.8 21.3 - - + -
70N ASP 3.1 20.3 + - - +
71N THR* 3.5 10.5 - - - +
73N ARG* 1.3 73.4 - - + +
75N ALA* 1.3 67.4 + - - +
77N LEU* 4.4 5.6 - - + -
78N THR* 2.8 48.6 + - + +
101N MET* 6.4 0.7 - - + -
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Residues in contact with ALA 75 (chain N).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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77J LEU* 5.1 1.1 - - - -
24N ILE* 4.0 15.0 + - + +
71N THR* 2.9 20.5 + - + +
72N LEU* 3.8 4.5 - - - +
74N ILE* 1.3 77.7 - - + +
76N TYR* 1.3 63.3 + - - +
78N THR* 3.7 5.6 - - - -
79N GLU* 3.2 3.8 + - - -
80N ALA* 3.1 35.4 + - + +
82N VAL* 4.9 4.5 - - + -
99N ILE* 5.2 2.5 - - + -
101N MET* 4.0 25.1 - - - -
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Residues in contact with TYR 76 (chain N).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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143B ARG* 3.8 28.8 + - - -
80M ALA* 5.4 2.2 - - + -
81M LYS 4.9 0.9 + - - -
101M MET* 3.6 31.2 - - + +
102M ALA* 3.1 31.2 + - - -
103M ASN* 3.5 5.0 + - - -
24N ILE* 3.5 41.4 - - + +
25N PHE 3.5 21.3 - - - -
26N SER 4.3 2.0 - - - -
27N TYR* 3.8 20.6 - - + -
72N LEU 2.9 18.6 + - - +
73N ARG 3.5 4.0 - - - +
75N ALA* 1.3 77.8 - - - +
77N LEU* 1.3 84.6 + - + +
79N GLU* 3.2 13.4 + - - +
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Residues in contact with LEU 77 (chain N).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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143B ARG* 5.7 3.6 + - - +
146B ARG* 4.9 10.9 + - - -
226B TYR* 4.9 2.7 - - + -
74M ILE* 3.9 33.4 - - + -
75M ALA* 5.2 1.1 - - - +
78M THR* 4.2 16.8 + - + +
80M ALA* 3.7 28.7 - - + -
101M MET* 4.0 12.1 - - + -
73N ARG* 3.0 40.4 + - + +
74N ILE* 3.3 11.2 + - + +
76N TYR* 1.3 100.3 - - + +
78N THR* 1.3 59.6 + - - +
79N GLU* 3.4 3.7 - - - +
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Residues in contact with THR 78 (chain N).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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17B LYS* 3.9 11.1 + - - -
226B TYR* 3.7 50.2 + - + -
77J LEU* 3.8 13.4 - - + +
74N ILE* 2.8 44.0 + - + +
75N ALA* 3.4 6.8 + - - -
77N LEU* 1.3 75.5 - - - +
79N GLU* 1.3 69.7 + - - +
80N ALA* 3.3 15.3 + - - +
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Residues in contact with GLU 79 (chain N).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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17B LYS* 3.5 20.2 + - - +
121B TYR* 2.7 40.2 + - - -
143B ARG* 3.5 45.2 + - + +
144B GLY* 4.0 6.1 + - - -
23N LYS* 2.9 47.6 + - + +
75N ALA 3.2 6.5 + - - -
76N TYR 3.2 6.4 + - - +
77N LEU 4.9 2.9 - - - +
78N THR* 1.3 81.8 - - - +
80N ALA* 1.3 64.2 + - - +
81N LYS* 3.4 2.1 + - - +
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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
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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