Contacts of the helix formed by residues 60 - 79 (chain J) 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 J).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
58J ILE* 3.3 18.5 - - - +
59J ASP* 1.3 77.9 - - - +
61J GLN* 1.3 58.8 + - - +
62J LYS 3.3 0.7 + - - -
63J LYS* 4.3 4.7 + - - +
64J ALA* 4.2 6.2 + - - +
34K LYS* 4.6 4.0 + - - +
36K GLU* 2.6 43.8 + - - +
52K VAL* 6.2 0.7 - - - -
53K PRO* 6.5 0.7 - - - -
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Residues in contact with GLN 61 (chain J).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
56J GLN 4.0 0.9 - - - +
57J HIS* 3.3 18.0 - - + -
58J ILE* 2.8 41.0 + - + +
60J SER* 1.3 77.1 + - - +
62J LYS* 1.3 59.1 + - - +
63J LYS 3.4 0.7 - - - -
64J ALA* 3.1 4.7 + - - +
65J ILE* 2.8 36.8 + - + +
88J TRP* 4.1 4.9 - - - -
752J GAL 3.0 28.9 + - - -
31K LEU* 2.8 28.0 + - - +
33K GLY* 3.5 18.7 - - - +
36K GLU* 3.5 20.6 - - - +
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Residues in contact with LYS 62 (chain J).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
53J PRO* 4.0 19.1 - - + +
54J GLY* 3.0 39.2 + - - +
57J HIS* 3.6 23.3 + - + +
58J ILE 4.0 5.8 - - - +
59J ASP* 3.1 29.4 + - - +
61J GLN* 1.3 78.9 - - - +
63J LYS* 1.3 64.0 - - + +
65J ILE* 3.4 8.1 + - + +
66J GLU* 3.4 24.8 + - - +
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Residues in contact with LYS 63 (chain J).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
235B ARG 4.6 22.7 - - - +
59J ASP 4.5 1.4 + - - -
60J SER 4.3 4.8 + - - +
61J GLN 3.4 0.2 - - - -
62J LYS* 1.3 79.6 - - + +
64J ALA* 1.3 57.4 + - - +
66J GLU* 3.3 9.5 + - - +
67J ARG* 3.0 26.7 + - - +
66K GLU* 4.6 31.3 - - + +
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Residues in contact with ALA 64 (chain J).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
60J SER 4.2 2.1 + - - +
61J GLN* 3.1 12.3 + - - +
63J LYS* 1.3 77.2 - - - +
65J ILE* 1.3 59.1 + - - +
67J ARG* 3.3 12.8 + - - +
68J MET* 2.9 29.8 + - - +
29K GLU* 4.6 0.9 - - - +
30K SER 4.1 7.4 - - - +
31K LEU* 3.6 29.6 - - + +
36K GLU* 4.2 16.2 - - + -
69K LYS* 6.2 1.6 - - - +
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Residues in contact with ILE 65 (chain J).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
50J VAL* 3.9 15.8 - - + +
51J GLU 4.1 8.7 - - - +
53J PRO* 4.4 14.8 - - + -
57J HIS* 3.4 43.3 - - + +
61J GLN* 2.8 25.7 + - + +
62J LYS* 3.6 11.2 - - + +
63J LYS 3.3 0.2 - - - -
64J ALA* 1.3 75.6 - - - +
66J GLU* 1.3 67.9 + - - +
68J MET* 3.3 7.4 + - - +
69J LYS* 3.2 44.2 + - - +
31K LEU* 4.0 22.0 - - + -
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Residues in contact with GLU 66 (chain J).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
53J PRO* 4.6 7.8 - - - +
62J LYS 3.4 14.2 + - - +
63J LYS* 3.3 9.8 + - + +
64J ALA 3.2 0.4 - - - -
65J ILE* 1.3 84.3 - - - +
67J ARG* 1.3 61.6 + - - +
69J LYS* 2.7 30.5 + - - +
70J ASP* 3.1 22.1 + - - +
63N LYS* 4.6 18.6 - - + +
67N ARG* 3.0 35.6 + - - +
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Residues in contact with ARG 67 (chain J).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
63J LYS 3.0 13.8 + - - +
64J ALA* 3.7 13.2 - - - +
65J ILE 3.3 0.2 - - - -
66J GLU* 1.3 76.2 - - - +
68J MET* 1.3 56.7 + - - +
70J ASP* 3.1 13.5 + - - +
71J THR* 2.8 30.7 + - - -
27K TYR* 4.5 2.1 + - - -
29K GLU* 3.1 31.9 - - - +
30K SER 6.1 0.4 - - - -
66K GLU* 3.0 51.3 + - - +
69K LYS* 3.4 39.2 + - - +
70K ASP* 2.7 28.4 + - - +
73K ARG* 3.9 11.1 - - - +
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Residues in contact with MET 68 (chain J).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
50J VAL* 3.8 23.3 - - + -
64J ALA 2.9 17.4 + - - +
65J ILE 3.7 4.7 - - - +
66J GLU 3.3 0.4 - - - -
67J ARG* 1.3 76.6 - - - +
69J LYS* 1.3 56.3 + - - +
71J THR* 3.1 3.6 + - - -
72J LEU* 2.9 41.9 + - + +
96J ILE* 3.9 19.5 - - + -
97J ALA 4.5 0.4 - - - +
98J ALA* 4.1 4.3 - - - -
99J ILE* 3.9 22.7 - - + -
29K GLU* 3.2 43.7 + - + +
30K SER 5.2 0.2 - - - -
31K LEU* 3.7 29.2 - - + +
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Residues in contact with LYS 69 (chain J).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
27J TYR* 3.8 8.5 + - - +
29J GLU* 6.3 0.7 - - + -
36J GLU* 4.3 16.8 + - - +
37J MET* 4.7 4.9 - - - +
38J ALA* 4.0 23.1 - - + +
50J VAL* 3.8 23.8 - - + +
51J GLU 5.2 0.8 + - - -
53J PRO* 5.0 3.6 - - - +
65J ILE* 3.2 28.7 + - - +
66J GLU* 2.7 40.5 + - - +
68J MET* 1.3 72.0 - - - +
70J ASP* 1.3 65.9 + - - +
72J LEU* 3.5 6.0 + - - +
73J ARG* 3.2 24.9 + - - +
64N ALA* 6.4 0.2 - - - +
67N ARG* 3.5 32.1 + - - +
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Residues in contact with ASP 70 (chain J).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
235B ARG* 5.0 11.6 - - - +
66J GLU* 3.1 16.9 + - - +
67J ARG* 3.2 13.5 - - - +
69J LYS* 1.3 75.4 - - - +
71J THR* 1.3 64.2 + - - +
73J ARG* 3.5 20.5 + - - +
74J ILE* 3.2 24.4 + - - +
70K ASP* 5.5 1.4 - - - +
73K ARG* 3.8 21.3 + - - +
67N ARG* 2.8 34.1 + - - +
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Residues in contact with THR 71 (chain J).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
67J ARG 2.8 9.9 + - - -
68J MET* 3.1 9.8 + - - -
70J ASP* 1.3 77.0 - - - +
72J LEU* 1.3 57.6 + - - +
74J ILE* 3.4 7.4 - - - +
75J ALA* 2.9 31.9 + - - +
99J ILE* 4.4 19.5 - - + -
101J MET* 4.2 20.6 - - + -
27K TYR* 4.8 0.7 - - + -
29K GLU* 2.7 32.9 + - - +
73K ARG* 2.9 30.9 + - - +
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Residues in contact with LEU 72 (chain J).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
24J ILE* 3.8 8.7 - - + +
27J TYR* 4.1 14.1 - - + -
38J ALA* 5.2 4.9 - - + -
40J ILE* 4.1 31.0 - - + -
50J VAL* 3.4 32.8 - - + -
68J MET* 2.9 30.7 + - + +
69J LYS* 4.0 5.2 - - - +
71J THR* 1.3 71.3 - - - +
73J ARG* 1.3 57.2 + - - +
75J ALA* 3.7 3.7 - - + +
76J TYR* 2.8 31.2 + - - +
96J ILE* 3.7 16.8 - - + -
99J ILE* 3.8 29.4 - - + -
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Residues in contact with ARG 73 (chain J).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
229B ASP* 5.1 6.7 + - - -
27J TYR* 3.8 26.6 - - + +
29J GLU* 4.2 2.9 + - - -
69J LYS 3.2 17.3 + - - +
70J ASP* 3.8 25.5 + - - +
72J LEU* 1.3 77.4 - - - +
74J ILE* 1.3 58.3 + - - +
76J TYR* 3.3 4.4 + - - +
77J LEU* 3.0 44.5 + - + +
67N ARG* 3.6 29.0 + - - +
70N ASP* 3.7 17.0 + - - +
71N THR* 2.8 54.6 + - - +
74N ILE* 4.2 14.1 - - - +
101N MET* 4.8 3.4 - - + -
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Residues in contact with ILE 74 (chain J).
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* 4.3 17.9 - - + +
227B GLN* 3.8 27.8 - - + +
70J ASP 3.2 11.5 + - - +
71J THR* 3.4 15.3 - - - +
73J ARG* 1.3 76.9 - - - +
75J ALA* 1.3 64.3 + - - +
77J LEU* 4.4 14.4 - - + +
78J THR* 2.8 46.5 + - + +
73K ARG* 4.1 13.7 - - - +
77K LEU* 3.7 29.2 - - + -
74N ILE* 5.7 1.3 - - + -
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Residues in contact with ALA 75 (chain J).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
24J ILE* 4.1 15.7 + - + +
71J THR* 2.9 21.2 + - + +
72J LEU* 3.7 4.9 - - + +
74J ILE* 1.3 75.3 - - - +
76J TYR* 1.3 65.6 + - - +
78J THR* 3.4 5.6 + - - -
79J GLU* 3.0 18.9 + - - -
80J ALA* 3.1 20.7 + - + +
82J VAL* 5.3 2.5 - - + -
99J ILE* 5.6 0.9 - - + -
101J MET* 4.1 24.7 - - + -
77K LEU* 5.0 2.0 - - + -
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Residues in contact with TYR 76 (chain J).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
24J ILE* 3.6 40.8 - - + +
25J PHE 3.6 21.1 - - - -
26J SER* 4.0 3.1 - - - -
27J TYR* 3.7 22.2 - - + -
72J LEU 2.8 19.5 + - - +
73J ARG 3.4 3.8 - - - +
75J ALA* 1.3 76.8 - - - +
77J LEU* 1.3 83.2 + - + +
79J GLU* 3.2 17.8 + - - +
80N ALA* 5.2 3.8 - - + -
81N LYS 4.8 2.1 + - - -
101N MET* 3.7 27.2 - - + +
102N ALA* 3.2 30.0 + - - -
103N ASN* 3.9 9.2 + - - -
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Residues in contact with LEU 77 (chain J).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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223B PHE* 5.1 0.5 - - - -
226B TYR* 4.5 12.0 - - + -
73J ARG* 3.0 31.7 + - + +
74J ILE* 3.9 14.8 - - + +
75J ALA 3.3 0.2 - - - -
76J TYR* 1.3 95.1 - - + +
78J THR* 1.3 61.6 + - + +
79J GLU* 3.7 5.5 + - - +
74N ILE* 3.8 40.2 - - + -
75N ALA* 5.1 1.3 - - - -
78N THR* 3.8 17.2 - - + +
80N ALA* 3.7 29.6 - - + -
101N MET* 4.4 9.0 - - + -
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Residues in contact with THR 78 (chain J).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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31B PHE* 5.5 2.3 - - - -
223B PHE* 3.4 62.0 - - + -
226B TYR* 4.5 4.0 - - + -
227B GLN* 5.4 0.4 - - - +
74J ILE* 2.8 41.9 + - + +
75J ALA* 3.4 6.8 + - - -
77J LEU* 1.3 75.3 - - - +
79J GLU* 1.3 68.9 + - - +
80J ALA* 3.3 15.8 + - - +
77K LEU* 4.0 10.6 - - + +
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Residues in contact with GLU 79 (chain J).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
18B GLN 5.0 7.3 - - - +
29B GLU* 4.1 19.8 - - - +
31B PHE* 5.7 6.2 - - + +
23J LYS* 3.6 47.8 + - + +
24J ILE 5.8 0.4 - - - +
75J ALA 3.0 7.3 + - - -
76J TYR 3.2 12.4 + - - +
77J LEU 4.4 5.4 - - - +
78J THR* 1.3 81.8 - - - +
80J ALA* 1.3 65.3 + - - +
81J LYS* 3.6 5.0 + - - +
103N ASN* 4.0 14.7 - - - +
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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