Contacts of the helix formed by residues 55 - 78 (chain B) in PDB entry 1IS2
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 THR 55 (chain B).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
55A THR* 3.8 32.8 - - + -
54B LEU* 1.3 77.9 - - - +
56B ARG* 1.3 65.6 + - - +
57B SER* 3.6 8.6 + - - -
58B GLN* 2.8 42.8 + - - +
59B ARG* 2.9 22.8 + - - +
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Residues in contact with ARG 56 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
639A SER* 6.2 0.4 - - - -
640A PRO* 5.7 10.5 - - + +
641A LEU* 3.5 26.8 - - + +
55B THR* 1.3 73.7 - - - +
57B SER* 1.3 62.9 + - - +
59B ARG* 3.1 9.6 + - - +
60B TYR* 3.0 22.5 + - - +
225B ASP* 3.2 33.5 + - - -
227B GLY* 3.7 14.1 + - - -
228B PRO* 3.9 17.2 - - + +
229B LYS* 3.3 14.4 - - - +
233B GLU* 2.7 45.9 + - + +
235B MET 3.1 25.3 + - - -
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Residues in contact with SER 57 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
641A LEU* 4.3 12.1 - - - -
643A LYS* 4.9 15.7 + - - -
647A HIS* 2.9 33.0 + - - -
55B THR* 3.2 8.9 + - - -
56B ARG* 1.3 81.4 - - - +
58B GLN* 1.3 58.9 + - - +
60B TYR* 3.5 2.1 + - - +
61B GLU* 3.0 28.3 + - - +
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Residues in contact with GLN 58 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
53B PHE 4.7 1.0 - - - +
54B LEU* 3.5 29.7 - - + +
55B THR* 2.8 47.4 + - - +
57B SER* 1.3 75.7 - - - +
59B ARG* 1.3 65.3 + - - +
61B GLU* 3.4 10.1 + - - +
62B VAL* 3.0 31.9 + - + +
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Residues in contact with ARG 59 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
51B TYR* 3.3 51.0 + - + +
52B ASN* 4.0 17.8 + - - +
54B LEU* 4.0 14.2 + - + -
55B THR 2.9 20.7 + - - +
56B ARG* 3.4 9.2 - - - +
58B GLN* 1.3 74.5 - - - +
60B TYR* 1.3 67.8 + - - +
62B VAL* 3.2 3.5 + - - +
63B ALA* 3.0 22.5 + - - +
96B HIS* 4.2 0.8 - - - -
233B GLU* 3.4 49.2 + - + +
234B GLU* 3.1 33.2 + - + +
403B HIS* 5.5 4.6 + - - -
409B ASN* 4.2 15.0 - - - +
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Residues in contact with TYR 60 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
641A LEU* 4.6 15.3 - - + -
647A HIS* 3.7 35.8 - + + +
649A SER* 3.4 18.4 + - - -
654A LEU* 5.5 1.6 - - - +
56B ARG 3.0 12.3 + - - +
57B SER* 3.7 7.2 - - - +
59B ARG* 1.3 77.1 - - - +
61B GLU* 1.3 55.6 + - - +
63B ALA* 3.0 4.5 + - - +
64B VAL* 2.8 51.9 + - + +
99B PRO* 4.0 3.4 - - + -
182B LYS* 3.3 30.1 + - + +
183B THR* 2.8 26.8 + - - -
233B GLU 4.5 5.6 - - - +
234B GLU* 3.7 24.8 - - - +
235B MET 6.0 0.2 - - - -
236B ASP* 3.6 22.2 - - + -
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Residues in contact with GLU 61 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
647A HIS* 4.1 10.7 + - - +
648A GLU* 5.0 6.3 - - - +
649A SER* 4.0 31.4 + - - -
652A LYS* 5.6 2.1 - - - +
653A HIS* 4.2 17.7 + - - +
57B SER* 3.0 18.6 + - - +
58B GLN* 3.6 11.0 - - - +
59B ARG 3.2 0.4 - - - -
60B TYR* 1.3 78.1 - - - +
62B VAL* 1.3 60.0 + - + +
64B VAL* 3.4 2.3 + - - +
65B LYS* 2.9 27.8 + - + +
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Residues in contact with VAL 62 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
48B HIS* 3.5 42.2 - - + +
51B TYR* 4.4 7.2 - - + -
54B LEU* 3.9 17.9 - - + -
58B GLN* 3.0 20.0 + - + +
59B ARG 3.7 4.0 - - - +
61B GLU* 1.3 76.2 - - + +
63B ALA* 1.3 61.6 + - - +
65B LYS* 3.6 10.5 - - + +
66B LYS* 2.9 41.4 + - + +
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Residues in contact with ALA 63 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
51B TYR* 4.9 4.9 - - - +
59B ARG 3.0 12.8 + - - +
60B TYR 3.3 8.3 - - - +
62B VAL* 1.3 78.1 - - - +
64B VAL* 1.3 57.6 + - - +
66B LYS* 3.1 3.4 + - - +
67B SER* 2.8 32.7 + - - -
93B HIS* 3.7 13.8 - - + +
97B PRO 4.7 1.1 - - - +
99B PRO* 3.5 25.4 - - + -
234B GLU* 3.5 22.2 - - + +
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Residues in contact with VAL 64 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
649A SER* 3.9 15.3 - - - +
653A HIS* 4.2 11.9 - - + -
654A LEU* 4.0 31.6 - - + +
60B TYR* 2.8 60.7 + - + +
61B GLU 3.6 6.5 - - - +
63B ALA* 1.3 71.9 - - - +
65B LYS* 1.3 64.0 + - - +
67B SER* 3.4 2.1 + - - -
68B ALA* 3.1 23.6 + - - +
99B PRO* 3.8 14.6 - - + +
100B LEU* 5.5 0.2 - - - +
183B THR* 4.5 3.1 - - + +
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Residues in contact with LYS 65 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
653A HIS* 3.3 45.2 - - + +
44B PRO 5.4 0.4 + - - -
45B ASP* 3.5 26.2 + - - +
47B GLN 4.8 8.5 + - - -
48B HIS* 6.2 0.6 - - - +
61B GLU* 2.9 18.8 + - + +
62B VAL* 3.6 11.7 - - + +
64B VAL* 1.3 76.4 - - - +
66B LYS* 1.3 66.8 + - + +
68B ALA* 3.8 2.1 - - - +
69B THR* 3.1 32.4 + - - +
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Residues in contact with LYS 66 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
45B ASP 4.6 3.6 - - - +
46B PHE* 3.8 29.9 - - + +
48B HIS* 2.9 35.8 - - + +
51B TYR* 2.4 32.7 + - - -
62B VAL* 2.9 28.4 + - + +
63B ALA 3.6 2.5 - - - +
65B LYS* 1.3 79.0 - - + +
67B SER* 1.3 59.6 + - - +
69B THR* 3.4 6.1 + - - -
70B MET* 2.7 30.5 + - - +
92B VAL* 3.0 34.4 + - + +
93B HIS* 3.8 16.4 - - + +
94B ARG* 4.7 0.8 - - - +
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Residues in contact with SER 67 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
63B ALA 2.8 17.2 + - - -
64B VAL* 3.9 5.2 - - - -
66B LYS* 1.3 70.1 - - - +
68B ALA* 1.3 68.1 + - - +
70B MET* 2.9 25.9 + - - +
71B VAL* 3.0 13.3 + - - +
93B HIS* 3.1 19.4 + - - -
98B GLU* 2.6 30.7 + - - +
99B PRO* 4.1 3.5 - - - +
100B LEU* 3.5 18.2 - - - -
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Residues in contact with ALA 68 (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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653A HIS* 3.9 24.0 - - + +
654A LEU* 4.4 6.7 - - + -
64B VAL 3.1 18.3 + - - +
65B LYS 3.8 3.4 - - - +
67B SER* 1.3 76.7 - - - +
69B THR* 1.3 64.2 + - - +
71B VAL* 3.3 10.6 + - - +
72B LYS* 3.3 12.1 + - - +
100B LEU* 4.1 1.2 - - - +
130B LEU* 3.6 27.3 - - + +
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Residues in contact with THR 69 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
45B ASP* 4.2 15.1 + - + +
46B PHE* 3.9 12.6 - - + -
65B LYS* 3.1 22.2 + - - +
66B LYS* 3.8 4.9 - - - -
68B ALA* 1.3 79.6 - - - +
70B MET* 1.3 53.0 + - - +
72B LYS* 3.3 13.8 + - - +
73B LYS* 2.8 66.3 + - + +
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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
----------------------------------------------------------
46B PHE* 4.1 13.7 - - + -
66B LYS 2.7 14.2 + - - +
67B SER* 2.9 34.1 - - - +
69B THR* 1.3 77.0 - - - +
71B VAL* 1.3 55.7 + - + +
73B LYS* 3.7 0.5 - - - +
74B MET* 2.8 51.8 + - + +
88B PHE* 4.0 15.3 - - + -
89B LYS* 4.0 22.7 - - + -
92B VAL* 4.4 4.3 - - + -
93B HIS* 3.6 26.9 - - - +
98B GLU* 4.2 10.8 - - - +
100B LEU* 5.0 0.7 - - + -
104B LEU* 3.9 28.0 - - + -
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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
----------------------------------------------------------
67B SER 3.0 13.5 + - - +
68B ALA 3.3 6.3 + - - +
70B MET* 1.3 78.1 - - + +
72B LYS* 1.3 63.1 + - - +
74B MET* 3.5 9.0 + - + +
75B ARG* 3.1 27.2 + - + +
100B LEU* 4.2 10.5 - - + -
104B LEU* 4.5 25.8 - - + -
128B TRP 4.1 13.7 - - - +
130B LEU* 3.9 33.0 - - + -
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Residues in contact with LYS 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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68B ALA 3.3 8.7 + - - +
69B THR* 3.3 16.9 + - - +
70B MET 3.3 0.2 - - - -
71B VAL* 1.3 80.0 - - - +
73B LYS* 1.3 85.8 + - - +
75B ARG* 3.7 18.6 - - - +
76B GLU* 2.9 61.2 + - - +
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Residues in contact with LYS 73 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
43B ASP* 3.2 27.4 + - - +
45B ASP* 3.3 29.9 + - - +
46B PHE* 3.9 6.9 - - + -
69B THR* 2.8 39.4 + - + +
70B MET 3.8 2.5 - - - +
72B LYS* 1.3 95.1 - - - +
74B MET* 1.3 56.9 + - - +
76B GLU* 3.4 9.7 + - - +
77B TYR* 3.0 59.7 + - + +
88B PHE* 4.1 15.5 - - + -
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Residues in contact with MET 74 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
70B MET* 2.8 57.3 + - + +
71B VAL* 3.9 8.7 - - + +
73B LYS* 1.3 70.3 - - - +
75B ARG* 1.3 67.2 + - - +
77B TYR* 3.0 5.2 + - - -
78B GLY 2.9 19.2 + - - -
79B ILE* 3.1 43.4 + - + +
85B ILE* 4.2 26.5 - - + +
88B PHE* 3.4 34.8 - - + -
89B LYS* 5.1 1.1 - - + -
104B LEU* 4.6 9.6 - - + -
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Residues in contact with ARG 75 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
71B VAL* 3.1 18.0 + - + +
72B LYS* 3.7 19.2 + - - +
74B MET* 1.3 79.4 - - - +
76B GLU* 1.3 93.5 + - - +
78B GLY* 3.3 11.1 + - - -
79B ILE 4.8 2.7 + - - -
128B TRP* 5.3 11.1 + - - -
129B ASN* 6.3 0.6 - - - +
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Residues in contact with GLU 76 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
72B LYS* 2.9 59.3 + - - +
73B LYS* 3.8 12.9 - - + +
75B ARG* 1.3 97.0 + - - +
77B TYR* 1.3 66.9 + - + +
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Residues in contact with TYR 77 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
39B LEU* 4.1 39.0 + - + +
43B ASP* 5.0 7.4 + - - +
46B PHE* 5.9 1.3 - + - -
73B LYS* 3.0 53.8 + - + +
74B MET 3.0 1.1 + - - +
76B GLU* 1.3 81.3 - - + +
78B GLY* 1.3 60.4 + - - +
79B ILE* 3.4 23.2 + - + +
88B PHE* 4.0 23.1 - + - -
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Residues in contact with GLY 78 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
74B MET 2.9 4.7 + - - -
75B ARG* 3.3 10.9 + - - -
76B GLU 3.3 0.6 + - - -
77B TYR* 1.3 79.7 - - - +
79B ILE* 1.3 61.0 + - - +
80B SER* 3.1 18.1 + - - -
84B GLU* 5.4 0.3 - - - +
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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