Contacts of the helix formed by residues 49 - 68 in PDB entry 2IIL
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 49
.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
45 LEU 3.9 1.2 + - - -
46 ALA 3.0 20.6 + - - +
47 TYR* 4.0 2.0 - - - +
48 GLY* 1.4 67.6 - - - +
50 VAL* 1.3 58.1 + - - +
51 ILE* 3.0 5.2 - - - -
52 ILE* 2.9 43.5 + - + +
53 LEU* 3.4 4.0 + - - +
98 PHE* 5.5 0.6 - - - -
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Residues in contact with VAL 50
.
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
47 TYR* 3.1 39.7 + - + +
48 GLY* 3.5 13.0 - - - +
49 ALA* 1.3 74.6 - - - +
51 ILE* 1.3 52.7 + - - +
53 LEU* 4.7 3.4 - - - +
54 GLY* 2.7 34.9 + - - -
94 LEU* 3.4 25.5 - - + +
310 MET* 4.1 24.5 - - + +
311 ILE* 5.2 6.7 - - + -
313 THR* 5.4 0.4 - - - +
314 CYS* 3.7 17.6 - - - -
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Residues in contact with ILE 51
.
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
48 GLY 2.8 30.5 + - - +
49 ALA* 4.4 2.9 - - - -
50 VAL* 1.3 70.1 - - - +
52 ILE* 1.3 70.0 + - + +
54 GLY* 5.0 0.4 - - - -
55 VAL* 3.1 42.6 + - + +
90 ALA* 3.8 24.0 - - + +
91 ILE* 5.9 0.2 - - - -
94 LEU* 4.1 13.7 - - + +
95 PRO* 4.4 23.1 - - + -
98 PHE* 5.7 9.6 - - + -
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Residues in contact with ILE 52
.
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
49 ALA* 2.9 37.7 + - + +
51 ILE* 1.3 81.3 - - + +
53 LEU* 1.3 64.2 + - + +
55 VAL* 4.3 2.0 - - - +
56 SER* 3.6 18.5 + - - -
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Residues in contact with LEU 53
.
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
49 ALA 3.4 5.3 + - - +
50 VAL* 4.1 7.0 - - - +
51 ILE 3.4 0.4 - - - -
52 ILE* 1.3 81.9 - - + +
54 GLY* 1.3 59.3 + - - +
56 SER* 3.1 10.8 + - - +
57 GLY* 2.9 33.2 + - - +
314 CYS* 3.9 24.9 - - + -
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Residues in contact with GLY 54
.
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
50 VAL 2.7 23.8 + - - -
51 ILE* 4.1 0.4 - - - -
53 LEU* 1.3 72.2 - - - +
55 VAL* 1.3 60.3 + - - +
57 GLY* 5.4 0.2 - - - -
58 ASN* 2.8 37.9 + - - +
86 ASP 5.4 0.2 - - - +
87 LEU* 4.4 0.7 - - - +
90 ALA* 4.8 7.4 - - - -
313 THR* 4.5 7.9 - - - -
314 CYS* 3.6 16.1 - - - -
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Residues in contact with VAL 55
.
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
51 ILE* 3.1 29.3 + - + +
52 ILE* 4.3 2.9 - - - +
54 GLY* 1.3 74.2 - - - +
56 SER* 1.3 54.5 - - - +
59 LEU* 2.8 51.8 + - + +
87 LEU* 3.8 12.0 - - + +
90 ALA* 4.0 19.3 - - + -
91 ILE* 5.8 0.7 - - + +
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Residues in contact with SER 56
.
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
52 ILE 3.6 12.2 + - - -
53 LEU* 3.1 16.7 + - - +
55 VAL* 1.3 78.4 - - - +
57 GLY* 1.3 61.1 + - - +
59 LEU* 4.0 3.9 - - - +
60 ALA* 2.8 38.1 + - - +
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Residues in contact with GLY 57
.
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
53 LEU* 2.9 15.2 + - - -
54 GLY* 5.4 0.4 - - - -
56 SER* 1.3 81.1 + - - +
58 ASN* 1.3 57.8 + - - +
60 ALA* 3.8 4.7 - - - +
61 LEU* 3.2 31.7 + - - +
317 PRO* 4.3 11.5 - - - +
328 GLN* 4.7 4.3 + - - -
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Residues in contact with ASN 58
.
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
54 GLY* 2.8 28.0 + - - +
57 GLY* 1.3 71.0 - - - +
59 LEU* 1.3 60.9 + - - +
61 LEU* 3.2 3.5 + - - +
62 ILE* 3.0 14.4 + - - +
83 SER* 2.7 44.8 + - - +
86 ASP* 2.9 37.8 + - - +
87 LEU* 3.6 11.0 - - + -
313 THR* 2.9 19.1 - - - +
314 CYS* 4.6 1.0 - - - -
317 PRO* 3.1 19.2 - - - +
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Residues in contact with LEU 59
.
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
55 VAL* 2.8 35.3 + - + +
56 SER* 4.0 3.4 - - - +
58 ASN* 1.3 68.4 - - - +
60 ALA* 1.3 65.1 + - - +
62 ILE* 3.1 20.7 - - + +
63 ILE* 3.0 48.3 + - + +
87 LEU* 3.7 16.7 - - + +
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Residues in contact with ALA 60
.
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
56 SER 2.8 24.4 + - - +
57 GLY* 3.8 5.6 - - - +
59 LEU* 1.3 73.0 - - - +
61 LEU* 1.3 57.8 + - - +
63 ILE* 3.2 9.2 + - - +
64 ILE* 2.9 44.4 + - + +
328 GLN* 5.1 5.6 - - - +
332 GLN* 5.2 9.0 - - + +
335 PHE* 5.6 5.8 - - + -
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Residues in contact with LEU 61
.
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
57 GLY 3.2 13.2 + - - +
58 ASN* 3.2 8.7 + - - +
60 ALA* 1.3 77.6 - - - +
62 ILE* 1.3 61.2 + - - +
64 ILE* 3.4 9.4 + - + +
65 ILE* 3.1 33.7 + - + +
79 ILE* 3.3 35.2 - - + -
83 SER* 4.1 9.9 - - - +
317 PRO* 3.4 32.5 - - + +
320 TYR* 4.6 0.4 - - + -
327 PHE* 3.9 8.5 - - + -
328 GLN* 3.2 44.9 - - + +
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Residues in contact with ILE 62
.
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
58 ASN 3.0 15.5 + - - +
59 LEU* 3.1 40.8 - - + +
61 LEU* 1.3 71.4 - - - +
63 ILE* 1.3 62.5 + - + +
65 ILE* 3.6 1.9 + - - +
66 LEU* 3.2 29.0 + - + +
80 VAL* 3.7 28.1 - - + +
83 SER* 3.3 13.6 + - - +
84 PHE* 4.2 30.5 - - + -
87 LEU* 4.2 11.0 - - + -
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Residues in contact with ILE 63
.
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
59 LEU* 3.0 57.3 + - + +
60 ALA* 3.5 7.6 - - - +
62 ILE* 1.3 75.8 - - + +
64 ILE* 1.3 56.4 + - - +
66 LEU* 3.7 5.0 - - - +
67 LYS* 2.9 46.4 + - + +
335 PHE* 3.3 39.3 - - + -
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Residues in contact with ILE 64
.
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
60 ALA* 2.9 38.3 + - + +
61 LEU* 3.7 21.3 - - + +
63 ILE* 1.3 73.5 - - - +
65 ILE* 1.4 62.0 + - - +
67 LYS* 3.1 6.1 + - - -
68 GLN* 2.8 55.5 + - - +
327 PHE* 3.4 12.3 - - + -
328 GLN* 4.7 0.2 - - - +
331 LEU* 4.0 0.9 - - + +
332 GLN* 3.0 55.6 - - + +
335 PHE* 4.2 17.0 - - + -
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Residues in contact with ILE 65
.
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
61 LEU* 3.1 19.5 + - + +
62 ILE 3.9 3.8 - - - +
64 ILE* 1.4 72.3 - - - +
66 LEU* 1.3 54.7 + - - +
68 GLN* 2.9 14.5 - - - +
71 MET* 3.6 18.6 - - - +
72 ARG* 2.8 30.1 + - - +
76 ASN* 3.6 19.3 - - + +
77 ILE* 5.8 2.7 - - + -
79 ILE* 3.6 12.8 - - + +
80 VAL* 3.3 51.6 - - + +
327 PHE* 3.1 29.8 - - + -
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Residues in contact with LEU 66
.
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
62 ILE* 3.2 19.3 + - + +
63 ILE* 3.7 6.1 - - - +
65 ILE* 1.3 77.4 - - - +
67 LYS* 1.3 72.0 + - + +
69 LYS* 3.6 11.5 - - - +
72 ARG* 3.2 25.2 + - - +
80 VAL* 5.8 0.6 - - + +
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Residues in contact with LYS 67
.
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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63 ILE* 2.9 41.2 + - + +
64 ILE* 3.7 4.9 - - - +
66 LEU* 1.3 80.5 - - + +
68 GLN* 1.3 58.7 + - - +
69 LYS* 2.9 27.1 + - - +
335 PHE* 3.3 29.4 - - + -
360 SER* 4.9 0.2 - - - -
361 LYS* 3.1 43.4 + - + +
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Residues in contact with GLN 68
.
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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64 ILE* 2.8 50.0 + - - +
65 ILE 2.9 6.4 - - - +
66 LEU 4.0 0.7 - - - -
67 LYS* 1.3 75.0 - - - +
69 LYS* 1.3 62.2 + - - +
70 GLU 3.4 0.2 - - - -
71 MET* 3.3 23.7 + - + +
72 ARG* 2.8 22.4 + - - -
327 PHE* 2.9 30.8 - - - -
331 LEU* 3.5 26.4 + - + +
335 PHE* 5.3 1.6 - - - +
359 VAL* 3.7 26.2 + - + +
360 SER* 3.5 10.6 + - - +
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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