Contacts of the helix formed by residues 48 - 69 (chain A) in PDB entry 4IP8
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 GLY 48 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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9A GLU* 3.7 4.5 - - - -
45A ALA 3.1 13.0 + - - +
46A LYS 3.2 1.7 - - - -
47A ARG* 1.3 78.9 - - - +
49A PRO* 1.3 67.2 - - - +
50A GLY 3.0 3.1 - - - -
51A GLY* 2.7 24.6 + - - -
52A VAL* 3.2 10.8 + - - -
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Residues in contact with PRO 49 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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6A PHE* 3.8 16.5 - - + -
9A GLU* 3.6 11.4 - - - +
48A GLY* 1.3 82.6 - - - +
50A GLY* 1.3 59.8 + - - +
52A VAL* 3.5 12.2 + - + +
53A TRP* 3.2 22.9 + - - +
204A P4C 5.4 1.8 - - + +
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Residues in contact with GLY 50 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
6A PHE* 3.6 38.0 - - - -
9A GLU* 3.4 8.1 + - - -
10A ALA* 3.3 18.4 - - - +
48A GLY 2.9 1.6 + - - -
49A PRO* 1.3 80.2 - - - +
51A GLY* 1.3 57.0 + - - +
53A TRP* 3.3 3.5 + - - +
54A ALA 3.0 23.6 + - - -
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Residues in contact with GLY 51 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
9A GLU* 3.4 20.0 + - - +
13A GLY* 4.3 5.8 - - - -
44A ALA* 3.1 28.9 - - - +
47A ARG* 4.3 0.4 - - - -
48A GLY 2.7 12.4 + - - -
50A GLY* 1.3 69.0 - - - -
52A VAL* 1.3 57.1 + - - -
54A ALA* 3.8 1.5 - - - +
55A ALA* 2.8 32.4 + - - +
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Residues in contact with VAL 52 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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44A ALA 3.9 0.6 + - - -
45A ALA* 3.8 31.9 - - + +
48A GLY 3.2 9.9 + - - +
49A PRO* 3.7 14.1 - - + +
51A GLY* 1.3 75.1 - - - +
53A TRP* 1.3 63.9 + - - +
55A ALA* 3.4 5.4 + - - +
56A GLU* 3.1 39.5 + - - +
87A ARG* 3.9 16.1 - - + +
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Residues in contact with TRP 53 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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6A PHE* 3.7 30.3 - + + -
10A ALA* 4.0 15.9 - - + -
49A PRO 3.2 11.4 + - - +
50A GLY 3.4 6.3 - - - +
51A GLY 3.1 0.2 - - - -
52A VAL* 1.3 78.8 - - - +
54A ALA* 1.3 63.6 + - - +
56A GLU* 3.4 11.8 + - + +
57A ALA* 3.2 20.3 + - - +
204A P4C 2.8 73.2 + - + -
3B PHE* 3.4 51.4 - + - -
6B PHE* 3.8 29.4 - + + -
7B LEU* 4.1 12.6 - - + -
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Residues in contact with ALA 54 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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10A ALA 3.2 28.0 - - - +
13A GLY 4.5 0.2 - - - -
14A ALA* 4.0 13.7 - - - +
17A MET* 5.0 0.2 - - - -
50A GLY 3.0 12.9 + - - +
51A GLY 3.8 4.0 - - - +
53A TRP* 1.3 75.0 - - - +
55A ALA* 1.3 66.1 + - - +
57A ALA* 3.3 1.3 + - - +
58A ILE* 3.0 31.2 + - + +
3B PHE* 3.8 25.1 - - + -
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Residues in contact with ALA 55 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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17A MET* 4.1 15.9 - - - +
41A ASN* 3.4 22.0 - - - +
44A ALA* 3.9 15.7 - - + +
51A GLY 2.8 19.0 + - - +
52A VAL 3.6 5.4 - - - +
54A ALA* 1.3 77.4 - - - +
56A GLU* 1.3 58.1 + - - +
58A ILE* 3.8 0.5 - - - +
59A SER* 2.9 35.9 + - - -
87A ARG* 3.9 10.3 - - + +
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Residues in contact with GLU 56 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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52A VAL* 3.1 27.8 + - - +
53A TRP* 3.7 12.9 - - + +
54A ALA 3.3 0.2 - - - -
55A ALA* 1.3 79.4 - - - +
57A ALA* 1.3 61.7 + - - +
59A SER* 3.4 0.9 + - - -
60A ASP* 3.0 33.5 + - - +
87A ARG* 3.2 34.8 + - - +
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Residues in contact with ALA 57 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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53A TRP 3.2 7.3 + - - +
54A ALA 3.7 5.8 - - - +
56A GLU* 1.3 80.5 - - - +
58A ILE* 1.3 58.6 + - - +
60A ASP* 3.5 8.2 - - - +
61A ALA* 3.0 25.3 + - - +
204A P4C 5.1 8.3 + - - +
0B MET* 3.8 11.4 + - - +
2B SER* 6.0 0.7 - - - +
3B PHE* 3.6 41.7 - - + -
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Residues in contact with ILE 58 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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14A ALA* 3.7 37.9 - - + +
17A MET* 3.9 32.1 - - + -
54A ALA* 3.0 23.2 + - + +
55A ALA 4.1 2.0 - - - +
57A ALA* 1.3 75.2 - - + +
59A SER* 1.3 56.2 + - - +
61A ALA* 3.1 5.2 + - - +
62A ARG* 2.6 34.7 + - + +
202A P4C 4.1 21.5 - - - +
0B MET* 3.7 26.2 - - + -
3B PHE* 5.5 1.8 - - + -
4C PHE* 5.1 4.0 - - + -
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Residues in contact with SER 59 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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17A MET* 3.7 3.1 - - - +
41A ASN* 3.2 20.3 + - - -
55A ALA 2.9 22.8 + - - -
56A GLU 3.7 1.8 - - - -
58A ILE* 1.3 77.4 - - - +
60A ASP* 1.3 60.0 + - - +
62A ARG* 3.3 18.4 + - - +
63A GLU* 2.9 30.1 + - - +
83A ASN* 3.5 15.1 + - - -
87A ARG* 3.2 23.6 + - - -
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Residues in contact with ASP 60 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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56A GLU* 3.0 19.5 + - - +
57A ALA* 3.5 12.0 - - - +
59A SER* 1.3 77.5 - - - +
61A ALA* 1.3 62.2 + - - +
63A GLU* 3.4 6.5 + - - +
64A ASN* 3.1 23.7 + - - +
87A ARG* 5.7 0.9 + - - -
0B MET 6.3 0.4 - - - +
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Residues in contact with ALA 61 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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57A ALA 3.0 15.4 + - - +
58A ILE* 3.1 7.8 + - - +
60A ASP* 1.3 74.1 - - - +
62A ARG* 1.3 65.0 + - - +
64A ASN* 3.2 5.3 + - - +
65A ILE* 3.1 28.9 + - + +
202A P4C 4.4 9.0 - - - +
0B MET* 3.6 34.3 - - + +
18D TRP* 3.9 16.6 - - + -
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Residues in contact with ARG 62 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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17A MET* 4.5 7.6 - - + +
37A HIS* 3.4 30.8 + - - +
41A ASN* 4.1 3.0 - - - +
58A ILE* 2.6 20.8 + - + +
59A SER* 3.5 22.0 + - - +
61A ALA* 1.3 74.0 - - - +
63A GLU* 1.3 69.0 + - - +
65A ILE* 3.2 2.5 + - - +
66A GLN* 2.9 46.8 + - - +
79A ASP* 4.1 17.6 - - - +
80A GLN* 6.2 0.4 - - - +
83A ASN* 2.5 48.0 + - - +
202A P4C 3.5 45.7 - - - +
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Residues in contact with GLU 63 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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59A SER 2.9 18.1 + - - +
60A ASP* 3.8 7.1 - - - +
62A ARG* 1.3 81.9 - - - +
64A ASN* 1.3 65.2 + - - +
66A GLN* 3.9 9.6 - - - +
67A ARG* 3.0 46.1 + - + +
71A HIS* 5.9 1.5 - - + -
76A SER* 4.4 22.8 - - - +
79A ASP* 6.0 0.6 - - + +
80A GLN* 2.5 44.1 + - - +
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Residues in contact with ASN 64 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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60A ASP 3.1 13.7 + - - +
61A ALA* 3.4 12.6 - - - +
63A GLU* 1.3 78.4 - - - +
65A ILE* 1.3 60.3 + - - +
67A ARG* 4.7 1.3 - - - -
68A PHE 3.2 16.3 + - - -
18D TRP* 4.4 12.1 - - + -
21D TYR* 2.8 37.7 + - - -
22D SER* 5.6 2.8 + - - -
25D ARG* 2.9 33.9 + - - +
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Residues in contact with ILE 65 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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61A ALA 3.1 17.0 + - - +
62A ARG* 3.2 5.6 + - - +
64A ASN* 1.3 74.1 - - - +
66A GLN* 1.3 67.6 + - - +
68A PHE* 3.0 19.1 + - - +
69A PHE* 3.2 30.1 + - + -
202A P4C 3.6 33.9 - - - +
18D TRP* 4.3 11.9 - - + -
21D TYR* 3.5 18.8 - - + +
65D ILE* 4.1 19.1 - - + -
69D PHE* 4.6 1.6 - - + -
203D P4C 4.1 32.1 - - - +
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Residues in contact with GLN 66 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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24A MET* 5.0 5.7 - - - +
33A ASP* 5.1 3.2 + - - +
37A HIS* 4.3 9.5 + - - -
62A ARG* 2.9 47.6 + - - +
63A GLU* 3.9 5.8 - - - +
65A ILE* 1.3 77.5 - - - +
67A ARG* 1.3 63.3 + - - +
69A PHE* 3.0 13.6 + - - +
70A GLY 3.1 0.9 + - - -
71A HIS* 3.1 54.3 + - + +
79A ASP* 3.8 13.2 + - - +
202A P4C 4.4 12.5 + - - +
68D PHE* 6.3 0.8 - - - -
69D PHE* 4.0 27.3 - - + -
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Residues in contact with ARG 67 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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63A GLU* 3.0 40.1 + - + +
64A ASN* 3.7 5.6 - - - +
65A ILE 3.2 0.2 - - - -
66A GLN* 1.3 72.9 - - - +
68A PHE* 1.3 65.7 + - - +
70A GLY* 3.1 12.6 + - - -
71A HIS* 3.8 22.4 + - + +
72A GLY 6.5 0.2 - - - -
73A ALA* 6.5 0.9 - - - +
76A SER* 5.1 8.8 + - - +
25D ARG* 3.5 24.5 + - - +
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Residues in contact with PHE 68 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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64A ASN 3.2 3.0 + - - -
65A ILE* 3.0 11.6 + - - +
67A ARG* 1.3 80.1 - - - +
69A PHE* 1.3 91.9 + + - +
70A GLY 3.5 0.7 + - - -
21D TYR* 3.6 26.0 - + - +
24D MET* 4.6 23.6 - - + -
25D ARG* 3.2 54.5 - - + +
33D ASP* 6.0 0.9 - - - -
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Residues in contact with PHE 69 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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65A ILE* 3.2 33.1 + - + -
66A GLN 3.0 10.2 + - - +
68A PHE* 1.3 105.1 - + - +
70A GLY* 1.3 56.2 + - - +
71A HIS 3.7 0.2 - - - -
21D TYR* 6.3 0.4 - + - -
65D ILE* 4.4 4.9 - - + -
66D GLN* 4.3 28.9 - - + -
69D PHE* 3.5 59.3 - + + -
203D P4C 5.3 4.3 - - - -
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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
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Atomic class I II III IV V VI VII VIII
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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