Contacts of the helix formed by residues 48 - 69 (chain D) 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 D).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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9D GLU* 3.9 1.8 - - - -
45D ALA 3.1 10.3 + - - +
46D LYS 3.2 0.8 - - - -
47D ARG* 1.3 81.3 - - - +
49D PRO* 1.3 69.0 - - - +
50D GLY 3.1 2.9 - - - -
51D GLY 2.7 20.3 + - - -
52D VAL* 2.9 16.9 + - - +
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Residues in contact with PRO 49 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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6D PHE* 3.9 14.6 - - + -
9D GLU* 3.2 17.0 - - - +
48D GLY* 1.3 82.5 - - - +
50D GLY* 1.3 60.9 + - - +
52D VAL* 3.4 10.7 + - + +
53D TRP* 3.0 24.9 + - - +
202D P4C 5.4 5.0 - - - +
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Residues in contact with GLY 50 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
6D PHE* 3.5 29.9 - - - -
9D GLU* 3.0 23.0 + - - -
10D ALA* 3.3 18.0 - - - +
49D PRO* 1.3 77.4 - - - +
51D GLY* 1.3 56.5 + - - +
53D TRP* 3.4 3.1 - - - +
54D ALA 3.0 21.8 + - - -
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Residues in contact with GLY 51 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
9D GLU* 3.6 18.4 + - - +
13D GLY* 4.2 5.6 - - - -
44D ALA* 3.2 28.6 - - - +
47D ARG* 4.3 0.9 - - - -
48D GLY 2.7 12.0 + - - -
50D GLY* 1.3 70.0 - - - +
52D VAL* 1.3 63.1 + - - -
54D ALA* 3.1 3.4 + - - +
55D ALA* 2.9 25.6 + - - +
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Residues in contact with VAL 52 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
44D ALA 4.0 1.0 + - - -
45D ALA* 3.9 28.3 - - + +
48D GLY 2.9 19.8 + - - +
49D PRO* 3.7 9.9 - - + +
51D GLY* 1.3 74.2 - - - +
53D TRP* 1.3 63.4 + - - +
55D ALA* 3.3 5.4 + - - +
56D GLU* 3.1 45.3 + - - +
87D ARG* 4.1 17.5 - - + +
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Residues in contact with TRP 53 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
3C PHE* 3.5 49.1 - + - -
6C PHE* 3.8 31.0 - + + -
7C LEU* 4.1 13.7 - - + -
6D PHE* 3.7 31.0 - + + -
7D LEU* 5.7 0.2 - - + -
10D ALA* 3.9 18.4 - - + -
49D PRO 3.0 17.1 + - - +
50D GLY 3.4 2.5 - - - +
52D VAL* 1.3 78.6 - - - +
54D ALA* 1.3 61.3 - - - +
56D GLU* 3.4 17.7 + - + +
57D ALA* 3.2 20.7 + - + +
202D P4C 3.1 66.6 + - - -
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Residues in contact with ALA 54 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
3C PHE* 3.9 20.9 - - + -
10D ALA* 3.3 27.4 - - - +
13D GLY 4.3 1.6 - - - -
14D ALA* 3.9 15.3 - - - +
17D MET* 5.0 0.2 - - - -
50D GLY 3.0 11.1 + - - +
51D GLY 3.1 7.4 + - - +
53D TRP* 1.3 76.6 - - - +
55D ALA* 1.3 63.3 + - - +
57D ALA* 3.3 1.9 + - - +
58D ILE* 2.9 32.2 + - + +
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Residues in contact with ALA 55 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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17D MET* 4.0 14.9 - - - +
41D ASN* 3.1 26.0 - - - +
44D ALA* 3.9 16.3 - - + +
51D GLY 2.9 17.0 + - - +
52D VAL* 3.6 6.7 - - - +
54D ALA* 1.3 76.2 - - - +
56D GLU* 1.3 57.1 + - - +
59D SER* 2.7 38.9 + - - -
87D ARG* 3.9 7.2 - - + +
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Residues in contact with GLU 56 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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52D VAL* 3.1 28.1 + - - +
53D TRP* 3.7 23.0 - - - +
54D ALA 3.3 0.2 - - - -
55D ALA* 1.3 77.5 - - - +
57D ALA* 1.3 63.5 + - - +
59D SER* 3.8 0.5 - - - -
60D ASP* 3.1 34.2 + - - +
87D ARG* 3.4 34.5 + - - +
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Residues in contact with ALA 57 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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0C MET* 3.8 10.8 + - - +
2C SER* 5.9 0.9 - - - +
3C PHE* 3.7 39.3 - - + -
53D TRP* 3.2 7.9 + - + +
54D ALA 3.7 6.1 - - - +
56D GLU* 1.3 79.0 - - - +
58D ILE* 1.3 59.0 + - + +
60D ASP* 3.5 6.9 + - - +
61D ALA* 3.0 26.9 + - - +
202D P4C 5.3 6.3 - - - +
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Residues in contact with ILE 58 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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4B PHE* 5.2 6.5 - - + -
0C MET* 4.1 26.0 - - + -
3C PHE* 5.8 1.8 - - + -
14D ALA* 3.6 38.4 - - + +
17D MET* 3.9 18.4 - - + -
18D TRP 5.6 0.2 - - - +
54D ALA* 2.9 20.0 + - + +
55D ALA 4.1 1.6 - - - +
57D ALA* 1.3 75.6 - - + +
59D SER* 1.3 61.7 + - - +
61D ALA* 3.6 2.3 - - + +
62D ARG* 2.8 28.1 + - - +
203D P4C 3.7 34.1 - - - +
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Residues in contact with SER 59 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
17D MET* 3.6 5.1 - - - +
41D ASN* 3.1 19.2 + - - -
55D ALA 2.7 24.6 + - - -
56D GLU 3.8 1.8 - - - -
58D ILE* 1.3 74.8 - - - +
60D ASP* 1.3 60.8 + - - +
62D ARG* 3.2 12.9 + - - +
63D GLU* 2.9 35.0 + - - +
83D ASN* 3.5 17.2 - - - -
87D ARG* 3.1 23.8 + - - -
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Residues in contact with ASP 60 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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56D GLU* 3.1 21.9 + - - +
57D ALA* 3.6 6.5 - - - +
59D SER* 1.3 81.2 - - - +
61D ALA* 1.3 60.5 + - - +
63D GLU* 3.4 18.2 + - - +
64D ASN* 3.0 22.2 + - - +
87D ARG* 5.4 1.9 + - - -
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Residues in contact with ALA 61 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
18A TRP* 3.8 15.6 - - + -
0C MET* 3.6 33.2 - - + +
57D ALA 3.0 17.4 + - - +
58D ILE* 3.6 5.8 - - + +
60D ASP* 1.3 76.2 - - - +
62D ARG* 1.3 58.7 + - - +
64D ASN* 3.2 9.2 + - - +
65D ILE* 3.0 34.9 + - + +
203D P4C 6.5 0.4 - - - -
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Residues in contact with ARG 62 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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37D HIS* 3.3 31.2 + - - -
41D ASN* 4.3 0.8 - - - +
58D ILE 2.8 17.7 + - - +
59D SER* 3.6 12.5 + - - +
61D ALA* 1.3 73.4 - - - +
63D GLU* 1.3 78.5 + - - +
65D ILE* 3.3 6.2 + - - +
66D GLN* 2.8 63.6 + - + +
79D ASP* 4.1 8.5 - - - +
83D ASN* 2.4 47.4 + - - +
203D P4C 3.3 58.3 + - - +
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Residues in contact with GLU 63 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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59D SER 2.9 19.0 + - - +
60D ASP* 3.6 22.1 - - - +
62D ARG* 1.3 92.1 - - - +
64D ASN* 1.3 63.4 + - - +
66D GLN* 3.7 9.5 - - - +
67D ARG* 3.2 28.6 + - - +
71D HIS* 6.3 0.2 - - - -
76D SER* 3.2 30.1 + - - +
79D ASP* 5.6 0.4 - - + -
80D GLN* 2.9 48.0 + - - +
83D ASN* 4.6 4.5 + - - -
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Residues in contact with ASN 64 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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18A TRP* 4.6 10.7 - - + -
21A TYR* 2.8 36.5 + - - -
25A ARG* 2.8 51.3 + - - +
60D ASP 3.0 13.4 + - - +
61D ALA* 3.2 14.1 + - - +
63D GLU* 1.3 78.7 - - - +
65D ILE* 1.3 61.6 + - - +
67D ARG* 3.5 4.1 + - - +
68D PHE 3.2 4.3 + - - -
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Residues in contact with ILE 65 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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18A TRP* 4.5 8.1 - - + -
21A TYR* 3.3 25.1 - - + +
65A ILE* 4.1 24.0 - - + -
69A PHE* 4.4 4.3 - - + -
202A P4C 4.0 35.2 - - - +
61D ALA* 3.0 21.7 + - + +
62D ARG* 3.8 3.6 - - - +
64D ASN* 1.3 71.1 - - - +
66D GLN* 1.3 68.8 + - + +
68D PHE* 2.9 17.3 + - - +
69D PHE* 3.3 32.3 + - + -
203D P4C 4.6 15.7 - - - +
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Residues in contact with GLN 66 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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69A PHE* 4.3 26.5 - - + -
33D ASP* 4.7 9.3 + - - -
37D HIS* 4.2 9.9 + - - -
62D ARG* 2.8 58.5 + - + +
63D GLU* 3.7 8.2 - - - +
64D ASN 3.4 0.2 - - - -
65D ILE* 1.3 73.5 - - + +
67D ARG* 1.3 58.6 + - - +
69D PHE* 3.3 12.1 + - - +
70D GLY 3.4 0.9 + - - -
71D HIS* 3.1 52.9 + - + +
76D SER* 5.9 0.3 - - - -
79D ASP* 3.9 11.2 + - - +
203D P4C 5.2 2.0 - - - +
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Residues in contact with ARG 67 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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25A ARG* 3.8 22.7 - - - +
63D GLU* 3.2 19.0 + - - +
64D ASN* 3.7 7.4 - - - +
66D GLN* 1.3 73.2 - - - +
68D PHE* 1.3 67.7 + - - +
69D PHE 3.0 1.3 - - - -
70D GLY* 3.1 11.1 + - - -
71D HIS* 3.5 34.6 + - + +
73D ALA* 4.5 20.2 - - - +
76D SER* 4.8 10.3 - - - +
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Residues in contact with PHE 68 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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21A TYR* 3.6 26.9 - + - +
24A MET* 4.2 30.7 - - + -
25A ARG* 3.5 51.1 - - + +
28A ASN* 6.3 1.6 - - - -
66A GLN* 6.3 0.9 - - - -
202A P4C 4.8 1.1 - - - -
64D ASN 3.2 4.9 + - - -
65D ILE* 2.9 11.1 + - + +
67D ARG* 1.3 77.2 - - - +
69D PHE* 1.3 87.8 + + - +
70D GLY 3.3 0.6 + - - -
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Residues in contact with PHE 69 (chain D).
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* 4.6 1.6 - - + -
66A GLN* 4.0 30.1 - - + -
69A PHE* 3.5 57.8 - + + -
71A HIS* 6.2 1.1 - - - -
202A P4C 4.2 7.9 - - - -
65D ILE* 3.3 38.3 + - + -
66D GLN 3.3 7.8 + - - +
67D ARG 3.0 0.4 - - - -
68D PHE* 1.3 103.6 - + - +
70D GLY* 1.3 55.6 + - - +
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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