Contacts of the helix formed by residues 48 - 69 (chain C) 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 C).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
9C GLU* 4.1 1.6 - - - -
45C ALA 3.0 10.9 + - - +
46C LYS 3.2 1.7 - - - -
47C ARG* 1.3 80.2 - - - +
49C PRO* 1.3 71.5 - - - +
50C GLY 3.3 2.5 - - - -
51C GLY* 2.9 17.7 + - - -
52C VAL* 3.1 16.3 + - - +
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Residues in contact with PRO 49 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
6C PHE* 3.9 14.8 - - + -
9C GLU* 3.5 16.4 - - - +
48C GLY* 1.3 82.9 - - - +
50C GLY* 1.3 60.8 + - - +
52C VAL* 3.3 12.1 + - + +
53C TRP* 3.1 22.0 + - - +
202C P4C 5.9 0.3 - - - +
202D P4C 6.0 2.2 - - - -
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Residues in contact with GLY 50 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
6C PHE* 3.3 36.9 - - - -
9C GLU* 3.1 14.1 + - - -
10C ALA* 3.2 21.0 - - - +
49C PRO* 1.3 78.9 - - - +
51C GLY* 1.3 57.6 + - - +
53C TRP* 3.5 2.6 - - - +
54C ALA 3.1 20.4 + - - -
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Residues in contact with GLY 51 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
9C GLU* 3.7 19.3 - - - +
10C ALA* 4.4 0.2 - - - -
13C GLY* 4.3 5.6 - - - -
44C ALA* 3.3 28.2 - - - +
47C ARG* 4.5 1.1 - - - -
48C GLY 2.9 6.5 + - - -
50C GLY* 1.3 74.3 - - - +
52C VAL* 1.3 64.6 + - - +
53C TRP 3.1 1.3 - - - -
54C ALA* 3.3 1.4 + - - +
55C ALA* 2.9 25.3 + - - +
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Residues in contact with VAL 52 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
44C ALA 4.1 0.6 + - - -
45C ALA* 3.9 26.0 - - + +
48C GLY 3.1 16.4 + - - +
49C PRO* 3.5 11.0 - - + +
51C GLY* 1.3 74.5 - - - +
53C TRP* 1.3 63.8 + - - +
55C ALA* 3.3 6.3 + - - +
56C GLU* 3.1 39.6 + - - +
87C ARG* 3.9 22.4 - - + +
205C P4C 5.9 2.9 - - - -
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Residues in contact with TRP 53 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
6C PHE* 3.7 31.4 - + + -
7C LEU* 5.8 0.2 - - + -
10C ALA* 3.9 17.7 - - + -
49C PRO 3.1 10.1 + - - +
50C GLY 3.5 6.1 - - - +
51C GLY 3.1 0.2 - - - -
52C VAL* 1.3 81.9 - - - +
54C ALA* 1.3 60.7 - - - +
56C GLU* 3.6 12.6 + - + +
57C ALA* 3.3 21.9 + - + +
202C P4C 3.7 37.7 + - - +
2D SER* 4.7 2.5 + - - -
3D PHE* 3.6 57.0 - + - +
6D PHE* 3.7 35.7 - + + -
7D LEU* 4.0 14.4 - - + -
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Residues in contact with ALA 54 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
10C ALA 3.2 27.4 - - - +
13C GLY 4.3 0.9 - - - -
14C ALA* 3.9 15.5 - - - +
17C MET* 5.0 0.2 - - - -
50C GLY 3.1 11.6 + - - +
51C GLY 3.3 6.9 + - - +
53C TRP* 1.3 77.1 - - - +
55C ALA* 1.3 57.6 + - - +
57C ALA* 3.3 2.3 + - - +
58C ILE* 2.9 36.9 + - + +
3D PHE* 3.8 22.0 - - + -
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Residues in contact with ALA 55 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
17C MET* 4.0 16.1 - - - +
41C ASN* 3.2 25.8 - - - +
44C ALA* 3.9 16.1 - - + +
51C GLY 2.9 17.9 + - - +
52C VAL* 3.5 6.3 - - - +
54C ALA* 1.3 77.4 - - - +
56C GLU* 1.3 56.9 + - - +
58C ILE 3.3 0.2 + - - -
59C SER* 2.8 35.2 + - - -
87C ARG* 3.9 6.3 - - - +
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Residues in contact with GLU 56 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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52C VAL* 3.1 29.1 + - - +
53C TRP* 3.7 13.1 - - + +
55C ALA* 1.3 76.1 - - - +
57C ALA* 1.3 64.7 + - - +
59C SER* 3.7 0.7 - - - -
60C ASP* 3.0 33.8 + - - +
87C ARG* 3.7 34.2 + - - +
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Residues in contact with ALA 57 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
53C TRP* 3.3 13.0 + - - +
54C ALA 3.5 7.6 - - - +
56C GLU* 1.3 80.0 - - - +
58C ILE* 1.3 58.6 + - - +
60C ASP* 3.4 7.6 + - - +
61C ALA* 3.1 26.2 + - - +
0D MET* 3.9 12.7 + - + +
2D SER* 6.0 0.4 - - - +
3D PHE* 3.8 34.1 - - + -
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Residues in contact with ILE 58 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
4A PHE* 5.1 6.5 - - + -
14C ALA* 3.6 38.4 - - + +
17C MET* 3.8 28.3 - - + -
54C ALA* 2.9 22.1 + - + +
55C ALA 4.0 2.5 - - - +
57C ALA* 1.3 73.4 - - + +
59C SER* 1.3 61.1 + - - +
61C ALA* 3.3 1.8 + - - +
62C ARG* 2.8 27.4 + - - +
203C P4C 3.8 23.7 - - - +
204C P4C 3.9 13.2 - - - +
0D MET* 4.0 27.8 - - + -
3D PHE* 5.7 1.8 - - + -
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Residues in contact with SER 59 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
17C MET* 3.6 3.9 - - - +
41C ASN* 3.1 28.4 + - - -
55C ALA 2.8 19.3 + - - -
56C GLU 3.7 1.6 - - - -
58C ILE* 1.3 77.0 - - - +
60C ASP* 1.3 59.3 + - - +
62C ARG* 3.1 15.8 + - - +
63C GLU* 2.9 30.5 + - - +
83C ASN* 3.5 17.5 + - - -
87C ARG* 3.3 14.9 + - - -
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Residues in contact with ASP 60 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
56C GLU* 3.0 18.3 + - - +
57C ALA* 3.5 10.7 - - - +
59C SER* 1.3 77.1 - - - +
61C ALA* 1.3 58.1 + - - +
63C GLU* 3.6 11.7 + - - +
64C ASN* 3.1 26.0 + - - +
87C ARG* 5.4 1.7 + - - -
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Residues in contact with ALA 61 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
18B TRP* 3.7 28.9 - - + -
57C ALA 3.1 14.1 + - - +
58C ILE* 3.6 7.4 - - - +
59C SER 3.2 0.2 - - - -
60C ASP* 1.3 73.6 - - - +
62C ARG* 1.3 66.2 + - - +
64C ASN* 3.2 5.9 + - - +
65C ILE* 3.0 28.5 + - - +
203C P4C 4.3 8.5 - - - -
0D MET* 3.8 22.2 - - + +
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Residues in contact with ARG 62 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
17C MET* 5.1 0.4 - - - +
37C HIS* 3.2 31.2 + - - +
41C ASN* 4.3 1.0 - - - +
58C ILE 2.8 17.0 + - - +
59C SER* 3.1 22.5 + - - +
61C ALA* 1.3 78.4 - - - +
63C GLU* 1.3 62.9 + - - +
65C ILE* 3.3 4.6 + - - +
66C GLN* 2.8 65.5 + - - +
79C ASP* 4.1 11.5 - - - +
80C GLN* 6.4 0.2 - - - +
83C ASN* 2.3 49.1 + - - +
203C P4C 3.4 45.7 - - - -
204C P4C 3.6 13.4 + - - -
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Residues in contact with GLU 63 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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59C SER 2.9 16.5 + - - +
60C ASP* 3.8 9.8 - - - +
62C ARG* 1.3 80.7 - - - +
64C ASN* 1.3 68.2 + - - +
66C GLN* 3.8 10.8 - - + +
67C ARG* 3.0 44.4 + - + +
71C HIS* 5.8 0.9 - - + -
76C SER* 4.4 19.4 - - - +
79C ASP* 6.5 0.7 - - + -
80C GLN* 3.0 33.4 + - + +
83C ASN* 6.1 0.2 - - - +
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Residues in contact with ASN 64 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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18B TRP* 4.7 8.6 - - + -
21B TYR* 2.6 39.9 + - + -
22B SER* 5.9 0.8 + - - -
25B ARG* 3.1 53.5 + - - +
60C ASP 3.1 15.2 + - - +
61C ALA* 3.2 13.2 + - - +
63C GLU* 1.3 80.4 - - - +
65C ILE* 1.3 62.8 + - - +
67C ARG* 3.3 2.2 + - - +
68C PHE 3.1 3.3 + - - -
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Residues in contact with ILE 65 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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18B TRP* 4.4 11.0 - - + -
21B TYR* 3.4 27.4 - - + +
65B ILE* 4.0 20.9 - - + -
69B PHE* 4.3 4.0 - - + -
203B P4C 3.8 29.4 - - - -
61C ALA 3.0 24.1 + - - +
62C ARG* 3.8 4.7 - - - +
64C ASN* 1.3 73.3 - - - +
66C GLN* 1.3 66.2 + - - +
68C PHE* 2.9 18.7 + - - +
69C PHE* 3.3 31.4 - - + -
203C P4C 4.6 24.0 - - - -
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Residues in contact with GLN 66 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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69B PHE* 4.3 27.6 - - + -
33C ASP* 4.4 8.9 + - - -
37C HIS* 4.3 8.3 + - - -
62C ARG* 2.8 61.2 + - + +
63C GLU* 3.8 8.2 - - - +
65C ILE* 1.3 73.2 - - + +
67C ARG* 1.3 60.8 + - - +
69C PHE* 3.2 5.9 + - - +
70C GLY 3.2 17.0 + - - +
71C HIS* 3.5 43.2 + - + +
79C ASP* 3.8 10.8 + - - +
203C P4C 4.4 6.1 + - - +
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Residues in contact with ARG 67 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
25B ARG* 3.8 13.6 + - - +
63C GLU* 3.0 34.9 + - + +
64C ASN* 3.6 5.8 - - - +
66C GLN* 1.3 74.6 - - + +
68C PHE* 1.3 65.5 + - - +
70C GLY* 3.0 12.5 + - - -
71C HIS* 3.0 28.2 + - + +
73C ALA* 4.0 23.7 - - - +
76C SER* 3.6 23.3 - - - +
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Residues in contact with PHE 68 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
21B TYR* 3.6 23.6 - + - +
24B MET* 4.3 28.0 - - + -
25B ARG* 3.3 50.0 - - + +
203B P4C 4.8 2.7 - - - -
64C ASN 3.1 4.6 + - - -
65C ILE 2.9 12.7 + - - +
67C ARG* 1.3 78.8 - - - +
69C PHE* 1.3 87.8 + + - +
70C GLY 3.6 0.2 + - - -
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Residues in contact with PHE 69 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
65B ILE* 4.5 0.4 - - + -
66B GLN* 4.4 17.3 - - + -
69B PHE* 3.4 59.9 - + + -
203B P4C 4.1 17.9 - - - -
65C ILE* 3.3 36.7 + - + -
66C GLN 3.2 7.3 + - - +
67C ARG 3.1 0.2 - - - -
68C PHE* 1.3 100.5 - + - +
70C GLY* 1.3 63.2 + - - +
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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