Contacts of the helix formed by residues 48 - 69 (chain B) 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 B).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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9B GLU* 3.8 4.0 - - - -
45B ALA 3.1 11.6 + - - +
46B LYS 3.3 1.2 - - - -
47B ARG* 1.3 79.7 - - - +
49B PRO* 1.3 68.0 - - - +
50B GLY 3.1 2.7 - - - -
51B GLY* 2.7 23.9 + - - -
52B VAL* 3.1 12.9 + - - +
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Residues in contact with PRO 49 (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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204A P4C 6.4 0.4 - - - -
6B PHE* 3.8 16.7 - - + -
9B GLU* 3.6 13.7 - - - +
48B GLY* 1.3 83.1 - - - +
50B GLY* 1.3 59.9 + - - +
52B VAL* 3.5 11.9 + - + +
53B TRP* 3.2 21.8 + - - +
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Residues in contact with GLY 50 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
6B PHE* 3.6 27.9 - - - -
9B GLU* 3.2 19.7 + - - -
10B ALA* 3.3 17.5 - - - +
48B GLY 2.9 1.6 + - - -
49B PRO* 1.3 79.1 - - - +
51B GLY* 1.3 56.8 + - - +
53B TRP* 3.3 3.8 + - - +
54B ALA 3.0 22.5 + - - -
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Residues in contact with GLY 51 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
9B GLU* 3.5 20.0 + - - +
13B GLY* 4.3 5.6 - - - -
44B ALA* 3.1 29.5 - - - +
47B ARG* 4.3 0.7 - - - -
48B GLY 2.7 13.3 + - - -
50B GLY* 1.3 68.8 - - - -
52B VAL* 1.3 58.5 + - - -
54B ALA* 3.3 1.8 + - - +
55B ALA* 2.8 31.4 + - - +
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Residues in contact with VAL 52 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
44B ALA 4.0 0.6 + - - -
45B ALA* 3.9 26.7 - - + +
48B GLY 3.1 15.6 + - - +
49B PRO* 3.7 11.0 - - + +
51B GLY* 1.3 74.8 - - - +
53B TRP* 1.3 63.7 + - - +
55B ALA* 3.3 7.2 + - - +
56B GLU* 3.1 33.4 + - - +
87B ARG* 4.0 20.1 - - + +
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Residues in contact with TRP 53 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
3A PHE* 3.5 50.5 - + - -
6A PHE* 3.8 26.7 - + + -
7A LEU* 4.0 13.7 - - + -
6B PHE* 3.8 32.1 - + + -
10B ALA* 4.0 17.5 - - + -
49B PRO 3.2 11.0 + - - +
50B GLY 3.5 6.1 - - - +
51B GLY 3.2 0.2 - - - -
52B VAL* 1.3 81.5 - - - +
54B ALA* 1.3 60.1 + - - +
56B GLU* 3.5 10.6 + - + +
57B ALA* 3.2 20.6 + - - +
202B P4C 2.6 66.5 + - - +
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Residues in contact with ALA 54 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
3A PHE* 4.1 23.6 - - + -
10B ALA* 3.3 28.5 - - - +
13B GLY 4.5 0.7 - - - -
14B ALA* 4.2 13.7 - - + +
17B MET* 5.0 0.2 - - - -
50B GLY 3.0 13.0 + - - +
51B GLY* 3.8 4.0 - - - +
53B TRP* 1.3 73.2 - - - +
55B ALA* 1.3 66.9 + - - +
57B ALA* 4.5 0.4 - - - -
58B ILE* 2.9 33.0 + - + +
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Residues in contact with ALA 55 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
17B MET* 3.9 14.4 - - - +
41B ASN* 3.4 24.7 - - - +
44B ALA* 3.9 15.6 - - + +
51B GLY 2.8 17.9 + - - +
52B VAL* 3.6 5.4 - - - +
54B ALA* 1.3 77.0 - - - +
56B GLU* 1.3 56.8 + - - +
58B ILE 3.8 0.2 - - - -
59B SER* 2.8 35.9 + - - -
87B ARG* 3.8 12.1 - - + +
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Residues in contact with GLU 56 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
52B VAL* 3.1 23.1 + - - +
53B TRP* 3.6 13.5 - - + +
55B ALA* 1.3 77.3 - - - +
57B ALA* 1.3 65.0 + - - +
59B SER* 3.3 1.2 + - - -
60B ASP* 2.9 37.7 + - - +
87B ARG* 3.3 34.0 + - - +
202B P4C 6.2 1.8 - - - -
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Residues in contact with ALA 57 (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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0A MET* 3.8 10.1 + - - +
3A PHE* 3.7 42.2 - - + -
53B TRP 3.2 9.6 + - - +
54B ALA 3.3 3.1 + - - +
56B GLU* 1.3 80.8 - - - +
58B ILE* 1.3 58.0 + - + +
60B ASP* 3.5 8.0 - - - +
61B ALA* 2.9 27.2 + - - +
202B P4C 4.8 12.9 - - - -
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Residues in contact with ILE 58 (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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0A MET* 3.9 29.6 - - + -
3A PHE* 5.7 1.3 - - + -
14B ALA* 3.6 40.4 - - + +
17B MET* 3.8 33.4 - - + -
18B TRP 5.6 0.4 - - - +
54B ALA* 2.9 21.6 + - + +
57B ALA* 1.3 75.2 - - + +
59B SER* 1.3 60.0 + - - +
61B ALA* 3.6 2.1 - - + +
62B ARG* 2.8 28.6 + - - +
203B P4C 3.9 21.0 - - - +
4D PHE* 5.2 4.3 - - + -
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Residues in contact with SER 59 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
17B MET* 3.6 3.7 - - - +
41B ASN* 3.1 28.1 + - - -
55B ALA 2.8 22.8 + - - -
56B GLU 3.7 2.0 - - - -
58B ILE* 1.3 74.2 - - - +
60B ASP* 1.3 61.8 + - - +
62B ARG* 3.3 16.5 + - - +
63B GLU* 2.9 30.2 + - - +
83B ASN* 3.5 17.0 + - - -
87B ARG* 3.2 16.2 + - - -
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Residues in contact with ASP 60 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
0A MET 6.3 0.2 - - - +
56B GLU* 2.9 25.6 + - - +
57B ALA* 3.5 7.5 - - - +
59B SER* 1.3 77.5 - - - +
61B ALA* 1.3 62.4 + - - +
63B GLU* 3.4 12.6 + - - +
64B ASN* 3.1 21.5 + - - +
87B ARG* 5.5 1.0 + - - -
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Residues in contact with ALA 61 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
0A MET* 3.6 34.1 - - + +
57B ALA 2.9 17.2 + - - +
58B ILE* 3.6 6.3 - - + +
59B SER 3.2 0.2 - - - -
60B ASP* 1.3 74.9 - - - +
62B ARG* 1.3 59.2 + - - +
64B ASN* 3.2 6.6 + - - +
65B ILE* 3.0 33.6 + - + +
203B P4C 6.0 0.9 - - - -
18C TRP* 3.8 17.2 - - + -
203C P4C 6.3 0.4 - - - -
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Residues in contact with ARG 62 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
17B MET* 4.8 2.4 - - - +
24B MET* 6.0 0.7 - - - -
37B HIS* 3.3 23.0 + - - +
41B ASN* 4.3 2.6 - - - +
58B ILE 2.8 20.6 + - - +
59B SER* 3.5 22.2 + - - +
61B ALA* 1.3 70.5 - - - +
63B GLU* 1.3 72.5 + - - +
65B ILE* 3.2 8.0 + - - +
66B GLN* 2.9 53.3 + - - +
79B ASP* 4.1 14.3 - - - +
80B GLN* 6.1 0.4 - - - +
83B ASN* 2.4 47.5 + - - +
203B P4C 3.3 60.2 + - - +
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Residues in contact with GLU 63 (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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59B SER 2.9 17.3 + - - +
60B ASP* 3.6 13.2 - - - +
62B ARG* 1.3 82.5 - - - +
64B ASN* 1.3 63.4 + - - +
66B GLN* 3.4 11.3 + - - +
67B ARG* 2.4 60.6 + - - +
71B HIS* 6.2 0.2 - - - -
76B SER* 4.5 11.3 + - - +
79B ASP* 6.5 0.7 - - + -
80B GLN* 3.1 38.5 - - + +
83B ASN* 5.8 0.4 + - - +
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Residues in contact with ASN 64 (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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60B ASP 3.1 10.9 + - - +
61B ALA* 3.3 13.0 - - - +
63B GLU* 1.3 80.5 - - - +
65B ILE* 1.3 62.7 + - - +
67B ARG* 3.4 6.8 + - - +
68B PHE 3.1 4.5 + - - -
18C TRP* 4.5 11.9 - - + +
21C TYR* 3.0 33.1 + - - -
22C SER* 5.9 1.4 + - - -
25C ARG* 3.0 52.4 + - - +
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Residues in contact with ILE 65 (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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61B ALA* 3.0 18.9 + - + +
62B ARG* 3.2 9.2 + - - +
64B ASN* 1.3 75.7 - - - +
66B GLN* 1.3 65.3 + - - +
68B PHE* 3.0 19.4 + - - +
69B PHE* 3.2 30.2 + - + -
203B P4C 4.2 15.5 - - - -
18C TRP* 4.0 12.1 - - + -
21C TYR* 3.3 34.5 - - + +
65C ILE* 4.0 21.3 - - + -
69C PHE* 4.5 0.2 - - + -
203C P4C 3.8 24.9 - - - +
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Residues in contact with GLN 66 (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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24B MET* 5.5 3.2 - - - +
33B ASP* 4.3 7.5 + - - -
37B HIS* 4.3 9.9 + - - -
62B ARG* 2.9 51.9 + - - +
63B GLU* 3.8 6.2 - - - +
65B ILE* 1.3 77.7 - - - +
67B ARG* 1.3 61.0 + - - +
69B PHE* 3.1 11.6 + - - +
70B GLY 3.2 0.5 + - - -
71B HIS* 3.0 52.3 + - + +
79B ASP* 3.8 16.3 + - - +
203B P4C 4.3 17.3 + - - +
69C PHE* 4.4 18.3 - - + -
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Residues in contact with ARG 67 (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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63B GLU* 2.4 60.7 + - - +
64B ASN* 3.7 9.0 - - - +
66B GLN* 1.3 73.2 - - - +
68B PHE* 1.3 67.2 + - - +
70B GLY* 2.9 14.4 + - - -
71B HIS* 3.8 19.7 + - + +
73B ALA* 5.6 6.1 - - - +
76B SER* 3.8 19.3 + - - +
77B LEU* 6.4 0.2 - - - +
25C ARG* 3.8 21.8 - - - +
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Residues in contact with PHE 68 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
64B ASN 3.1 4.8 + - - -
65B ILE 3.0 11.1 + - - +
67B ARG* 1.3 77.2 - - - +
69B PHE* 1.3 92.0 + + - +
70B GLY 3.5 2.3 + - - -
21C TYR* 3.3 18.6 - + - +
24C MET* 4.2 26.0 - - + -
25C ARG* 3.0 53.3 - - + +
33C ASP* 5.8 2.5 - - - -
203C P4C 4.4 6.7 - - - -
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Residues in contact with PHE 69 (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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65B ILE* 3.2 33.1 + - + -
66B GLN 3.1 9.5 + - - +
67B ARG 3.0 1.2 - - - -
68B PHE* 1.3 96.9 - + - +
70B GLY* 1.3 58.1 + - - +
71B HIS 3.6 0.4 + - - -
65C ILE* 4.3 4.9 - - + -
66C GLN* 4.3 24.0 - - + -
69C PHE* 3.4 59.3 - + + -
203C P4C 3.8 20.2 - - - -
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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