Contacts of the helix formed by residues 46 - 66 (chain C) in PDB entry 1J7H
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 ASP 46 (chain C).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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44C PRO* 3.1 2.5 - - + +
45C ALA* 1.3 74.6 - - - +
47C ILE* 1.3 56.6 + - - +
48C VAL* 2.9 10.9 - - - +
49C ALA* 2.6 50.2 + - + +
50C GLN* 2.7 14.6 + - - +
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Residues in contact with ILE 47 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
45C ALA 2.7 14.1 + - - +
46C ASP* 1.3 69.2 - - - +
48C VAL* 1.3 55.7 + - + +
50C GLN* 3.2 28.3 - - + +
51C ALA* 2.8 36.6 + - - +
81C ASP* 6.0 2.0 - - + -
84C ASP* 3.3 45.3 - - + +
87C ALA* 5.3 2.2 - - + -
88C VAL* 3.8 23.6 - - + -
120C GLY* 5.1 10.1 - - - +
121C LEU* 4.4 2.9 - - + +
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Residues in contact with VAL 48 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
46C ASP* 2.7 13.0 + - - +
47C ILE* 1.3 77.2 - - + +
49C ALA* 1.3 59.6 + - - +
51C ALA* 3.3 5.1 + - + +
52C ARG* 2.9 31.1 + - + +
87C ALA* 4.5 24.2 - - + +
88C VAL* 5.9 0.9 - - - +
91C GLU* 5.0 21.2 - - + +
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Residues in contact with ALA 49 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
44C PRO* 4.4 8.7 - - + -
46C ASP* 2.6 33.7 + - + +
48C VAL* 1.3 75.7 - - - +
50C GLN* 1.3 56.8 + - - +
52C ARG* 3.2 4.0 + - - +
53C GLN* 3.0 44.5 + - - +
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Residues in contact with GLN 50 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
35C PRO* 3.1 30.7 - - + +
43C VAL* 3.0 25.5 - - - +
44C PRO* 2.5 39.5 - - + +
45C ALA* 3.2 17.0 - - - +
46C ASP 2.7 15.0 + - - +
47C ILE* 3.2 24.9 - - - +
49C ALA* 1.3 75.6 - - - +
51C ALA* 1.3 60.5 + - - +
53C GLN* 4.5 1.3 - - - -
54C SER* 3.1 22.7 + - - -
120C GLY* 3.8 16.8 - - - +
121C LEU* 3.4 17.6 - - + +
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Residues in contact with ALA 51 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
47C ILE 2.8 23.7 + - - +
48C VAL* 3.6 7.0 - - + +
49C ALA 3.2 0.2 - - - -
50C GLN* 1.3 79.8 - - - +
52C ARG* 1.3 58.5 + - - +
54C SER* 4.0 3.5 - - - -
55C LEU* 3.5 27.8 + - + +
88C VAL* 4.1 29.1 - - + +
91C GLU* 5.4 3.8 - - - +
121C LEU* 3.7 16.8 - - + -
123C ILE* 4.7 1.2 - - - +
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Residues in contact with ARG 52 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
48C VAL* 2.9 18.7 + - + +
49C ALA* 3.2 6.3 + - - +
51C ALA* 1.3 75.8 - - - +
53C GLN* 1.3 74.7 + - - +
55C LEU* 3.2 16.9 + - - +
56C GLU* 3.1 64.1 + - - +
59C LYS* 5.9 2.4 - - - +
91C GLU* 3.7 30.4 + - - +
95C PHE* 5.5 10.9 - - - +
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Residues in contact with GLN 53 (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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35C PRO* 4.7 11.2 - - + +
36C VAL 5.7 1.1 - - - +
38C PRO* 4.2 31.0 - - + +
44C PRO* 4.6 8.0 - - + +
49C ALA* 3.0 31.0 + - - +
50C GLN* 4.0 6.3 - - - +
51C ALA 3.5 0.2 - - - -
52C ARG* 1.3 87.2 - - - +
54C SER* 1.3 60.4 + - - +
56C GLU* 3.1 8.8 + - + +
57C ASN* 2.5 37.5 + - - +
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Residues in contact with SER 54 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
33C GLN* 4.2 0.5 - - - +
34C ILE* 3.8 9.9 + - - -
35C PRO* 3.8 18.0 - - - +
50C GLN 3.1 18.9 + - - -
51C ALA 4.0 2.2 - - - -
53C GLN* 1.3 77.0 - - - +
55C LEU* 1.3 59.6 + - - +
57C ASN* 3.5 7.3 + - - +
58C VAL* 2.8 31.7 + - - +
121C LEU* 3.3 16.8 - - - +
123C ILE* 2.9 32.8 - - - +
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Residues in contact with LEU 55 (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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51C ALA* 3.5 16.0 + - + +
52C ARG* 3.2 22.8 + - - +
53C GLN 3.2 0.6 - - - -
54C SER* 1.3 76.4 - - - +
56C GLU* 1.3 59.2 + - - +
58C VAL* 3.6 4.8 + - + +
59C LYS* 3.1 29.5 + - - +
88C VAL* 6.2 2.7 - - + -
91C GLU* 4.5 12.6 - - - +
92C TYR* 3.8 28.3 - - + -
95C PHE* 3.2 51.4 - - + -
96C PHE* 4.7 0.7 - - + -
123C ILE* 4.1 17.0 - - + -
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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
----------------------------------------------------------
10C LYS* 4.4 24.2 - - + -
52C ARG* 3.1 41.7 + - - +
53C GLN* 3.1 13.5 + - + +
55C LEU* 1.3 75.6 - - - +
57C ASN* 1.3 57.4 + - - +
59C LYS* 3.3 9.9 + - - +
60C ALA* 2.6 38.0 + - + +
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Residues in contact with ASN 57 (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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10C LYS* 3.5 24.4 + - - -
11C ALA* 3.6 9.0 - - - +
12C PRO* 3.7 15.8 - - + +
33C GLN* 4.1 13.5 - - + -
34C ILE 4.5 10.3 + - - +
36C VAL* 5.3 9.5 + - - +
53C GLN* 2.5 37.0 + - - +
54C SER* 3.8 6.7 - - - +
56C GLU* 1.3 79.0 - - - +
58C VAL* 1.3 60.4 + - - +
60C ALA* 3.3 6.9 + - - +
61C ILE* 3.0 33.0 + - - +
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Residues in contact with VAL 58 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
30C THR* 3.3 32.9 - - + +
33C GLN* 3.4 27.8 - - + -
54C SER 2.8 25.7 + - - +
55C LEU* 3.9 6.5 - - + +
57C ASN* 1.3 76.4 - - - +
59C LYS* 1.3 61.0 + - - +
61C ILE* 3.8 1.2 + - - +
62C ILE* 3.0 36.4 + - + +
72C ILE* 5.8 2.7 - - + -
123C ILE* 3.4 33.4 - - + +
125C ALA* 5.0 6.3 - - + +
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Residues in contact with LYS 59 (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 ARG* 5.9 2.7 - - - +
55C LEU 3.1 18.2 + - - +
56C GLU* 3.8 11.4 - - - +
58C VAL* 1.3 75.3 - - - +
60C ALA* 1.3 56.8 + - - +
61C ILE 3.2 0.4 - - - -
62C ILE* 3.3 6.9 + - + -
63C GLU* 2.6 69.7 + - + +
68C THR* 4.2 12.7 - - - +
69C ALA* 4.0 38.8 - - + +
95C PHE* 5.8 4.3 - - + -
99C ASN* 3.4 25.2 + - - +
101C HIS* 4.2 9.4 + - + -
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Residues in contact with ALA 60 (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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8C THR* 4.0 3.0 + - - -
10C LYS* 3.3 45.2 - - + +
11C ALA 4.6 0.7 - - - +
56C GLU* 2.6 23.5 + - + +
57C ASN* 3.3 6.5 + - - +
59C LYS* 1.3 74.3 - - - +
61C ILE* 1.3 57.2 + - - +
63C GLU* 3.8 7.2 - - - +
64C LYS* 2.9 30.7 + - - +
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Residues in contact with ILE 61 (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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6C ILE* 3.5 15.1 - - + +
8C THR* 3.9 17.9 - - + -
11C ALA* 3.1 31.2 - - + -
20C GLN 4.1 7.0 - - - +
21C ALA* 3.2 34.8 - - + -
30C THR* 5.1 1.1 - - + -
33C GLN* 3.2 38.8 - - + +
57C ASN 3.0 19.9 + - - +
58C VAL* 3.9 4.3 - - - +
59C LYS 3.2 0.2 - - - -
60C ALA* 1.3 75.6 - - - +
62C ILE* 1.3 65.8 + - + +
64C LYS* 3.3 3.5 + - - +
65C ALA* 3.2 21.7 + - - +
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Residues in contact with ILE 62 (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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6C ILE* 6.0 2.7 - - + -
28C VAL* 4.4 9.4 - - + -
30C THR* 3.2 29.6 - - + -
58C VAL* 3.0 29.4 - - + +
59C LYS* 3.3 8.0 + - - +
61C ILE* 1.3 76.4 - - + +
63C GLU* 1.3 59.6 + - - +
65C ALA* 3.3 7.8 + - + +
66C GLY 3.2 6.4 + - - -
67C LEU* 3.0 49.6 + - + -
68C THR* 4.2 7.6 - - - +
69C ALA* 5.4 2.0 - - - -
72C ILE* 4.6 23.6 - - + -
125C ALA* 5.5 1.8 - - + +
127C ALA* 4.3 17.5 - - + -
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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
----------------------------------------------------------
59C LYS* 2.6 54.1 + - + +
60C ALA* 3.8 7.9 - - - +
62C ILE* 1.3 69.6 - - - +
64C LYS* 1.3 61.9 + - - +
65C ALA 3.0 4.7 - - - -
66C GLY* 3.1 14.2 + - - -
67C LEU 3.6 13.4 + - - +
68C THR* 4.3 9.7 - - - +
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Residues in contact with LYS 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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7C HIS* 3.4 23.8 + - - +
8C THR* 3.8 25.8 - - - +
9C GLU* 4.7 4.0 - - - +
60C ALA 2.9 19.7 + - - +
61C ILE 3.3 5.4 + - - +
63C GLU* 1.3 74.7 - - - +
65C ALA* 1.3 58.9 + - - +
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Residues in contact with ALA 65 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
6C ILE* 4.2 20.6 - - + -
23C ASP* 4.4 17.5 - - + +
28C VAL* 5.1 5.6 - - + -
61C ILE 3.2 11.8 + - - +
62C ILE* 3.5 12.1 - - + +
63C GLU 3.0 0.8 - - - -
64C LYS* 1.3 80.1 - - - +
66C GLY* 1.3 58.3 + - - +
67C LEU* 5.7 1.3 - - + -
129C ARG* 4.0 12.6 + - - +
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Residues in contact with GLY 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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62C ILE 3.2 0.6 + - - -
63C GLU 3.1 10.8 + - - -
64C LYS 3.5 0.2 - - - -
65C ALA* 1.3 79.2 - - - +
67C LEU* 1.3 70.3 + - - +
129C ARG* 3.8 16.1 + - - +
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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