Contacts of the helix formed by residues 47 - 66 (chain C) in PDB entry 1XRG
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 47 (chain C).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
46C GLY* 1.3 73.9 - - - -
48C ILE* 1.3 61.2 + - - -
49C GLU 3.2 2.9 - - - -
50C GLU* 2.8 13.5 + - - -
51C GLN* 2.9 33.4 + - - +
117C LEU* 4.3 7.6 - - - -
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Residues in contact with ILE 48 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
47C GLY* 1.3 71.4 - - - -
49C GLU* 1.3 60.6 + - + +
51C GLN* 4.5 1.1 - - - -
52C ALA* 2.7 30.2 + - - +
80C ILE* 5.3 0.9 - - + -
85C SER* 4.4 22.2 - - - +
88C LYS* 4.4 17.9 - - + -
89C VAL* 3.7 33.4 - - + +
117C LEU* 3.8 38.6 - - + +
118C ILE* 4.0 20.4 - - + -
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Residues in contact with GLU 49 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
47C GLY 3.2 0.6 - - - -
48C ILE* 1.3 82.7 - - + +
50C GLU* 1.3 78.2 + - - +
52C ALA* 3.5 2.0 + - - +
53C LYS* 3.1 24.1 + - + +
88C LYS* 3.3 36.4 + - - +
91C GLU* 5.1 5.7 - - - +
92C VAL* 4.0 21.4 - - + +
95C LYS* 4.7 11.6 + - - -
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Residues in contact with GLU 50 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
44C VAL* 3.8 7.1 - - + +
45C ASP 3.4 24.9 - - - +
46C GLY* 3.7 5.1 - - - -
47C GLY* 2.8 31.4 + - - +
49C GLU* 1.3 91.1 + - + +
51C GLN* 1.3 65.1 + - - +
53C LYS* 3.5 8.5 + - - +
54C GLN* 3.2 22.0 + - - +
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Residues in contact with GLN 51 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
35C PRO* 3.4 37.3 - - + +
43C VAL* 3.8 17.9 - - + +
44C VAL* 4.0 14.9 + - + +
46C GLY 4.9 6.4 + - - +
47C GLY* 2.9 18.4 + - - +
48C ILE* 3.8 3.8 - - - +
50C GLU* 1.3 76.0 - - - +
52C ALA* 1.3 62.8 + - - +
54C GLN 3.1 1.7 + - - -
55C VAL* 2.9 22.0 + - - +
115C GLY 5.2 1.0 + - - -
116C VAL* 4.5 3.4 - - - +
117C LEU* 2.7 51.9 + - - +
118C ILE* 3.8 8.9 + - + -
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Residues in contact with ALA 52 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
48C ILE 2.7 23.2 + - - +
49C GLU 3.8 3.8 - - - +
51C GLN* 1.3 73.8 - - - +
53C LYS* 1.3 62.7 + - - +
55C VAL* 3.4 2.6 + - - +
56C LEU* 3.2 29.6 + - + +
89C VAL* 4.6 14.1 - - + -
92C VAL* 4.0 21.8 - - + -
118C ILE* 3.9 27.6 - - + +
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Residues in contact with LYS 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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49C GLU* 3.1 19.3 + - + +
50C GLU* 3.7 7.4 - - - +
52C ALA* 1.3 76.5 - - - +
54C GLN* 1.3 60.7 + - - +
56C LEU* 3.2 4.7 + - - +
57C GLU* 2.9 47.7 + - + +
92C VAL* 3.7 15.7 - - + +
96C TYR* 3.6 19.6 + - + +
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Residues in contact with GLN 54 (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* 3.7 17.9 - - + -
36C ILE 3.4 17.9 - - - +
37C ASN* 4.0 11.8 + - - +
38C PRO* 3.4 15.4 - - - +
44C VAL* 3.5 22.8 - - + +
50C GLU 3.2 10.0 + - - +
51C GLN 3.1 8.3 + - - +
53C LYS* 1.3 79.5 + - - +
55C VAL* 1.3 66.2 + - - +
57C GLU* 4.3 13.5 - - - +
58C ASN* 3.0 46.8 + - - -
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Residues in contact with VAL 55 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
33C GLN* 3.7 19.7 - - + +
34C ILE* 3.6 10.3 - - - -
35C PRO* 3.4 32.3 - - + -
51C GLN 2.9 18.1 + - - +
52C ALA* 3.7 6.5 - - - +
54C GLN* 1.3 76.9 - - - +
56C LEU* 1.3 53.9 + - - +
58C ASN* 3.4 3.7 + - - +
59C LEU* 2.8 31.8 + - + +
118C ILE* 3.8 18.2 - - + +
120C ILE* 3.7 37.5 - - + -
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Residues in contact with LEU 56 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
52C ALA* 3.2 20.6 + - + +
53C LYS 3.7 3.6 - - - +
55C VAL* 1.3 73.6 - - - +
57C GLU* 1.3 60.9 + - - +
59C LEU* 3.6 15.1 - - + +
60C LYS* 2.8 29.6 + - - +
70C LEU* 4.7 1.9 - - + +
89C VAL* 5.4 1.1 - - + +
92C VAL* 3.9 9.4 - - + -
93C TYR* 3.7 32.8 - - + +
96C TYR* 3.8 35.4 - - + -
97C PHE* 3.8 28.0 - - + -
120C ILE* 4.1 22.9 - - + -
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Residues in contact with GLU 57 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
53C LYS* 2.9 40.0 + - + +
54C GLN* 3.8 17.5 - - - +
56C LEU* 1.3 75.5 - - - +
58C ASN* 1.3 58.5 + - - +
60C LYS* 3.3 20.5 + - - +
61C ASN* 2.9 43.9 + - - +
96C TYR* 2.3 34.8 + - - +
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Residues in contact with ASN 58 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
10C LYS 4.3 1.9 - - - +
11C ALA* 4.0 6.6 - - + +
12C PRO* 3.3 27.4 - - + +
33C GLN* 3.6 17.2 + - + +
34C ILE 3.1 21.4 + - - -
36C ILE 2.9 23.0 + - - +
38C PRO* 3.8 6.9 - - - +
54C GLN* 3.0 38.3 + - - +
55C VAL 3.5 5.2 - - - +
57C GLU* 1.3 77.9 - - - +
59C LEU* 1.3 56.7 + - - +
61C ASN* 3.4 3.9 + - - +
62C VAL* 3.0 33.4 + - - +
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Residues in contact with LEU 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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30C THR* 3.7 31.0 - - + +
33C GLN* 3.8 18.1 - - + +
55C VAL* 2.8 20.8 + - + +
56C LEU* 3.6 17.7 - - + +
58C ASN* 1.3 71.1 - - - +
60C LYS* 1.3 66.2 + - - +
62C VAL* 3.4 2.2 + - + +
63C LEU* 2.9 37.7 + - + +
70C LEU* 4.4 3.4 - - + -
76C THR* 5.0 0.7 - - + -
97C PHE* 4.2 25.6 - - + -
120C ILE* 4.4 18.6 - - + +
122C ALA* 3.8 24.9 - - + +
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Residues in contact with LYS 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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56C LEU 2.8 18.1 + - - +
57C GLU* 3.3 26.9 + - - +
59C LEU* 1.3 72.6 - - - +
61C ASN* 1.3 64.9 + - - +
63C LEU* 3.1 4.7 + - - +
64C GLU* 2.9 60.2 + - + +
70C LEU* 3.9 38.2 - - + +
96C TYR* 4.8 7.1 - - + -
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Residues in contact with ASN 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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8C THR* 3.9 4.5 + - - +
10C LYS* 3.6 56.1 - - + +
11C ALA* 4.7 1.3 - - + -
57C GLU* 2.9 30.9 + - - +
58C ASN 4.0 3.1 - - - +
59C LEU 3.3 0.2 - - - -
60C LYS* 1.3 81.5 - - - +
62C VAL* 1.3 61.2 + - - +
64C GLU* 4.2 13.9 + - - +
65C ALA* 3.0 30.8 + - - +
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Residues in contact with VAL 62 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
6C VAL* 3.7 5.0 - - + +
8C THR* 4.3 5.8 - - + -
11C ALA* 3.7 19.3 - - + -
20C GLN* 3.6 29.2 - - + +
21C ALA* 3.4 31.2 - - + -
30C THR* 4.4 11.2 - - + -
33C GLN* 3.8 17.0 - - - +
58C ASN 3.0 21.3 + - - +
59C LEU* 3.8 4.3 - - - +
61C ASN* 1.3 77.5 - - - +
63C LEU* 1.3 62.1 + - - +
65C ALA* 3.4 3.9 + - - +
66C ALA* 3.0 19.9 + - - +
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Residues in contact with LEU 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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28C VAL* 4.4 5.2 - - + -
30C THR* 3.9 20.6 - - + -
59C LEU* 2.9 34.2 + - + +
60C LYS 3.5 3.4 - - - +
62C VAL* 1.3 76.0 - - - +
64C GLU* 1.3 56.6 + - - +
66C ALA* 2.8 21.7 + - - +
68C SER* 3.0 27.7 + - - +
69C SER* 3.8 17.0 - - - +
70C LEU* 3.9 20.9 - - + +
73C VAL* 3.3 27.1 - - + -
122C ALA* 4.8 1.3 - - + -
124C ALA* 3.6 28.3 - - + -
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Residues in contact with GLU 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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60C LYS* 2.9 48.8 + - + +
61C ASN* 4.2 14.3 + - - +
63C LEU* 1.3 75.9 - - - +
65C ALA* 1.3 60.0 + - - +
67C GLY* 3.1 13.5 + - - -
68C SER 3.4 15.2 - - - +
69C SER* 4.5 12.8 - - - -
70C LEU* 5.5 1.7 + - - +
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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
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6C VAL* 3.8 14.7 - - + +
7C LYS 4.7 3.4 - - - +
8C THR* 3.6 27.4 - - + +
61C ASN 3.0 22.1 + - - +
62C VAL 3.6 4.3 - - - +
64C GLU* 1.3 75.3 - - - +
66C ALA* 1.3 59.2 + - - +
67C GLY 3.5 0.3 + - - -
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Residues in contact with ALA 66 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
6C VAL* 3.6 27.1 - - + -
21C ALA* 5.1 0.2 - - + -
23C VAL* 4.0 6.8 - - + +
28C VAL* 3.8 27.8 - - + -
62C VAL 3.0 9.2 + - - +
63C LEU 2.8 13.4 + - - +
65C ALA* 1.3 77.6 - - - +
67C GLY* 1.3 56.2 + - - +
68C SER 3.3 0.4 + - - -
126C LYS* 3.2 28.6 + - - +
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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