Contacts of the helix formed by residues 53 - 68 (chain C) in PDB entry 1M6X
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 LYS 53 (chain C).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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4C PHE* 4.0 0.9 - - - -
43C TRP* 5.2 0.2 - - - -
51C ALA 5.7 0.9 - - - +
52C ILE* 1.3 79.4 - - - +
54C ARG* 1.3 66.4 + - - +
55C ALA 3.5 2.0 - - - +
56C THR* 3.3 13.1 + - - +
57C PHE* 2.9 21.1 + - - +
223C LYS 4.4 1.4 + - - -
225C SER* 3.7 21.5 + - - -
260C ASN 3.6 13.0 - - - +
261C ARG* 4.3 13.0 - - + +
22I A 2.9 66.7 + - + +
23I A 4.5 10.1 + - - +
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Residues in contact with ARG 54 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
2C SER* 4.0 6.5 + - - -
4C PHE* 3.3 52.9 - - + +
5C ASP* 2.5 39.8 + - - -
53C LYS* 1.3 71.8 - - - +
55C ALA* 1.3 67.2 + - - +
57C PHE* 2.9 5.0 + - - +
58C MET* 2.8 35.9 + - + +
258C ARG* 3.4 47.2 - - - +
259C VAL 2.4 30.3 + - - -
260C ASN* 3.2 23.9 + - + +
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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
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53C LYS* 3.5 1.4 - - + +
54C ARG* 1.3 79.5 - - - +
56C THR* 1.3 58.1 - - - +
58C MET* 3.1 10.8 + - - +
59C SER* 2.8 30.1 + - - -
22I A 4.1 4.3 - - + -
23I A 3.5 52.8 + - + +
24I T 5.2 7.2 - - + +
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Residues in contact with THR 56 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
43C TRP* 4.0 14.1 - - + -
52C ILE* 4.3 7.2 - - + -
53C LYS* 3.3 10.3 + - - +
54C ARG 3.2 0.8 - - - -
55C ALA* 1.3 73.8 - - - +
57C PHE* 1.3 67.7 + - - +
59C SER* 3.2 3.7 + - - +
60C TYR* 3.0 56.6 + - + -
21I G 4.1 4.7 - - + -
22I A 2.7 53.1 + - + +
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Residues in contact with PHE 57 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
3C GLN* 4.7 4.7 - - + -
4C PHE* 3.4 47.8 - + + -
7C LEU* 3.4 31.6 - - + -
36C ALA* 3.6 38.6 - - + -
39C THR* 3.6 21.1 - - + -
40C TYR 4.7 1.1 - - - -
52C ILE* 3.7 19.0 - - + +
53C LYS 2.9 13.7 + - - +
54C ARG 3.4 5.8 - - - +
56C THR* 1.3 76.2 - - - +
58C MET* 1.3 65.6 + - - +
60C TYR* 3.9 0.5 - - - +
61C ASN* 2.7 56.0 + - + +
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Residues in contact with MET 58 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
2C SER* 5.5 3.4 - - - +
3C GLN* 5.7 1.6 - - - -
4C PHE* 4.3 14.4 - - - -
54C ARG* 2.8 32.5 + - + +
55C ALA* 3.2 11.4 - - - +
57C PHE* 1.3 94.2 - - + +
59C SER* 1.3 63.6 + - - +
61C ASN* 3.6 4.8 - - - +
62C THR* 3.0 25.9 + - - -
7G C 5.8 0.7 - - + -
8G C 3.9 35.2 - - + +
9G T 3.4 34.7 + - + +
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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
----------------------------------------------------------
55C ALA 2.8 18.5 + - - -
56C THR* 3.7 5.8 - - - -
58C MET* 1.3 72.2 - - - +
60C TYR* 1.3 73.1 + - - +
62C THR* 3.2 8.9 + - - -
63C ILE* 3.0 36.8 + - - +
82C LYS* 4.7 2.9 + - - -
9G T 6.3 0.2 - - - -
10G A 6.1 3.1 - - - +
11G T 4.4 10.7 + - - +
22I A 4.6 12.0 + - - -
23I A 4.6 13.9 - - - -
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Residues in contact with TYR 60 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
39C THR* 3.9 17.0 - - + -
43C TRP* 4.3 5.8 - + + -
52C ILE* 5.3 1.3 - - + -
56C THR* 3.0 36.2 + - + +
57C PHE 3.9 1.6 - - - +
59C SER* 1.3 81.7 - - - +
61C ASN* 1.3 68.1 + - - +
63C ILE* 3.0 13.8 + - + +
64C ILE* 2.8 26.4 + - - +
81C TYR* 3.6 39.7 - + + -
82C LYS* 3.6 37.8 - - + +
20I A 3.7 1.0 - - - +
21I G 3.0 53.8 + + - +
22I A 5.3 1.1 - - - -
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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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3C GLN* 3.7 27.1 + - - +
35C ALA* 3.6 11.9 - - - +
36C ALA* 3.4 29.8 - - - +
39C THR* 3.4 12.0 + - - +
57C PHE* 2.7 45.0 + - + +
58C MET* 3.6 7.4 - - - +
60C TYR* 1.3 71.3 - - - +
62C THR* 1.3 58.0 + - - +
64C ILE* 3.4 0.5 + - - +
65C SER* 2.8 31.3 + - - -
8G C 5.8 0.5 - - - +
9G T 4.6 6.3 + - - +
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Residues in contact with THR 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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58C MET 3.0 12.4 + - - -
59C SER* 3.3 10.2 - - - -
60C TYR 3.1 0.8 - - - -
61C ASN* 1.3 79.5 - - - +
63C ILE* 1.3 59.3 + - + +
65C SER* 3.2 5.7 + - - -
66C ASN* 2.8 47.5 + - - +
9G T 2.6 66.3 + - + +
10G A 3.8 5.5 + - + +
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Residues in contact with ILE 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* 3.1 23.8 - - - +
60C TYR* 3.0 15.8 + - + +
62C THR* 1.3 77.4 - - + +
64C ILE* 1.3 62.5 + - - +
66C ASN* 3.5 6.7 + - - +
67C SER* 2.9 25.3 + - - -
80C LYS* 3.8 23.6 - - + +
81C TYR* 4.6 3.1 - - - +
82C LYS* 3.9 34.3 - - + +
107C TYR* 3.6 41.5 - - + +
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Residues in contact with ILE 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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35C ALA* 4.0 17.0 - - - -
38C LEU* 3.9 25.6 - - + +
39C THR* 3.4 39.9 - - - +
60C TYR 2.8 19.6 + - - +
61C ASN 3.8 2.7 - - - +
63C ILE* 1.3 70.2 - - + +
65C SER* 1.3 55.2 + - - +
67C SER* 2.7 14.3 + - - -
68C LEU* 2.7 36.9 + - + -
79C PHE* 3.8 24.7 - - + -
80C LYS 3.6 16.2 - - - +
81C TYR* 4.4 12.3 - - + -
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Residues in contact with SER 65 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
32C ALA 5.6 1.2 + - - -
35C ALA* 4.1 17.9 - - - +
61C ASN* 2.8 26.5 + - - -
62C THR* 3.5 7.0 - - - -
64C ILE* 1.3 77.2 - - - +
66C ASN* 1.3 62.1 + - - +
68C LEU* 3.9 13.7 + - - +
9G T 4.5 12.2 + - - -
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Residues in contact with ASN 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 THR* 2.8 35.6 + - - +
63C ILE* 3.8 7.1 - - - +
65C SER* 1.3 74.7 - - - +
67C SER* 1.3 60.6 + - - +
68C LEU 4.7 2.1 - - - +
9G T 5.0 8.3 + - - +
10G A 3.2 25.2 + - - -
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Residues in contact with SER 67 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
63C ILE 2.9 19.4 + - - -
64C ILE* 2.7 13.9 + - - -
66C ASN* 1.3 72.1 - - - +
68C LEU* 1.3 65.7 + - - +
69C SER* 3.3 10.2 + - - -
78C GLN* 3.9 5.9 + - - +
79C PHE* 3.7 3.0 - - - -
80C LYS* 2.8 53.9 + - - +
105C ILE* 6.3 0.4 - - - -
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Residues in contact with LEU 68 (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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31C ILE 3.7 22.9 - - - +
32C ALA* 3.8 20.0 - - - +
34C CYS* 3.8 10.5 - - - -
35C ALA* 4.6 9.4 - - + +
38C LEU* 4.2 8.7 - - + -
64C ILE* 2.7 22.7 + - + +
65C SER* 4.2 10.3 - - - +
66C ASN 3.6 3.8 - - - +
67C SER* 1.3 74.4 + - - +
69C SER* 1.3 67.7 + - - +
70C PHE* 4.5 7.4 - - + -
77C LEU* 3.8 31.2 - - + -
78C GLN 3.6 12.8 - - - +
79C PHE* 4.0 7.9 - - + -
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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
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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