Contacts of the helix formed by residues 53 - 68 (chain D) 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 D).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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4D PHE* 4.0 0.9 - - - -
43D TRP* 5.3 0.4 - - - -
51D ALA 5.7 0.9 - - - +
52D ILE* 1.3 79.2 - - - +
54D ARG* 1.3 67.0 + - - +
55D ALA 3.5 3.1 - - - +
56D THR* 3.2 13.6 + - - +
57D PHE* 2.9 21.0 + - - +
222D THR 5.5 0.2 + - - -
223D LYS 4.7 0.2 + - - -
225D SER* 3.4 24.2 + - - -
260D ASN 3.4 10.5 - - - +
261D ARG* 4.0 11.9 - - + +
22J A 2.9 60.4 + - + +
23J A 4.7 8.5 + - - +
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Residues in contact with ARG 54 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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2D SER* 4.0 5.9 + - - -
4D PHE* 3.3 50.8 - - + +
5D ASP* 2.5 40.2 + - - -
53D LYS* 1.3 70.2 - - - +
55D ALA* 1.3 66.7 + - - +
57D PHE* 3.0 4.7 + - - +
58D MET* 2.8 36.6 + - + +
258D ARG* 3.4 45.8 - - - +
259D VAL 2.3 30.7 + - - -
260D ASN* 2.8 30.7 + - + +
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Residues in contact with ALA 55 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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53D LYS* 3.5 1.4 - - + +
54D ARG* 1.3 79.2 - - - +
56D THR* 1.3 57.8 + - - +
58D MET* 3.2 10.5 + - - +
59D SER* 2.8 30.6 + - - -
22J A 4.0 7.0 - - + -
23J A 3.3 51.7 + - + +
24J T 5.3 5.4 - - + +
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Residues in contact with THR 56 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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43D TRP* 4.1 11.7 - - + -
52D ILE* 4.3 7.6 - - + -
53D LYS* 3.2 10.4 + - - +
54D ARG 3.2 0.6 - - - -
55D ALA* 1.3 74.8 - - - +
57D PHE* 1.3 67.5 + - - +
59D SER* 3.2 2.5 + - - +
60D TYR* 3.0 56.8 + - + -
21J G 4.0 7.0 - - + -
22J A 2.5 53.1 + - + +
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Residues in contact with PHE 57 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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3D GLN* 4.7 5.6 - - + -
4D PHE* 3.4 47.8 - + + -
7D LEU* 3.4 30.7 - - + -
36D ALA* 3.6 38.4 - - + -
39D THR* 3.6 21.1 - - + -
40D TYR 4.7 1.3 - - - -
52D ILE* 3.7 18.8 - - + +
53D LYS 2.9 13.5 + - - +
54D ARG 3.4 5.6 - - - +
56D THR* 1.3 77.0 - - - +
58D MET* 1.3 65.2 + - - +
60D TYR* 3.8 0.5 - - - +
61D ASN* 2.7 59.1 + - + +
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Residues in contact with MET 58 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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2D SER* 5.5 4.0 - - - +
3D GLN* 5.7 1.8 - - - -
4D PHE* 4.4 14.4 - - - -
54D ARG* 2.8 32.0 + - + +
55D ALA* 3.2 11.9 - - - +
57D PHE* 1.3 93.0 - - + +
59D SER* 1.3 62.6 + - - +
61D ASN* 3.7 5.2 - - - +
62D THR* 3.0 26.1 + - - -
7H C 5.9 0.4 - - + -
8H C 4.1 33.9 - - + +
9H T 3.5 34.1 + - + +
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Residues in contact with SER 59 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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55D ALA 2.8 18.5 + - - -
56D THR* 3.2 6.0 + - - -
58D MET* 1.3 72.1 - - - +
60D TYR* 1.3 73.5 + - - +
62D THR* 3.2 10.1 + - - -
63D ILE* 3.0 36.4 + - - +
82D LYS* 4.6 2.3 + - - -
10H A 6.2 1.1 - - - +
11H T 4.6 7.6 + - - -
22J A 4.4 17.1 + - - -
23J A 4.6 13.7 - - - +
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Residues in contact with TYR 60 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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39D THR* 4.0 16.4 - - + -
43D TRP* 4.3 5.8 - + + -
52D ILE* 5.3 1.6 - - + -
56D THR* 3.0 36.4 + - + +
57D PHE* 3.9 1.8 - - - +
59D SER* 1.3 82.8 - - - +
61D ASN* 1.3 68.7 + - - +
63D ILE* 2.9 14.8 + - + +
64D ILE* 2.8 26.3 + - + +
81D TYR* 3.6 40.6 - + + -
82D LYS* 3.6 32.3 - - + +
20J A 3.6 3.6 - - - +
21J G 2.8 57.0 + + - +
22J A 5.3 0.9 - - - -
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Residues in contact with ASN 61 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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3D GLN* 3.7 27.2 + - - +
35D ALA* 3.6 12.3 - - - +
36D ALA* 3.4 27.8 - - - +
39D THR* 3.4 11.3 + - - +
57D PHE* 2.7 44.7 + - + +
58D MET* 3.7 6.8 - - - +
60D TYR* 1.3 72.3 - - - +
62D THR* 1.3 59.2 + - - +
64D ILE* 3.4 0.5 + - - +
65D SER* 2.9 30.6 + - - -
8H C 6.0 0.2 - - - +
9H T 4.6 6.2 + - - +
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Residues in contact with THR 62 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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58D MET 3.0 12.6 + - - -
59D SER* 3.3 10.3 - - - -
60D TYR 3.1 0.8 - - - -
61D ASN* 1.3 78.9 - - - +
63D ILE* 1.3 58.5 - - + +
65D SER* 3.2 5.0 + - - -
66D ASN* 2.8 46.5 + - - +
9H T 2.8 66.8 + - + +
10H A 3.9 5.9 + - + +
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Residues in contact with ILE 63 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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59D SER* 3.0 24.0 + - - +
60D TYR* 2.9 14.9 + - + +
62D THR* 1.3 78.7 - - + +
64D ILE* 1.3 61.4 + - + +
66D ASN* 3.5 6.7 + - - +
67D SER* 2.8 26.2 + - - -
80D LYS* 3.8 22.9 - - + +
81D TYR* 4.7 3.4 - - - +
82D LYS* 3.9 35.7 - - + +
107D TYR* 3.7 41.1 - - + +
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Residues in contact with ILE 64 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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35D ALA* 4.0 16.6 - - + -
38D LEU* 3.9 26.0 - - + +
39D THR* 3.3 39.5 - - - +
60D TYR 2.8 19.3 + - - +
61D ASN 3.8 2.9 - - - +
63D ILE* 1.3 71.2 - - + +
65D SER* 1.3 58.4 + - - +
67D SER* 2.7 14.8 + - - -
68D LEU* 2.6 37.5 + - + -
79D PHE* 3.8 24.5 - - + -
80D LYS 3.7 15.9 - - - +
81D TYR* 4.4 11.7 - - + -
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Residues in contact with SER 65 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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32D ALA 5.6 1.0 + - - -
35D ALA* 4.1 18.1 - - - +
61D ASN* 2.9 25.9 + - - -
62D THR* 3.5 6.7 - - - -
64D ILE* 1.3 77.1 - - - +
66D ASN* 1.3 63.3 + - - +
68D LEU* 3.9 12.8 + - - +
9H T 4.4 12.9 + - - -
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Residues in contact with ASN 66 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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62D THR* 2.8 35.4 + - - +
63D ILE* 3.8 7.3 - - - +
65D SER* 1.3 75.3 - - - +
67D SER* 1.3 58.5 + - - +
68D LEU 4.6 1.9 - - - +
9H T 5.0 7.8 + - - +
10H A 3.2 26.1 + - - -
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Residues in contact with SER 67 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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63D ILE 2.8 21.0 + - - -
64D ILE* 2.7 15.3 + - - -
66D ASN* 1.3 73.0 - - - +
68D LEU* 1.3 66.1 + - - +
69D SER* 3.3 8.7 + - - -
78D GLN* 3.9 6.6 + - - +
79D PHE* 3.7 3.1 - - - -
80D LYS* 2.7 53.1 + - - +
105D ILE* 6.2 0.6 - - - +
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Residues in contact with LEU 68 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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31D ILE 3.7 23.6 - - - +
32D ALA* 3.8 19.3 - - - +
34D CYS* 3.7 10.5 - - - -
35D ALA* 4.6 8.5 - - + +
38D LEU* 4.2 8.7 - - + -
64D ILE* 2.6 21.8 + - + +
65D SER* 4.1 9.6 - - - +
66D ASN 3.6 4.3 - - - +
67D SER* 1.3 75.2 + - - +
69D SER* 1.3 67.6 + - - +
70D PHE* 4.5 7.4 - - + -
77D LEU* 3.8 29.8 - - + -
78D GLN 3.5 13.2 - - - +
79D PHE* 4.0 8.3 - - + -
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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
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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