Contacts of the helix formed by residues 53 - 68 (chain B) 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 B).
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
4B PHE* 4.0 0.9 - - - -
43B TRP* 5.3 0.4 - - - -
51B ALA 4.4 1.5 + - - +
52B ILE* 1.3 78.7 - - - +
54B ARG* 1.3 66.5 + - - +
55B ALA 4.7 1.8 - - - +
56B THR* 3.2 9.4 + - - +
57B PHE* 2.9 21.7 + - - +
222B THR 5.4 0.2 + - - -
223B LYS 4.3 4.8 + - - -
225B SER* 3.1 26.7 + - - -
260B ASN 3.6 7.4 - - - +
261B ARG* 3.9 31.0 - - + +
22G A 2.8 61.0 + - + +
23G A 4.9 10.8 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with ARG 54 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
2B SER* 4.1 6.3 + - - -
4B PHE* 3.3 50.7 - - + +
5B ASP* 2.6 39.8 + - - -
53B LYS* 1.3 70.6 - - - +
55B ALA* 1.3 66.3 + - - +
57B PHE* 3.0 4.7 + - - +
58B MET* 2.8 36.9 + - + +
258B ARG* 3.3 44.3 - - - +
259B VAL 2.4 28.5 + - - -
260B ASN* 2.8 36.7 + - + +
----------------------------------------------------------
Back to top of page
Residues in contact with ALA 55 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
53B LYS 3.5 0.4 - - - -
54B ARG* 1.3 79.4 - - - +
56B THR* 1.3 57.6 + - - +
58B MET* 3.1 11.4 + - - +
59B SER* 2.8 29.9 + - - -
22G A 3.8 11.4 - - + -
23G A 3.3 47.7 + - + +
24G T 5.3 6.3 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with THR 56 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
43B TRP* 4.1 12.6 - - + -
52B ILE* 4.3 6.7 - - + -
53B LYS* 3.2 10.3 + - - +
54B ARG 3.2 0.6 - - - -
55B ALA* 1.3 74.6 - - - +
57B PHE* 1.3 68.2 + - - +
59B SER* 3.2 2.7 + - - -
60B TYR* 3.0 56.8 + - + -
21G G 3.5 11.2 - - + +
22G A 2.7 48.5 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with PHE 57 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
3B GLN* 4.7 5.2 - - + -
4B PHE* 3.4 47.8 - + + -
7B LEU* 3.4 31.6 - - + -
36B ALA* 3.7 38.6 - - + -
39B THR* 3.6 20.9 - - + -
40B TYR* 4.7 1.3 - - - -
52B ILE* 3.6 18.3 - - + +
53B LYS 2.9 13.5 + - - +
54B ARG 3.4 6.1 - - - +
56B THR* 1.3 75.5 - - - +
58B MET* 1.3 65.2 + - - +
60B TYR* 3.9 0.3 - - - +
61B ASN* 2.7 56.5 + - + +
----------------------------------------------------------
Back to top of page
Residues in contact with MET 58 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
2B SER* 5.5 2.9 - - - +
3B GLN* 5.7 1.6 - - - -
4B PHE* 4.3 13.0 - - - -
54B ARG* 2.8 32.5 + - + +
55B ALA* 3.2 11.7 - - - +
57B PHE* 1.3 94.2 - - + +
59B SER* 1.3 62.9 + - - +
61B ASN* 3.7 4.6 - - - +
62B THR* 3.0 26.4 + - - -
8F C 4.3 38.6 - - + +
9F T 3.6 32.0 - - + +
----------------------------------------------------------
Back to top of page
Residues in contact with SER 59 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
55B ALA 2.8 17.8 + - - -
56B THR 3.2 4.2 + - - -
58B MET* 1.3 72.4 - - - +
60B TYR* 1.3 74.5 + - - +
62B THR* 3.2 8.9 + - - -
63B ILE* 3.0 36.7 + - - +
82B LYS* 4.7 2.3 + - - -
9F T 6.2 0.2 - - - -
10F A 6.1 1.8 - - - +
11F T 4.4 10.6 + - - -
22G A 4.5 15.8 + - - -
23G A 4.5 14.4 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with TYR 60 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
39B THR* 3.9 16.6 - - + -
43B TRP* 4.3 6.3 - + + -
52B ILE* 5.3 0.9 - - + -
56B THR* 3.0 36.4 + - + +
57B PHE 3.9 2.0 - - - +
59B SER* 1.3 81.5 - - - +
61B ASN* 1.3 68.7 + - - +
63B ILE* 3.0 13.9 + - + +
64B ILE* 2.8 27.1 + - + +
81B TYR* 3.6 39.3 - + + -
82B LYS* 3.5 33.4 - - + +
20G A 3.3 17.0 - - - +
21G G 3.0 41.6 + + - +
22G A 5.2 1.3 - - - -
----------------------------------------------------------
Back to top of page
Residues in contact with ASN 61 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
3B GLN* 3.7 27.1 + - - +
35B ALA* 3.6 12.5 - - - +
36B ALA* 3.4 28.6 - - - +
39B THR* 3.4 11.6 + - - +
57B PHE* 2.7 45.1 + - + +
58B MET* 3.7 6.8 - - - +
60B TYR* 1.3 73.2 - - - +
62B THR* 1.3 57.5 + - - +
64B ILE* 3.5 0.7 + - - +
65B SER* 2.9 31.1 + - - -
8F C 5.9 0.2 - - - +
9F T 4.8 6.0 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with THR 62 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
58B MET 3.0 12.7 + - - -
59B SER* 3.3 10.2 - - - -
60B TYR 3.1 0.6 - - - -
61B ASN* 1.3 77.6 - - - +
63B ILE* 1.3 59.5 + - + +
65B SER* 3.2 5.7 + - - -
66B ASN* 2.8 49.3 + - - +
9F T 2.8 63.6 + - + +
10F A 3.9 6.9 + - + +
----------------------------------------------------------
Back to top of page
Residues in contact with ILE 63 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
59B SER* 3.2 23.8 - - - +
60B TYR* 3.0 14.1 + - + +
62B THR* 1.3 78.6 - - + +
64B ILE* 1.3 62.5 + - + +
66B ASN* 3.5 6.9 + - - +
67B SER* 2.8 25.3 + - - -
80B LYS* 3.9 22.9 - - + +
81B TYR* 4.7 3.4 - - - +
82B LYS* 3.9 34.3 - - + +
107B TYR* 3.6 42.6 - - + +
----------------------------------------------------------
Back to top of page
Residues in contact with ILE 64 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
35B ALA* 4.0 16.4 - - + -
38B LEU* 3.9 32.3 - - + +
39B THR* 3.3 39.7 - - - +
60B TYR 2.8 19.2 + - - +
61B ASN 3.8 2.9 - - - +
63B ILE* 1.3 71.8 - - + +
65B SER* 1.3 55.3 + - - +
67B SER* 2.7 15.2 + - - -
68B LEU* 2.7 37.5 + - + -
79B PHE* 3.8 17.9 - - + -
80B LYS 3.6 15.9 - - - +
81B TYR* 4.4 12.6 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with SER 65 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
32B ALA 5.6 1.0 + - - -
35B ALA* 4.1 18.2 - - - +
61B ASN* 2.9 25.8 + - - -
62B THR* 3.5 6.7 - - - -
64B ILE* 1.3 77.1 - - - +
66B ASN* 1.3 63.6 + - - +
67B SER 3.5 0.2 + - - -
68B LEU* 3.8 13.6 + - - +
9F T 4.6 12.2 + - - -
----------------------------------------------------------
Back to top of page
Residues in contact with ASN 66 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
62B THR* 2.8 33.0 + - - +
63B ILE* 3.8 6.0 - - - +
65B SER* 1.3 76.4 - - - +
67B SER* 1.3 60.1 + - - +
68B LEU 4.7 1.6 - - - +
9F T 5.0 6.9 + - - +
10F A 3.0 28.4 + - - -
----------------------------------------------------------
Back to top of page
Residues in contact with SER 67 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
63B ILE 2.8 21.8 + - - -
64B ILE* 2.7 14.4 + - - -
66B ASN* 1.3 72.5 - - - +
68B LEU* 1.3 66.5 + - - +
69B SER* 3.3 9.2 + - - -
78B GLN* 3.8 6.9 + - - +
79B PHE* 3.7 3.1 - - - -
80B LYS* 2.8 53.4 + - - +
105B ILE* 6.3 0.4 - - - -
----------------------------------------------------------
Back to top of page
Residues in contact with LEU 68 (chain B).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
31B ILE 3.7 22.7 - - - +
32B ALA* 3.8 20.2 - - - +
34B CYS* 3.8 9.6 - - - -
35B ALA* 4.6 9.9 - - + +
38B LEU* 4.2 8.7 - - + -
64B ILE* 2.7 22.3 + - + +
65B SER* 4.1 10.5 - - - +
66B ASN 3.6 3.8 - - - +
67B SER* 1.3 74.0 + - - +
69B SER* 1.3 67.0 + - - +
70B PHE* 4.5 7.2 - - + -
77B LEU* 3.8 30.7 - - + -
78B GLN 3.5 13.0 - - - +
79B PHE* 4.0 8.1 - - + -
----------------------------------------------------------
Back to top of page
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) + - + + + + + -
------------------------------------------------------------
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