Contacts of the helix formed by residues 34 - 48 (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 CYS 34 (chain B).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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19B PHE* 3.6 24.7 - - + -
22B ARG* 3.6 22.6 - - - +
23B PHE* 4.7 3.6 - - + -
30B LYS 3.8 3.4 + - - -
31B ILE* 3.2 23.0 + - - +
33B SER* 1.3 76.7 - - - +
35B ALA* 1.3 56.8 + - - +
36B ALA 3.4 0.2 - - - -
37B GLU* 2.9 8.1 + - - +
38B LEU* 2.6 56.9 + - - -
68B LEU* 3.8 13.2 - - - -
77B LEU* 4.4 9.4 - - - -
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Residues in contact with ALA 35 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
32B ALA 4.6 7.5 + - - +
33B SER* 2.8 7.5 + - - +
34B CYS* 1.3 79.7 - - - +
36B ALA* 1.3 64.8 + - - +
38B LEU* 3.2 3.5 + - - +
39B THR* 2.9 26.7 + - - -
61B ASN* 3.6 15.7 - - - +
64B ILE* 4.0 21.8 - - + +
65B SER* 4.1 19.7 - - - +
68B LEU* 4.6 3.3 - - + +
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Residues in contact with ALA 36 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
3B GLN* 3.9 23.1 - - + +
7B LEU* 4.6 7.8 - - + +
33B SER 3.8 5.8 + - - +
34B CYS 3.2 0.8 + - - -
35B ALA* 1.3 77.2 - - - +
37B GLU* 1.3 65.8 + - + +
39B THR* 3.2 6.5 + - - -
40B TYR* 3.1 19.1 + - - +
57B PHE* 3.7 24.0 - - + -
61B ASN* 3.4 10.9 - - - +
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Residues in contact with GLU 37 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
7B LEU* 5.2 3.1 - - + -
15B LEU* 4.4 25.6 - - + +
18B GLN* 3.9 18.1 - - - +
19B PHE* 3.0 37.8 + - + -
22B ARG* 2.8 44.6 + - - -
33B SER 4.9 1.1 + - - +
34B CYS* 2.9 7.4 + - - +
36B ALA* 1.3 75.4 - - + +
38B LEU* 1.3 60.1 + - - +
40B TYR* 3.1 9.4 + - - +
41B LEU* 2.8 36.3 + - + +
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Residues in contact with LEU 38 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
19B PHE* 3.9 27.0 - - + -
34B CYS* 2.6 40.4 + - - +
35B ALA 3.4 4.9 - - - +
37B GLU* 1.3 72.8 - - - +
39B THR* 1.3 56.9 + - - +
41B LEU* 3.7 3.7 - - - +
42B CYS* 2.9 35.4 + - - -
64B ILE* 3.9 15.5 - - + -
68B LEU* 4.2 4.5 - - + -
77B LEU* 4.5 2.7 - - + -
79B PHE* 3.2 54.3 - - + -
93B LEU* 4.0 16.4 - - + -
102B PHE* 5.2 2.2 - - + -
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Residues in contact with THR 39 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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35B ALA 2.9 16.1 + - - -
36B ALA 3.2 9.6 - - - -
37B GLU 3.1 0.2 - - - -
38B LEU* 1.3 73.2 - - - +
40B TYR* 1.3 68.4 + - - +
42B CYS* 3.2 5.4 + - - +
43B TRP* 3.0 22.0 + - - +
52B ILE* 4.6 6.3 - - + -
57B PHE* 3.6 30.7 - - + +
60B TYR* 3.9 28.0 - - + -
61B ASN* 3.4 17.5 + - - -
64B ILE* 3.3 18.7 - - + +
81B TYR* 4.7 2.2 - - + -
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Residues in contact with TYR 40 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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7B LEU* 3.9 31.2 - - + -
12B PRO* 3.9 20.9 - - + +
15B LEU* 3.4 33.8 - - + +
16B VAL* 5.6 2.7 - - + -
36B ALA 3.1 7.7 + - - +
37B GLU* 3.1 10.0 + - - +
39B THR* 1.3 80.5 - - - +
41B LEU* 1.3 73.8 + - + +
43B TRP* 3.3 4.9 + - - +
44B MET* 2.9 70.6 + - + +
52B ILE* 5.0 3.8 - - + -
57B PHE* 4.7 1.3 - - - -
262B THR* 4.0 16.8 - - + -
120D VAL* 6.4 1.8 - - + -
123D LEU* 3.3 22.6 - - + +
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Residues in contact with LEU 41 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
15B LEU* 5.9 1.1 - - + -
16B VAL* 4.2 26.2 - - + +
19B PHE* 3.3 49.6 - - + -
37B GLU* 2.8 21.6 + - + +
38B LEU* 3.7 4.5 - - - +
40B TYR* 1.3 89.3 - - + +
42B CYS* 1.3 63.1 + - - +
43B TRP 3.0 0.3 + - - -
44B MET* 3.2 5.8 + - + +
45B ILE* 2.9 32.5 + - + +
93B LEU* 4.5 13.5 - - + -
96B LEU* 3.9 15.3 - - + -
116D ILE* 4.8 10.5 - - + -
120D VAL* 5.4 1.6 - - + -
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Residues in contact with CYS 42 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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38B LEU* 2.9 26.8 + - - +
39B THR 3.7 0.7 - - - +
41B LEU* 1.3 73.0 - - - +
43B TRP* 1.3 58.9 + - - +
45B ILE* 4.5 0.7 - - - -
46B THR* 2.8 31.9 + - - +
79B PHE* 3.6 36.1 - - - -
81B TYR* 3.6 26.8 + - + -
89B LEU* 3.7 31.4 - - + +
93B LEU* 4.4 8.1 - - - -
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Residues in contact with TRP 43 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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39B THR* 3.0 16.6 + - + +
40B TYR* 3.6 3.4 - - - +
42B CYS* 1.3 74.0 - - - +
44B MET* 1.3 82.9 + - + +
45B ILE 3.0 1.5 + - - -
46B THR* 3.2 2.3 + - - -
47B HIS* 2.8 76.6 + + + +
50B THR* 2.8 31.8 + - + -
51B ALA 3.1 17.2 + - - -
52B ILE* 3.4 33.3 - - + +
56B THR* 4.1 13.7 - - + -
60B TYR* 4.3 4.5 - + + -
81B TYR* 3.5 18.8 + - - +
21G G 3.5 22.7 - - - -
22G A 4.1 16.8 - - - -
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Residues in contact with MET 44 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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40B TYR* 2.9 63.0 + - + +
41B LEU* 3.7 7.2 - - + +
43B TRP* 1.3 99.7 - - + +
45B ILE* 1.3 59.0 + - + +
48B ASN* 2.7 30.2 + - - +
49B GLY 3.2 14.5 + - - +
50B THR 3.4 18.4 - - - +
51B ALA* 4.3 1.6 - - - -
52B ILE* 4.2 3.1 - - + +
262B THR* 4.0 15.9 - - - +
119D ILE* 4.0 15.1 - - + +
123D LEU* 3.8 19.7 - - + -
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Residues in contact with ILE 45 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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41B LEU* 2.9 26.5 + - + +
44B MET* 1.3 80.5 - - + +
46B THR* 1.3 63.1 + - + +
47B HIS 2.9 6.1 + - - -
48B ASN* 3.1 9.2 + - - +
88B ILE* 5.1 7.0 - - + +
89B LEU* 3.6 30.5 - - + -
92B SER* 3.5 37.5 - - - +
93B LEU* 4.5 12.8 - - + +
114D SER 5.4 8.9 + - - +
116D ILE* 3.8 29.6 - - + -
119D ILE* 4.3 13.7 - - + +
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Residues in contact with THR 46 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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42B CYS 2.8 18.2 + - - +
43B TRP* 3.2 1.7 + - - -
45B ILE* 1.3 80.0 - - + +
47B HIS* 1.3 87.4 + - - +
81B TYR* 3.8 9.8 + - + -
83B THR* 4.6 9.6 - - - +
85B LYS* 3.9 39.9 + - + +
88B ILE* 6.4 1.6 - - + -
89B LEU* 4.0 24.5 - - + -
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Residues in contact with HIS 47 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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43B TRP* 2.8 63.1 + + + +
46B THR* 1.3 110.0 + - - +
48B ASN* 1.3 74.9 + - - +
49B GLY 3.7 0.9 - - - -
50B THR* 3.1 32.1 + - + +
81B TYR* 4.7 1.1 - + - -
21G G 2.4 35.2 + - - -
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Residues in contact with ASN 48 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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44B MET 2.7 11.9 + - - -
45B ILE 3.1 7.9 + - - +
46B THR 3.6 0.2 - - - -
47B HIS* 1.3 83.8 - - - +
49B GLY* 1.3 57.4 + - - +
50B THR* 3.0 5.4 + - - -
114D SER* 3.1 33.9 + - - +
119D ILE* 4.0 11.4 - - - +
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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
------------------------------------------------------------
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