Contacts of the helix formed by residues 34 - 48 (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 CYS 34 (chain C).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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19C PHE* 3.5 25.4 - - + -
22C ARG* 3.6 22.6 - - - +
23C PHE* 4.7 2.7 - - + -
30C LYS 3.8 3.0 + - - -
31C ILE* 3.2 23.4 + - - +
33C SER* 1.3 75.4 - - - +
35C ALA* 1.3 56.2 + - - +
36C ALA 3.4 0.4 - - - -
37C GLU* 2.9 7.7 + - - +
38C LEU* 2.6 56.9 + - - -
68C LEU* 3.8 13.7 - - - -
77C LEU* 4.4 9.6 - - - -
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Residues in contact with ALA 35 (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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32C ALA 4.6 8.0 + - - +
33C SER* 2.8 7.3 + - - +
34C CYS* 1.3 80.2 - - - +
36C ALA* 1.3 65.1 + - - +
38C LEU* 3.2 3.8 + - - +
39C THR* 2.9 25.6 + - - -
61C ASN* 3.6 16.4 - - - +
64C ILE* 4.0 22.5 - - + +
65C SER* 4.1 18.8 - - - +
68C LEU* 4.9 2.7 - - + -
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Residues in contact with ALA 36 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
3C GLN* 3.9 22.4 - - + +
7C LEU* 4.6 7.4 - - + +
33C SER 3.8 5.8 + - - +
34C CYS 3.4 0.4 - - - -
35C ALA* 1.3 77.8 - - - +
37C GLU* 1.3 66.0 + - + +
39C THR* 3.2 6.3 + - - -
40C TYR* 3.1 18.7 + - - +
57C PHE* 3.6 24.9 - - + -
61C ASN* 3.4 11.5 - - - +
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Residues in contact with GLU 37 (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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7C LEU* 5.1 2.7 - - + -
15C LEU* 4.4 26.9 - - + +
18C GLN* 4.0 17.7 - - - +
19C PHE* 3.0 44.3 + - + -
22C ARG* 2.7 38.4 + - - -
33C SER 4.9 0.8 + - - +
34C CYS* 2.9 7.4 + - - +
36C ALA* 1.3 78.4 - - + +
38C LEU* 1.3 57.8 + - - +
40C TYR* 3.1 9.1 + - - +
41C LEU* 2.9 35.4 + - + +
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Residues in contact with LEU 38 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
19C PHE* 3.9 25.7 - - + -
34C CYS* 2.6 41.9 + - - +
35C ALA 3.4 4.5 - - - +
37C GLU* 1.3 72.3 - - - +
39C THR* 1.3 58.2 + - - +
41C LEU* 3.7 3.7 - - - +
42C CYS* 2.9 34.8 + - - -
64C ILE* 3.9 15.5 - - + -
68C LEU* 4.2 4.3 - - + -
77C LEU* 4.5 2.5 - - + -
79C PHE* 3.2 55.4 - - + -
93C LEU* 4.0 17.5 - - + -
102C PHE* 5.2 2.7 - - + -
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Residues in contact with THR 39 (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 2.9 15.6 + - - -
36C ALA 3.2 9.4 - - - -
37C GLU 3.1 0.2 - - - -
38C LEU* 1.3 74.0 - - - +
40C TYR* 1.3 68.5 + - - +
42C CYS* 3.2 5.3 + - - +
43C TRP* 3.0 22.2 + - + +
52C ILE* 4.6 6.3 - - + -
57C PHE* 3.6 31.2 - - + +
60C TYR* 3.9 27.1 - - + -
61C ASN* 3.4 20.8 + - - -
64C ILE* 3.4 16.2 - - - +
81C TYR* 4.7 2.6 - - + -
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Residues in contact with TYR 40 (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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120B VAL* 6.1 1.6 - - + -
123B LEU* 3.2 22.6 - - + +
7C LEU* 3.9 31.2 - - + -
12C PRO* 3.9 21.8 - - + +
15C LEU* 3.5 33.6 - - + +
16C VAL* 5.6 2.9 - - + -
36C ALA 3.1 8.5 + - - +
37C GLU* 3.4 8.7 - - - +
39C THR* 1.3 81.3 - - - +
41C LEU* 1.3 74.0 + - + +
43C TRP* 3.3 4.9 + - - +
44C MET* 2.9 71.2 + - + +
52C ILE* 5.0 4.3 - - + -
57C PHE* 4.7 1.3 - - - -
262C THR* 4.5 15.7 - - + -
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Residues in contact with LEU 41 (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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116B ILE* 4.6 15.9 - - + -
120B VAL* 5.1 1.6 - - + -
15C LEU* 5.9 1.3 - - + -
16C VAL* 4.2 26.5 - - + +
19C PHE* 3.4 48.7 - - + -
37C GLU* 2.9 20.3 + - + +
38C LEU* 3.7 4.9 - - - +
40C TYR* 1.3 87.1 - - + +
42C CYS* 1.3 67.4 + - - +
43C TRP 3.0 0.3 + - - -
44C MET* 3.1 6.5 + - + +
45C ILE* 2.9 33.0 + - + +
93C LEU* 4.6 13.7 - - + -
96C LEU* 3.9 9.9 - - + -
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Residues in contact with CYS 42 (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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38C LEU* 2.9 29.0 + - - +
39C THR 3.7 0.9 - - - +
41C LEU* 1.3 72.5 - - - +
43C TRP* 1.3 59.9 + - - +
45C ILE* 4.5 0.7 - - - -
46C THR* 2.9 31.4 + - - +
79C PHE* 3.6 36.1 - - - -
81C TYR* 3.6 26.6 + - + -
89C LEU* 3.7 31.2 - - + +
93C LEU* 4.5 5.4 - - - -
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Residues in contact with TRP 43 (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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39C THR* 3.0 12.3 + - + +
40C TYR* 3.5 7.9 - - - +
42C CYS* 1.3 73.3 - - - +
44C MET* 1.3 91.4 + - + +
45C ILE 3.0 1.7 + - - -
46C THR* 3.2 2.5 + - - -
47C HIS* 2.8 73.3 + + + +
50C THR* 2.9 23.8 + - + -
51C ALA 3.1 17.0 + - - -
52C ILE* 3.4 34.0 - - + +
53C LYS 5.2 0.2 - - - -
56C THR* 4.0 15.3 - - + -
60C TYR* 4.3 4.9 - + + -
81C TYR* 3.5 19.0 + - + +
21I G 3.7 21.3 - - - -
22I A 4.0 20.0 - - - -
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Residues in contact with MET 44 (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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116B ILE* 6.6 0.2 - - + -
119B ILE* 4.0 10.7 - - + +
120B VAL* 6.5 0.9 - - + -
123B LEU* 3.6 33.2 - - + -
40C TYR* 2.9 58.5 + - + +
41C LEU* 3.7 6.7 - - + +
43C TRP* 1.3 97.8 - - + +
45C ILE* 1.3 55.3 + - + +
48C ASN* 2.7 34.5 + - - -
49C GLY 3.2 14.0 + - - +
50C THR 3.4 17.9 - - - +
51C ALA* 4.3 1.3 - - - -
52C ILE* 4.2 4.5 - - + +
262C THR* 4.1 14.6 - - - +
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Residues in contact with ILE 45 (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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114B SER* 4.7 13.8 + - - +
116B ILE* 3.7 28.9 - - + -
119B ILE* 4.1 15.2 - - + +
41C LEU* 2.9 26.2 + - + +
43C TRP 3.0 0.6 + - - -
44C MET* 1.3 79.9 - - + +
46C THR* 1.3 61.9 + - + +
47C HIS 2.9 6.1 + - - -
48C ASN* 3.1 9.2 + - - +
88C ILE* 5.1 7.2 - - + +
89C LEU* 3.6 30.3 - - + -
92C SER* 3.5 37.2 - - - +
93C LEU* 4.5 12.1 - - + +
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Residues in contact with THR 46 (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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42C CYS 2.9 17.7 + - - +
43C TRP* 3.8 1.7 - - - -
45C ILE* 1.3 80.0 - - + +
47C HIS* 1.3 86.8 + - - +
81C TYR* 3.8 9.4 + - + -
83C THR* 4.6 10.5 - - - +
85C LYS* 3.8 38.9 + - + +
88C ILE* 6.4 1.1 - - + -
89C LEU* 4.0 24.0 - - + -
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Residues in contact with HIS 47 (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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43C TRP* 2.8 62.0 + + + +
44C MET 3.6 0.7 - - - +
46C THR* 1.3 109.1 + - - +
48C ASN* 1.3 74.8 + - - +
50C THR* 3.1 31.7 + - + +
81C TYR* 4.6 1.3 - + - -
21I G 2.4 34.3 + - - -
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Residues in contact with ASN 48 (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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114B SER* 4.5 14.5 + - - +
119B ILE* 4.1 22.3 - - - +
44C MET 2.7 11.2 + - - -
45C ILE 3.1 7.9 + - - +
46C THR 3.7 0.2 - - - -
47C HIS* 1.3 83.0 - - - +
49C GLY* 1.3 56.2 + - - +
50C THR* 3.0 5.0 + - - -
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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