Contacts of the helix formed by residues 34 - 48 (chain A) 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 A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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19A PHE* 3.5 26.0 - - + -
22A ARG* 3.6 22.9 - - - +
23A PHE* 4.7 2.7 - - + -
30A LYS 3.8 3.6 + - - -
31A ILE* 3.1 22.8 + - - +
33A SER* 1.3 75.2 - - - +
35A ALA* 1.3 56.5 + - - +
36A ALA 3.4 0.4 - - - -
37A GLU* 2.8 7.7 + - - +
38A LEU* 2.6 53.1 + - - -
68A LEU* 3.8 17.7 - - - -
77A LEU* 4.4 10.1 - - - -
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Residues in contact with ALA 35 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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32A ALA 4.6 7.6 + - - +
33A SER* 2.8 7.3 + - - +
34A CYS* 1.3 80.7 - - - +
36A ALA* 1.3 63.9 + - - +
38A LEU* 3.2 3.4 + - - +
39A THR* 2.9 25.8 + - - -
61A ASN* 3.6 16.6 - - - +
64A ILE* 4.0 21.9 - - + +
65A SER* 4.1 18.6 - - - +
68A LEU* 4.6 3.8 - - + +
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Residues in contact with ALA 36 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
3A GLN* 3.9 23.5 + - + +
7A LEU* 4.6 8.0 - - + +
33A SER 3.8 5.5 + - - +
34A CYS 3.4 0.6 - - - -
35A ALA* 1.3 77.6 - - - +
37A GLU* 1.3 65.3 - - + +
39A THR* 3.2 5.5 + - - -
40A TYR* 3.1 19.2 + - - +
57A PHE* 3.6 24.6 - - + -
61A ASN* 3.4 10.7 - - - +
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Residues in contact with GLU 37 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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7A LEU* 5.1 2.7 - - + -
15A LEU* 4.4 26.5 - - + +
18A GLN* 3.5 18.0 - - - +
19A PHE* 3.0 44.6 + - + -
22A ARG* 2.8 36.7 + - - -
33A SER 4.9 0.7 + - - +
34A CYS* 2.8 7.4 + - - +
36A ALA* 1.3 78.4 - - + +
38A LEU* 1.3 62.5 + - - +
40A TYR* 3.1 9.5 + - - +
41A LEU* 2.8 36.2 + - + +
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Residues in contact with LEU 38 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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19A PHE* 3.9 25.5 - - + -
34A CYS* 2.6 40.8 + - - +
35A ALA 3.4 5.2 - - - +
37A GLU* 1.3 73.0 - - - +
39A THR* 1.3 56.9 + - - +
41A LEU* 3.7 3.9 - - + +
42A CYS* 2.9 36.0 + - - -
64A ILE* 3.9 15.3 - - + -
68A LEU* 4.2 4.9 - - + -
77A LEU* 4.5 2.5 - - + -
79A PHE* 3.2 55.4 - - + -
93A LEU* 4.0 17.3 - - + -
102A PHE* 5.2 2.5 - - + -
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Residues in contact with THR 39 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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35A ALA 2.9 15.5 + - - -
36A ALA 3.2 9.9 - - - -
38A LEU* 1.3 73.9 - - - +
40A TYR* 1.3 68.9 + - - +
42A CYS* 3.1 5.8 + - - +
43A TRP* 3.0 21.7 + - + +
52A ILE* 4.6 6.7 - - + -
57A PHE* 3.6 30.1 - - + +
60A TYR* 3.9 26.9 - - + -
61A ASN* 3.4 17.8 + - - -
64A ILE* 3.3 18.8 - - - +
81A TYR* 4.7 2.4 - - + -
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Residues in contact with TYR 40 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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7A LEU* 3.9 31.2 - - + -
12A PRO* 3.9 21.3 - - + +
15A LEU* 3.5 34.4 - - + +
16A VAL* 5.6 2.5 - - + -
36A ALA 3.1 8.1 + - - +
37A GLU* 3.1 9.1 + - - +
39A THR* 1.3 81.0 - - - +
41A LEU* 1.3 73.7 + - + +
43A TRP* 3.3 5.4 + - - +
44A MET* 2.9 70.1 + - + +
52A ILE* 5.0 4.3 - - + -
57A PHE* 4.7 1.3 - - - -
262A THR* 4.5 15.9 - - + -
120C VAL* 6.3 1.6 - - + -
123C LEU* 3.2 23.7 - - + +
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Residues in contact with LEU 41 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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15A LEU* 5.9 0.9 - - + -
16A VAL* 4.3 26.5 - - + +
19A PHE* 3.3 50.5 - - + -
37A GLU* 2.8 19.0 + - + +
38A LEU* 3.7 4.9 - - - +
40A TYR* 1.3 88.1 - - + +
42A CYS* 1.3 67.7 + - - +
43A TRP 3.0 0.5 + - - -
44A MET* 3.1 6.5 + - + +
45A ILE* 2.9 32.2 + - + +
93A LEU* 4.5 12.8 - - + -
96A LEU* 3.9 14.4 - - + -
116C ILE* 4.7 12.1 - - + -
120C VAL* 5.3 1.8 - - + -
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Residues in contact with CYS 42 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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38A LEU* 2.9 29.0 + - - +
39A THR 3.7 0.9 - - - +
41A LEU* 1.3 73.2 - - - +
43A TRP* 1.3 58.5 + - - +
45A ILE* 3.7 0.6 + - - +
46A THR* 2.8 31.9 + - - +
79A PHE* 3.5 37.0 - - - -
81A TYR* 3.6 26.8 + - + -
89A LEU* 3.7 31.4 - - + +
93A LEU* 4.4 5.8 - - - -
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Residues in contact with TRP 43 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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39A THR* 3.0 13.2 + - + +
40A TYR* 3.6 7.2 - - - +
42A CYS* 1.3 73.8 - - - +
44A MET* 1.3 81.7 + - + +
45A ILE 3.0 1.9 + - - -
46A THR* 3.2 2.8 + - - -
47A HIS* 2.8 75.3 + + + +
50A THR* 2.8 32.4 + - + -
51A ALA 3.1 17.0 + - - -
52A ILE* 3.4 33.8 - - + +
53A LYS 5.2 0.4 - - - -
56A THR* 4.0 19.3 - - + -
60A TYR* 4.3 6.1 - + + -
81A TYR* 3.5 17.9 + - - +
21H G 3.5 22.4 - - - -
22H A 4.5 10.3 - - - -
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Residues in contact with MET 44 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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40A TYR* 2.9 63.3 + - + +
41A LEU* 3.6 6.5 - - + +
43A TRP* 1.3 100.1 - - + +
45A ILE* 1.3 55.0 + - + +
47A HIS* 5.1 0.2 - - - -
48A ASN* 2.7 34.2 + - - +
49A GLY 3.1 14.4 + - - +
50A THR 3.4 17.9 - - - +
51A ALA* 4.3 1.1 - - - -
52A ILE* 4.2 3.4 - - + +
262A THR* 3.9 15.3 - - - +
116C ILE* 6.6 0.4 - - + -
119C ILE* 3.9 11.1 - - + +
120C VAL* 6.5 0.7 - - + -
123C LEU* 3.7 25.8 - - + -
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Residues in contact with ILE 45 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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41A LEU* 2.9 27.3 + - + +
44A MET* 1.3 80.0 - - + +
46A THR* 1.3 62.7 + - + +
47A HIS 2.9 6.4 + - - -
48A ASN* 3.1 9.2 + - - +
88A ILE* 5.1 7.0 - - + +
89A LEU* 3.6 31.0 - - + -
92A SER* 3.4 37.5 - - - +
93A LEU* 4.5 12.3 - - + +
114C SER* 5.7 4.0 + - - +
116C ILE* 3.7 29.6 - - + -
119C ILE* 4.1 14.5 - - + +
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Residues in contact with THR 46 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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42A CYS 2.8 18.9 + - - +
43A TRP* 3.7 1.6 - - - -
45A ILE* 1.3 80.3 - - + +
47A HIS* 1.3 87.0 + - - +
81A TYR* 3.8 9.3 + - + -
83A THR* 4.5 13.0 - - - +
85A LYS* 3.8 39.5 + - + +
88A ILE* 6.4 1.6 - - + -
89A LEU* 4.0 21.5 - - + -
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Residues in contact with HIS 47 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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43A TRP* 2.8 59.8 + + + +
44A MET 3.7 0.4 - - - -
46A THR* 1.3 109.9 + - - +
48A ASN* 1.3 73.1 + - - +
49A GLY 3.7 0.2 - - - -
50A THR* 3.0 32.2 + - + +
81A TYR* 4.6 0.4 - - - -
21H G 2.8 42.1 + - - -
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Residues in contact with ASN 48 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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44A MET 2.7 11.9 + - - -
45A ILE 3.1 7.8 + - - +
46A THR 3.6 0.2 - - - -
47A HIS* 1.3 82.1 - - - +
49A GLY* 1.3 56.8 + - - +
50A THR* 3.0 5.7 + - - -
114C SER* 3.0 32.3 + - - +
119C ILE* 3.9 12.6 - - - +
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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