Contacts of the helix formed by residues 42 - 56 (chain A) in PDB entry 1MHQ
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 ASP 42 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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29A TRP* 5.7 1.2 - - - -
32A LYS* 4.0 27.0 + - + +
33A ALA* 4.3 1.4 - - - -
38A MET* 4.1 20.0 - - + +
40A GLU 3.7 2.8 + - - -
41A GLN* 1.3 69.2 - - - +
43A TRP* 1.3 62.0 + - - +
44A SER* 2.7 25.1 + - - -
45A ALA* 2.9 24.9 + - + +
46A ILE* 3.4 15.3 + - - +
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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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41A GLN* 2.9 24.9 + - + +
42A ASP* 1.3 72.9 + - - +
44A SER* 1.3 60.9 + - - +
46A ILE* 3.3 26.4 + - + +
47A GLN* 3.3 47.7 + - + +
84A THR* 4.8 10.2 - - + +
88A MET* 3.5 32.8 - - + -
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Residues in contact with SER 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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29A TRP* 6.2 0.2 - - - -
42A ASP* 2.7 15.9 + - - -
43A TRP* 1.3 74.9 - - - +
45A ALA* 1.3 56.5 + - - -
47A GLN* 3.2 17.3 + - - +
48A ASN* 2.9 41.9 + - - -
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Residues in contact with ALA 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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29A TRP* 3.8 21.6 - - + +
32A LYS* 3.7 13.7 - - + -
33A ALA* 3.6 26.9 - - + +
42A ASP* 2.9 27.2 + - - +
44A SER* 1.3 74.4 - - - +
46A ILE* 1.3 58.2 + - - +
48A ASN* 3.1 2.6 + - - +
49A PHE* 2.8 30.7 + - - +
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Residues in contact with ILE 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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33A ALA* 3.7 14.6 - - + +
41A GLN* 3.2 43.3 - - + +
42A ASP 3.4 10.3 - - - +
43A TRP* 3.4 32.3 - - + +
44A SER 3.3 0.6 - - - -
45A ALA* 1.3 75.1 - - - +
47A GLN* 1.3 64.9 + - - +
49A PHE* 3.1 5.1 + - - +
50A CYS* 3.1 24.0 + - - -
84A THR* 4.3 7.2 - - + +
85A VAL* 4.0 26.5 - - + +
88A MET* 3.7 27.8 - - + -
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Residues in contact with GLN 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* 3.3 31.9 - - + +
44A SER* 3.4 22.4 + - - +
45A ALA 3.2 0.2 - - - -
46A ILE* 1.3 77.3 - - - +
48A ASN* 1.3 62.7 + - - +
50A CYS* 3.6 3.8 + - - +
51A GLU* 3.3 23.0 + - - +
88A MET* 4.2 20.4 - - - +
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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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29A TRP* 3.0 59.3 - - + +
44A SER* 2.9 30.9 + - - -
45A ALA 3.1 4.2 + - - +
47A GLN* 1.3 77.2 - - - +
49A PHE* 1.3 62.5 + - - +
51A GLU* 3.4 13.5 + - - +
52A GLN* 3.2 26.2 + - - +
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Residues in contact with PHE 49 (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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26A LEU* 3.5 42.2 - - + -
29A TRP* 3.9 10.5 - - + +
30A LEU* 3.7 37.7 - - + +
33A ALA* 5.0 0.4 - - + -
45A ALA 2.8 13.4 + - - +
46A ILE* 3.4 9.9 - - - +
48A ASN* 1.3 76.3 - - - +
50A CYS* 1.3 63.0 + - - +
51A GLU 3.0 1.7 + - - -
52A GLN* 3.0 15.7 + - - +
53A VAL* 3.1 17.4 + - + +
63A ALA* 3.8 24.2 - - + -
66A LEU* 4.9 1.6 - - + -
67A LEU* 4.1 13.7 - - + -
85A VAL* 3.4 28.3 - - + -
89A CYS* 3.4 26.9 - - - -
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Residues in contact with CYS 50 (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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46A ILE 3.1 15.8 + - - +
47A GLN* 4.3 3.1 - - - +
49A PHE* 1.3 79.5 - - - +
51A GLU* 1.3 60.0 + - - +
53A VAL* 3.4 8.4 - - - +
54A ASN* 3.5 8.8 + - - -
85A VAL* 4.0 3.6 - - - -
88A MET* 3.8 13.7 - - + -
89A CYS* 2.1 61.7 - - - -
92A HIS* 4.8 11.4 - - + -
93A CYS* 3.2 26.9 - - - -
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Residues in contact with GLU 51 (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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47A GLN 3.3 17.0 + - - +
48A ASN* 3.7 13.8 - - - +
49A PHE 3.0 1.0 - - - -
50A CYS* 1.3 75.1 - - - +
52A GLN* 1.3 71.4 + - - +
53A VAL 3.1 1.3 - - - -
54A ASN* 3.0 14.4 + - - +
55A THR* 3.0 30.5 + - - +
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Residues in contact with GLN 52 (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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25A SER* 4.6 14.8 - - - +
26A LEU* 3.8 19.2 - - + +
29A TRP* 3.8 23.4 + - + +
48A ASN 3.2 14.6 + - - +
49A PHE* 3.0 9.5 + - - +
51A GLU* 1.3 83.3 - - - +
53A VAL* 1.3 59.0 + - - +
55A THR* 3.6 28.0 + - - +
56A ASP* 2.7 44.6 + - - +
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Residues in contact with VAL 53 (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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26A LEU* 3.7 18.2 - - + -
49A PHE* 3.1 26.4 + - + +
50A CYS* 3.4 16.2 - - - +
52A GLN* 1.3 79.4 - - - +
54A ASN* 1.3 60.7 + - - +
56A ASP 3.5 1.6 - - - +
59A GLY* 4.0 13.2 - - - -
60A PRO* 3.5 23.6 - - + +
63A ALA* 3.9 13.5 - - + -
89A CYS* 4.6 0.9 - - - -
93A CYS* 3.8 13.5 - - + -
97A PHE* 3.6 36.1 - - + -
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Residues in contact with ASN 54 (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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50A CYS 3.5 15.7 + - - -
51A GLU* 3.0 11.8 + - - +
53A VAL* 1.3 77.9 - - - +
55A THR* 1.3 66.2 + - - +
56A ASP 4.4 1.4 - - - +
60A PRO* 5.7 0.6 - - - +
92A HIS 3.9 7.5 + - - -
93A CYS* 3.1 16.9 - - - +
94A GLY* 2.8 29.7 + - - -
97A PHE* 5.4 0.5 - - - +
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Residues in contact with THR 55 (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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51A GLU* 3.0 21.8 + - - +
52A GLN* 3.0 31.2 + - - +
54A ASN* 1.3 79.8 - - - +
56A ASP* 1.3 66.2 + - - +
57A PRO* 3.6 5.9 - - - +
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Residues in contact with ASP 56 (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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26A LEU* 4.3 13.3 + - + +
52A GLN* 2.7 27.2 + - - +
53A VAL 3.5 5.0 - - - +
54A ASN 4.4 1.3 - - - +
55A THR* 1.3 77.4 - - + +
57A PRO* 1.3 91.6 - - - +
58A ASN* 2.8 33.8 + - - +
59A GLY* 3.0 19.2 + - - +
60A PRO* 3.5 9.2 - - - +
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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