Contacts of the helix formed by residues 53 - 66 (chain A) in PDB entry 2M9A
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 GLN 53 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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42A LEU* 4.4 0.9 - - - -
51A CYS* 3.3 11.1 - - - -
52A ARG* 1.4 86.9 - - + +
54A LYS* 1.4 95.1 + - - +
55A ALA* 3.2 27.4 - - - +
56A SER* 2.7 33.1 + - - +
57A LEU* 3.4 1.5 - - - +
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Residues in contact with LYS 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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42A LEU* 3.6 26.6 - - + +
52A ARG 4.2 0.4 + - - -
53A GLN* 1.4 88.0 + - - +
55A ALA* 1.3 78.3 + - + +
57A LEU* 3.1 11.1 - - - +
58A ASN* 3.0 33.5 - - - +
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Residues in contact with ALA 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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53A GLN* 3.2 22.2 + - - +
54A LYS* 1.3 87.8 - - + +
56A SER* 1.3 65.2 + - - +
58A ASN* 3.1 6.9 + - - +
59A TRP* 3.0 48.8 + - + +
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Residues in contact with SER 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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49A PHE* 3.8 11.4 - - - -
51A CYS* 3.0 21.6 - - - +
53A GLN* 2.7 34.8 + - - +
55A ALA* 1.3 78.2 - - - +
57A LEU* 1.4 56.6 + - - +
59A TRP* 4.7 2.1 - - - +
60A HIS* 3.5 18.9 + - - +
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Residues in contact with LEU 57 (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 LEU* 3.6 28.0 - - + -
43A GLN 3.5 31.0 - - - +
44A CYS* 3.7 11.9 - - + +
49A PHE* 4.0 17.3 - - + +
51A CYS* 3.2 34.2 - - - -
53A GLN 3.4 7.0 - - - +
54A LYS* 3.1 27.6 - - - +
56A SER* 1.4 76.5 - - - +
58A ASN* 1.4 56.6 - - + +
59A TRP 3.3 0.2 - - - -
60A HIS* 3.2 4.1 + - - +
61A MET* 2.8 50.6 + - + +
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Residues in contact with ASN 58 (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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54A LYS* 3.0 30.1 + - - +
55A ALA* 3.1 7.7 + - - +
57A LEU* 1.4 80.4 - - + +
59A TRP* 1.3 87.5 - - - +
61A MET* 3.3 24.4 + - + +
62A LYS* 3.1 21.5 + - - +
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Residues in contact with TRP 59 (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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55A ALA* 3.0 43.7 + - + +
56A SER* 4.8 1.6 - - - +
58A ASN* 1.3 90.6 - - - +
60A HIS* 1.3 61.0 + - - +
61A MET 3.2 0.2 - - - -
62A LYS* 3.2 32.7 + - + +
63A LYS* 2.9 38.6 + - - +
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Residues in contact with HIS 60 (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 CYS* 3.6 12.3 - - + -
47A CYS* 4.2 2.9 - - - -
48A GLY 5.4 0.2 - - - -
49A PHE* 3.4 50.1 - + + +
56A SER 3.5 16.4 + - - +
57A LEU* 3.2 8.0 + - - +
59A TRP* 1.3 77.7 - - - +
61A MET* 1.3 56.8 + - - -
63A LYS* 3.2 26.9 - - - +
64A HIS* 3.3 17.9 + + - -
69A PHE* 3.7 27.9 - + - -
102A ZN 2.0 36.3 - - - -
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Residues in contact with MET 61 (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 GLN 5.2 0.4 - - - +
44A CYS* 3.6 31.4 - - + -
45A GLU* 4.3 4.5 - - - -
46A ILE* 3.6 23.8 - - + -
57A LEU* 2.8 29.9 + - + +
58A ASN* 3.5 30.1 - - + +
59A TRP 3.2 0.4 - - - -
60A HIS* 1.3 69.5 - - - +
62A LYS* 1.3 61.1 + - - +
63A LYS 3.2 0.2 - - - -
64A HIS* 3.0 27.0 + - - +
65A ASP* 3.3 10.2 + - - +
75A ASN* 4.8 4.4 + - - +
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Residues in contact with LYS 62 (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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58A ASN* 3.1 14.0 + - - +
59A TRP* 3.2 40.6 - - + +
61A MET* 1.3 74.7 - - - +
63A LYS* 1.3 61.3 + - + +
65A ASP* 3.1 44.0 + - - +
66A ALA 4.2 1.7 + - - -
68A SER* 4.1 13.4 + - - +
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Residues in contact with LYS 63 (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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59A TRP* 2.9 26.6 + - - +
60A HIS* 3.2 21.2 - - + +
61A MET 3.2 0.2 - - - -
62A LYS* 1.3 77.8 - - + +
64A HIS* 1.3 54.9 + - - +
67A ASP* 3.2 3.8 - - - -
68A SER* 2.8 49.2 + - - +
69A PHE* 2.9 38.3 + - + +
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Residues in contact with HIS 64 (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 CYS* 3.9 0.2 - - - -
46A ILE* 3.4 25.0 - - + +
47A CYS* 4.0 8.7 - - + -
60A HIS* 3.3 25.8 + + - -
61A MET* 3.0 15.6 + - - +
63A LYS* 1.3 78.5 - - - +
65A ASP* 1.4 66.8 + - - +
67A ASP* 3.2 14.1 + - - +
69A PHE* 4.6 11.6 - + - +
73A SER* 4.2 2.3 - - - +
74A CYS 4.3 0.7 - - - -
75A ASN* 3.2 32.6 + - - +
102A ZN 2.1 37.0 - - - -
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Residues in contact with ASP 65 (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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61A MET 3.3 5.2 + - - +
62A LYS* 3.1 46.6 + - - +
64A HIS* 1.4 77.6 - - - +
66A ALA* 1.3 67.6 + - + +
75A ASN* 3.2 27.8 + - - +
87A VAL* 3.5 10.4 - - - +
88A VAL* 4.1 13.9 - - - +
91A LYS* 3.5 34.1 + - - +
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Residues in contact with ALA 66 (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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62A LYS 4.2 2.0 + - - -
65A ASP* 1.3 85.4 - - - +
67A ASP* 1.4 69.6 - - - +
68A SER* 3.7 2.6 + - - +
72A PHE* 3.5 6.4 - - - -
73A SER 3.3 18.2 + - - +
84A LYS* 3.6 41.2 - - + +
87A VAL* 3.7 16.2 - - + +
88A VAL* 4.2 6.1 - - + -
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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