Contacts of the helix formed by residues 56 - 66 (chain A) in PDB entry 8LDH
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 56 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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54A MET 3.4 0.6 - - - -
55A GLU* 1.3 93.1 - - - +
57A LYS* 1.3 59.1 + - - +
59A LYS* 3.1 8.0 + - - +
60A GLY* 2.9 27.9 + - - -
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Residues in contact with LYS 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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28A VAL* 3.4 30.1 - - + +
29A GLY* 5.4 1.5 + - - -
33A MET* 5.5 0.2 - - - +
54A MET* 3.5 27.7 + - + +
56A ASP* 1.3 80.5 - - + +
58A LEU* 1.3 57.0 + - - +
60A GLY* 3.9 1.4 - - - -
61A GLU* 2.4 64.2 + - - +
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Residues in contact with LEU 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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28A VAL* 3.9 26.6 - - + +
50A LEU* 3.5 26.5 - - + +
52A ASP* 3.7 21.8 - - + +
54A MET 3.0 12.7 + - - +
55A GLU* 3.2 12.3 - - - +
57A LYS* 1.3 75.8 - - - +
59A LYS* 1.3 65.8 + - - +
61A GLU* 3.2 3.2 + - - +
62A MET* 3.0 24.7 + - - +
79A SER* 3.6 13.9 - - - +
80A GLY* 3.3 40.4 - - - +
81A LYS* 3.7 4.9 - - + +
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Residues in contact with LYS 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 GLU 3.0 12.6 + - - +
56A ASP* 3.1 7.8 + - - +
58A LEU* 1.3 76.0 - - - +
60A GLY* 1.3 58.5 - - - +
62A MET* 3.0 15.7 - - - +
63A MET* 2.9 53.5 + - + +
79A SER* 4.4 3.8 - - - +
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Residues in contact with GLY 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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56A ASP 2.9 14.8 + - - -
57A LYS 3.9 2.0 - - - -
59A LYS* 1.3 79.7 - - - +
61A GLU* 1.3 55.9 + - - +
63A MET* 3.5 8.6 + - - +
64A ASP* 3.1 27.0 + - - +
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Residues in contact with GLU 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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28A VAL* 4.2 13.5 - - + -
33A MET* 3.7 37.3 - - + +
50A LEU* 4.4 6.1 - - + -
57A LYS* 2.4 64.1 + - - +
58A LEU* 3.2 5.8 + - - +
60A GLY* 1.3 74.4 - - - +
62A MET* 1.3 62.2 + - - +
63A MET 3.2 0.2 - - - -
64A ASP* 3.5 10.5 + - - +
65A LEU* 3.0 36.1 + - - +
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Residues in contact with MET 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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50A LEU* 4.6 6.8 - - + +
58A LEU 3.0 14.5 + - - +
59A LYS* 3.0 20.0 - - - +
61A GLU* 1.3 72.9 - - - +
63A MET* 1.3 56.4 - - - +
65A LEU* 3.5 6.4 + - - +
66A GLN* 2.8 63.6 + - - +
77A ILE* 3.8 5.6 - - + +
78A VAL* 3.0 26.0 - - + +
79A SER* 2.9 52.7 - - - +
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Residues in contact with MET 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 LYS* 2.9 47.4 + - + +
60A GLY* 3.9 7.9 - - - +
61A GLU 3.2 0.2 - - - -
62A MET* 1.3 77.6 - - + +
64A ASP* 1.3 68.8 + - - +
66A GLN* 3.0 19.1 + - - +
67A HIS* 2.8 55.8 + - + +
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Residues in contact with ASP 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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60A GLY 3.1 17.6 + - - +
61A GLU* 3.7 13.4 - - - +
63A MET* 1.3 79.9 - - - +
65A LEU* 1.3 66.8 + - + +
67A HIS* 3.1 19.1 + - - +
68A GLY* 3.7 4.2 + - - -
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Residues in contact with LEU 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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33A MET* 3.1 32.5 - - + -
36A ALA* 4.6 3.4 - - + -
37A ILE* 3.9 26.9 - - + -
40A LEU* 4.1 22.4 - - + -
50A LEU* 4.0 15.3 - - + -
61A GLU* 3.0 18.6 - - - +
62A MET 3.6 4.5 - - - +
64A ASP* 1.3 82.7 - - + +
66A GLN* 1.3 60.9 + - - +
68A GLY* 3.3 14.0 + - - -
69A SER* 4.0 2.9 + - - -
72A LEU* 4.3 12.5 - - + +
77A ILE* 4.5 16.8 - - + +
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Residues in contact with GLN 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 MET* 2.8 45.3 + - - +
63A MET* 3.0 22.4 + - - +
65A LEU* 1.3 68.5 - - - +
67A HIS* 1.3 69.3 + - + +
68A GLY 3.0 5.4 - - - -
69A SER* 2.4 32.7 + - - +
77A ILE* 3.3 38.1 - - + +
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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