Contacts of the helix formed by residues 73 - 87 (chain A) in PDB entry 5L0P
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 SER 73 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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43A LEU* 3.2 44.8 - - - +
44A ARG 4.1 8.7 + - - -
46A ILE* 4.7 6.2 - - - +
70A SER* 3.1 13.9 + - - -
72A HIS* 1.3 84.6 + - - +
74A GLY* 1.3 59.7 + - - +
75A ASP* 3.4 3.8 - - - -
76A GLU* 3.2 12.2 + - - +
77A LEU* 2.9 33.7 + - - +
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Residues in contact with GLY 74 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
66A PHE* 3.4 34.4 - - - +
67A ARG* 4.3 0.4 - - - -
70A SER* 2.7 30.5 + - - -
71A PRO 4.7 0.4 + - - -
72A HIS 4.0 0.2 - - - -
73A SER* 1.3 70.8 - - - +
75A ASP* 1.3 57.7 + - - +
77A LEU* 3.1 5.7 + - - -
78A TYR* 2.9 26.3 + - - +
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Residues in contact with ASP 75 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
63A LYS* 3.8 23.9 - - - +
67A ARG* 3.9 28.5 + - + +
71A PRO 5.7 1.0 - - - +
72A HIS 4.8 3.6 - - - +
73A SER* 3.9 6.6 - - - -
74A GLY* 1.3 71.6 + - - +
76A GLU* 1.3 84.8 + - - +
78A TYR* 3.5 3.4 + - - +
79A GLU* 3.1 30.4 + - - +
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Residues in contact with GLU 76 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
41A PHE* 4.5 30.2 - - - -
43A LEU* 4.3 26.0 - - + +
72A HIS 5.7 0.2 - - - +
73A SER* 3.2 17.9 - - - +
75A ASP* 1.3 87.9 + - - +
77A LEU* 1.3 64.2 + - - +
79A GLU* 3.4 5.5 + - - +
80A LEU* 3.0 25.7 + - - +
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Residues in contact with LEU 77 (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 TRP* 3.5 16.8 - - + -
34A LEU* 3.8 27.6 - - + -
37A ALA* 3.7 29.8 - - + -
43A LEU* 4.4 7.0 - - + -
46A ILE* 4.1 22.2 - - + -
51A PHE* 4.0 15.7 - - + -
66A PHE* 3.8 12.6 - - + -
70A SER* 4.4 7.9 - - - +
73A SER* 2.9 24.9 + - - +
74A GLY* 3.1 7.4 + - - +
76A GLU* 1.3 77.2 - - - +
78A TYR* 1.3 57.5 + - - +
80A LEU* 3.3 7.9 + - + +
81A LEU* 2.9 25.1 + - - +
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Residues in contact with TYR 78 (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 LEU 4.2 9.4 - - - -
62A THR* 4.0 3.9 - - - -
63A LYS* 3.5 54.0 + - + -
66A PHE* 3.4 28.3 - + + -
74A GLY 2.9 16.0 + - - +
75A ASP 3.7 4.7 - - - +
77A LEU* 1.3 76.7 - - - +
79A GLU* 1.3 74.3 + - - +
81A LEU* 3.3 4.0 + - + +
82A GLN* 2.8 69.2 + - + -
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Residues in contact with GLU 79 (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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63A LYS* 2.8 27.9 + - - +
75A ASP 3.1 18.3 + - - +
76A GLU* 3.9 7.2 - - - +
77A LEU 3.3 0.2 - - - -
78A TYR* 1.3 88.3 - - - +
80A LEU* 1.3 65.1 + - - +
82A GLN* 3.3 13.1 + - - +
83A HIS* 3.0 22.7 + - - +
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Residues in contact with LEU 80 (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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12A ILE* 4.2 33.7 - - + -
33A TRP* 3.6 25.8 - - + +
36A TRP* 4.2 4.7 - - + -
37A ALA* 3.6 30.7 - - + -
41A PHE* 3.9 20.0 - - + -
76A GLU* 3.0 20.5 + - - +
77A LEU* 3.4 11.7 - - + +
79A GLU* 1.3 74.8 - - - +
81A LEU* 1.3 63.2 + - - +
83A HIS* 3.1 8.5 + - - +
84A ILE* 3.0 33.6 + - + +
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Residues in contact with LEU 81 (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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22A PRO* 3.9 32.1 - - + -
25A TRP* 4.6 10.1 - - + -
33A TRP* 3.9 9.8 - - + -
58A LEU* 4.2 24.7 - - + +
59A LEU* 3.9 20.6 - - + -
66A PHE* 4.2 22.0 - - + -
77A LEU 2.9 14.2 + - - +
78A TYR* 3.3 10.5 - - + +
80A LEU* 1.3 76.4 - - - +
82A GLN* 1.3 75.2 + - - +
84A ILE* 3.1 7.1 + - + +
85A LEU* 2.9 31.0 + - + +
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Residues in contact with GLN 82 (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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78A TYR* 2.8 80.9 + - + +
79A GLU* 3.3 16.5 + - - +
81A LEU* 1.3 89.4 - - - +
83A HIS* 1.3 62.7 + - - +
85A LEU* 3.2 19.8 + - - +
86A LYS* 3.0 23.6 + - - +
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Residues in contact with HIS 83 (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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11A SER 3.8 20.9 + - - -
12A ILE* 3.4 36.1 - - + +
79A GLU 3.0 12.6 + - - +
80A LEU* 3.1 12.5 + - - +
82A GLN* 1.3 74.3 - - - +
84A ILE* 1.3 69.9 + - + +
86A LYS* 3.1 17.9 + - - +
87A GLN* 3.1 18.7 + - - +
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Residues in contact with ILE 84 (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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12A ILE* 5.5 3.4 - - + -
14A LEU* 3.7 27.4 - - + -
18A LEU 5.4 0.9 - - - +
19A ARG 6.5 0.2 - - - -
20A LEU 5.2 2.5 - - - +
22A PRO* 3.7 32.4 - - + +
25A TRP* 4.1 9.9 - - + -
33A TRP* 3.3 32.1 - - + +
80A LEU* 3.0 29.8 + - + +
81A LEU* 3.4 8.3 - - - +
83A HIS* 1.3 82.2 - - + +
85A LEU* 1.3 62.6 + - - +
87A GLN* 3.1 24.6 + - - +
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Residues in contact with LEU 85 (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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21A GLN* 6.1 1.8 - - + -
22A PRO* 4.0 22.4 - - + -
59A LEU* 3.8 35.4 - - + -
81A LEU* 2.9 22.9 + - + +
82A GLN* 3.2 30.5 + - - +
84A ILE* 1.3 78.0 - - - +
86A LYS* 1.3 63.0 + - - +
87A GLN 3.2 9.0 + - - +
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Residues in contact with LYS 86 (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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82A GLN 3.0 14.9 + - - +
83A HIS* 3.1 11.1 + - - +
85A LEU* 1.3 75.5 - - - +
87A GLN* 1.3 58.1 + - - +
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Residues in contact with GLN 87 (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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21A GLN* 5.6 5.6 - - - +
83A HIS* 3.1 19.7 + - - +
84A ILE* 3.1 24.8 + - - +
85A LEU 3.7 9.7 - - - +
86A LYS* 1.3 72.2 - - - +
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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