Contacts of the helix formed by residues 72 - 84 (chain A) in PDB entry 2LA6
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 72 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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14A ASN* 4.1 3.6 - - - -
39A ILE* 4.4 10.8 + - - +
70A PHE* 3.6 6.5 - - - +
71A ASP* 1.3 96.7 - - - +
73A PRO* 1.4 62.8 - - + +
74A PRO* 3.8 21.1 - - + +
75A SER* 3.3 15.5 + - - -
76A ALA* 3.1 21.5 + - - +
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Residues in contact with PRO 73 (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 ASP* 3.2 33.0 - - + +
13A ASN* 3.8 19.4 - - - +
14A ASN* 3.8 12.3 - - + +
71A ASP 4.2 3.4 - - - +
72A ASP* 1.4 80.0 - - + +
74A PRO* 1.4 68.3 - - + +
76A ALA* 3.4 1.6 + - - +
77A LYS* 3.0 29.3 + - - +
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Residues in contact with PRO 74 (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 ASP* 6.1 0.2 - - + -
72A ASP* 3.5 15.0 - - + +
73A PRO* 1.4 98.7 - - + +
75A SER* 1.3 56.2 + - - +
77A LYS* 4.0 7.2 - - + +
78A ALA* 3.1 28.9 + - - +
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Residues in contact with SER 75 (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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37A ILE* 3.1 16.5 - - - +
38A GLY* 3.2 28.6 + - - -
39A ILE 4.8 1.8 - - - -
70A PHE* 3.1 24.1 - - - -
72A ASP* 3.3 22.6 + - - -
73A PRO 3.3 0.6 - - - -
74A PRO* 1.3 77.2 - - - +
76A ALA* 1.3 60.2 + - - +
78A ALA* 4.4 0.7 - - - -
79A ALA* 3.0 27.2 + - - +
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Residues in contact with ALA 76 (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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13A ASN 3.3 24.2 - - - +
14A ASN* 3.7 21.3 - - - +
16A ILE* 3.3 20.8 - - + +
70A PHE* 3.8 15.2 - - + -
72A ASP 3.1 7.4 + - - +
73A PRO 3.4 4.0 + - - +
75A SER* 1.3 78.6 - - - +
77A LYS* 1.3 61.3 + - - +
79A ALA* 3.5 2.4 + - - +
80A ILE* 3.2 24.7 + - - +
97A PHE* 5.1 0.2 - - + -
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Residues in contact with LYS 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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10A HIS* 5.6 0.2 - - + -
12A ASP* 3.3 25.6 - - - +
73A PRO 3.0 16.6 + - - +
74A PRO* 4.0 8.3 - - + +
76A ALA* 1.3 72.1 - - - +
78A ALA* 1.3 69.5 + - + +
80A ILE* 3.1 7.3 + - + +
81A ASP* 3.1 38.3 + - + +
97A PHE* 3.8 24.1 - - + -
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Residues in contact with ALA 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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37A ILE* 3.7 23.3 - - + +
74A PRO 3.1 20.2 + - - +
75A SER* 4.4 0.7 - - - -
76A ALA 3.4 0.2 - - - -
77A LYS* 1.3 81.3 - - + +
79A ALA* 1.4 57.3 + - - +
81A ASP* 3.4 5.7 + - - +
82A TRP* 2.9 32.4 + - - +
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Residues in contact with ALA 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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16A ILE* 4.1 2.2 - - + -
34A PHE* 3.8 13.7 - - + -
37A ILE* 3.5 17.2 - - + +
70A PHE* 3.6 27.6 - - + -
75A SER 3.0 18.3 + - - +
76A ALA 3.6 5.4 - - - +
78A ALA* 1.4 75.2 - - - +
80A ILE* 1.3 56.8 + - - +
82A TRP* 4.4 0.2 - - - -
83A PHE* 2.9 37.9 + - + +
95A VAL* 4.4 3.6 - - - +
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Residues in contact with ILE 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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16A ILE* 3.6 16.6 - - + -
76A ALA 3.2 12.8 - - - +
77A LYS* 3.1 6.2 + - + +
79A ALA* 1.3 74.3 - - - +
81A ASP* 1.3 61.3 + - - +
84A ASP* 3.0 38.9 + - + +
95A VAL* 3.3 43.7 - - + +
96A SER* 3.5 16.6 - - - +
97A PHE* 3.5 44.2 - - + -
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Residues in contact with ASP 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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77A LYS* 3.1 31.6 + - - +
78A ALA* 3.9 7.6 - - - +
80A ILE* 1.3 79.5 - - - +
82A TRP* 1.3 63.8 + - - +
84A ASP* 4.7 6.5 + - - +
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Residues in contact with TRP 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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36A GLN* 3.0 23.3 + - - -
37A ILE* 3.7 21.9 - - + +
78A ALA 2.9 18.6 + - - +
79A ALA 4.0 2.2 - - - +
81A ASP* 1.3 83.3 + - - +
83A PHE* 1.3 92.6 + + - +
84A ASP 3.5 2.0 + - - +
86A LYS* 3.3 35.4 - - + +
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Residues in contact with PHE 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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33A TYR* 3.2 52.5 - + - -
34A PHE* 3.5 32.5 - + + -
36A GLN* 3.5 32.5 - - + -
37A ILE* 3.6 20.4 - - + -
79A ALA* 2.9 31.0 + - + +
82A TRP* 1.3 86.8 - + - +
84A ASP* 1.3 59.1 + - - +
85A GLY 3.2 1.0 + - - -
86A LYS* 3.0 27.2 + - + +
93A ILE* 3.3 26.2 - - + +
95A VAL* 3.8 7.9 - - + -
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Residues in contact with ASP 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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80A ILE* 3.0 23.0 + - + +
81A ASP* 4.9 5.4 - - - +
82A TRP 3.5 5.3 - - - +
83A PHE* 1.3 74.9 - - - +
85A GLY* 1.3 59.9 + - - +
86A LYS* 3.8 3.8 + - - +
93A ILE 4.1 0.2 - - - -
94A LYS* 3.1 43.3 + - - +
95A VAL* 3.2 28.2 + - - +
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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