Contacts of the helix formed by residues 70 - 85 (chain A) in PDB entry 1LWZ
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 70 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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68A HIS 4.1 3.3 + - - +
69A LYS* 1.4 68.8 - - - +
71A ILE* 1.3 68.3 + - + +
72A MET 3.1 3.4 - - - -
73A GLU* 2.8 21.5 + - + +
74A ASN* 2.7 27.6 + - - +
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Residues in contact with ILE 71 (chain A).
Click here for Legend to table.
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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69A LYS* 3.7 28.7 - - + +
70A GLN* 1.3 79.2 - - + +
72A MET* 1.3 67.9 + - - +
74A ASN* 3.4 10.9 + - - +
75A ALA* 3.2 21.1 + - - +
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Residues in contact with MET 72 (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 LEU* 5.2 15.5 - - + -
57A ARG* 5.4 19.3 - - + +
69A LYS* 3.1 34.5 - - + +
70A GLN 3.1 0.8 - - - -
71A ILE* 1.3 84.9 - - + +
73A GLU* 1.3 63.2 + - - +
75A ALA* 3.1 11.7 + - - +
76A GLU* 2.8 34.8 + - + +
79A ASN* 6.4 0.4 - - - +
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Residues in contact with GLU 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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69A LYS 4.9 1.7 + - - +
70A GLN* 2.8 19.6 + - + +
72A MET* 1.3 74.3 - - - +
74A ASN* 1.3 64.8 + - - +
76A GLU* 3.1 28.6 + - - +
77A ILE* 2.9 43.7 + - + +
122A LEU* 2.9 50.3 - - + +
123A LEU* 5.2 0.7 - - - +
126A PHE* 5.6 0.2 - - - +
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Residues in contact with ASN 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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70A GLN* 2.7 43.4 + - - +
71A ILE* 3.6 10.1 - - - +
73A GLU* 1.3 79.3 - - - +
75A ALA* 1.3 61.9 + - - +
77A ILE* 3.1 14.3 + - - +
78A ASN* 3.1 29.4 + - - +
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Residues in contact with ALA 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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71A ILE 3.2 9.8 + - - +
72A MET* 3.1 15.7 + - - +
74A ASN* 1.3 77.8 - - - +
76A GLU* 1.3 63.5 + - - +
78A ASN* 3.0 14.3 + - - +
79A ASN* 2.9 33.1 + - - +
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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
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56A LEU* 3.6 39.6 - - + +
72A MET* 2.8 25.3 + - + +
73A GLU* 3.1 33.6 - - - +
75A ALA* 1.3 77.9 - - - +
77A ILE* 1.3 61.1 + - + +
79A ASN* 3.2 12.6 + - - +
80A ILE* 3.1 31.9 + - + +
119A ILE* 3.9 6.3 - - - +
122A LEU* 5.0 0.3 - - - +
123A LEU* 3.3 27.9 - - - +
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Residues in contact with ILE 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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73A GLU* 2.9 44.1 + - + +
74A ASN* 3.1 13.0 + - - +
76A GLU* 1.3 76.6 - - + +
78A ASN* 1.3 66.6 + - - +
80A ILE* 3.1 13.2 + - + +
81A ILE* 3.0 24.4 + - + +
126A PHE* 3.2 58.1 - - + -
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Residues in contact with ASN 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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74A ASN* 3.1 18.7 + - - +
75A ALA* 3.0 15.2 + - - +
77A ILE* 1.3 79.7 - - - +
79A ASN* 1.3 63.1 + - - +
81A ILE* 2.7 39.5 - - + +
82A LYS* 2.8 10.2 + - - +
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Residues in contact with ASN 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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8A ILE* 3.0 29.4 - - - +
54A PHE* 4.0 24.7 - - + -
56A LEU* 5.3 0.8 - - - +
72A MET* 6.4 0.4 - - - +
75A ALA* 2.9 30.1 + - - +
76A GLU* 3.6 10.6 - - - +
77A ILE 3.2 0.2 - - - -
78A ASN* 1.3 75.1 - - - +
80A ILE* 1.3 58.7 + - + +
82A LYS* 3.8 3.8 - - - -
83A ILE* 2.8 50.0 + - + +
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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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27A LEU* 5.2 4.0 - - + +
29A LEU* 4.0 26.2 - - + -
54A PHE* 6.5 0.2 - - + -
56A LEU* 5.5 1.3 - - + -
76A GLU* 3.3 25.8 - - + +
77A ILE* 3.1 16.2 + - + +
79A ASN* 1.3 78.4 - - + +
81A ILE* 1.3 59.6 + - + +
83A ILE* 3.8 5.4 - - - +
84A VAL* 2.7 42.8 + - + +
86A LEU* 6.0 1.1 - - + -
106A ILE* 5.1 12.6 - - + -
123A LEU* 4.0 28.0 - - + -
126A PHE* 4.5 22.0 - - + -
127A ILE* 6.4 0.7 - - + -
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Residues in contact with ILE 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 ILE* 3.0 15.6 + - + +
78A ASN* 2.7 41.3 - - + +
80A ILE* 1.3 76.1 - - - +
82A LYS* 1.3 60.6 + - + +
84A VAL* 2.7 8.7 - - - +
85A GLY* 2.7 31.9 + - - -
86A LEU* 3.0 29.7 + - + +
87A GLN 5.8 3.8 - - - +
126A PHE* 3.5 29.2 - - + -
130A ASN* 5.6 1.1 - - - +
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Residues in contact with LYS 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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4A ARG 5.5 1.6 - - - -
5A ILE* 3.8 34.7 - - + +
6A LYS* 4.8 2.5 - - - +
7A GLY* 3.9 24.1 - - - +
8A ILE* 5.8 2.2 - - + -
78A ASN 2.8 16.6 + - - +
79A ASN* 3.9 4.7 - - - +
81A ILE* 1.3 81.4 - - + +
83A ILE* 1.3 66.1 + - + +
85A GLY* 3.3 9.0 + - - -
86A LEU 5.4 0.4 - - - -
102A ARG* 3.8 6.1 + - - -
518A GLU* 6.0 0.9 - - - -
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Residues in contact with ILE 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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5A ILE* 3.0 22.0 - - + -
8A ILE* 4.1 14.1 - - + -
11A LEU* 3.9 15.5 - - + -
27A LEU* 3.6 19.5 - - + -
29A LEU* 5.6 0.4 - - + -
54A PHE* 4.1 33.2 - - + -
79A ASN* 2.8 37.2 + - + +
80A ILE* 3.9 2.7 - - - +
82A LYS* 1.3 76.4 - - + +
84A VAL* 1.3 59.2 + - - +
102A ARG* 2.7 27.9 + - - +
103A TYR* 3.4 27.3 - - + -
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Residues in contact with VAL 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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27A LEU* 5.5 0.9 - - + -
80A ILE* 2.7 35.2 + - + +
81A ILE* 2.7 24.9 - - - +
83A ILE* 1.3 76.6 - - - +
85A GLY* 1.3 57.9 + - - +
86A LEU* 2.9 38.6 - - + +
101A LEU* 3.2 7.8 - - + +
102A ARG 2.7 22.6 + - - -
103A TYR* 3.3 30.0 + - + +
106A ILE* 4.8 13.7 - - + -
139A PHE* 5.1 7.0 - - + -
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Residues in contact with GLY 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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81A ILE 2.7 11.2 + - - -
82A LYS* 3.3 9.7 + - - -
84A VAL* 1.3 73.1 - - - +
86A LEU* 1.3 62.4 + - - +
87A GLN* 3.6 10.8 + - - +
100A THR* 4.6 4.4 + - - +
101A LEU* 2.7 26.1 - - - +
102A ARG* 4.2 13.7 - - - -
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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