Contacts of the helix formed by residues 69 - 84 (chain B) in PDB entry 1LUA
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 69 (chain B).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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11B THR* 4.4 6.2 + - - +
12B ASP* 4.8 3.4 + - - +
67B GLY 3.5 0.8 - - - -
68B GLY* 1.3 74.8 - - - +
70B MET* 1.3 63.8 + - - +
71B ALA* 2.9 23.7 + - - +
72B ALA* 3.0 23.5 + - + +
73B GLY* 3.0 18.5 + - - -
75B ARG* 4.8 4.4 + - - -
96B SER* 4.0 5.0 + - - -
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Residues in contact with MET 70 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
68B GLY 3.8 4.4 + - - -
69B ASP* 1.3 72.4 + - - +
71B ALA* 1.3 56.8 + - - +
73B GLY 3.2 0.5 + - - -
74B GLU* 2.9 58.8 + - + +
94B LEU* 3.5 32.1 - - + -
96B SER* 3.9 20.1 + - - +
97B ASN* 5.8 1.3 - - + +
99B SER* 4.2 20.9 - - - +
100B ASN* 5.3 4.3 - - - +
131B PRO* 3.7 35.7 - - + +
135B ARG* 4.2 14.6 - - + +
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Residues in contact with ALA 71 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
69B ASP* 2.9 10.6 + - - +
70B MET* 1.3 78.1 - - - +
72B ALA* 1.3 62.3 + - - +
74B GLU* 3.4 13.7 + - - +
75B ARG* 3.2 42.2 + - - +
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Residues in contact with ALA 72 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
11B THR* 4.1 20.6 - - + +
69B ASP* 3.0 29.9 + - + +
71B ALA* 1.3 76.5 - - - +
73B GLY* 1.3 63.8 + - - +
75B ARG* 3.3 27.3 + - - +
76B VAL* 3.1 27.4 + - + +
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Residues in contact with GLY 73 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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11B THR* 4.2 7.8 - - - +
65B VAL* 3.7 13.4 - - - +
69B ASP 3.0 10.5 + - - -
70B MET 3.2 1.1 + - - -
72B ALA* 1.3 79.1 - - - +
74B GLU* 1.3 55.9 + - - +
76B VAL 3.3 0.5 + - - -
77B PHE* 2.8 31.0 + - - +
94B LEU* 3.7 9.0 - - - +
96B SER* 3.4 22.0 - - - -
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Residues in contact with GLU 74 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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70B MET* 2.9 42.1 + - + +
71B ALA* 3.7 11.9 - - - +
73B GLY* 1.3 75.9 - - - +
75B ARG* 1.3 63.6 + - + +
77B PHE* 3.4 6.7 + - - +
78B GLU* 3.0 32.4 + - + +
94B LEU* 4.0 7.6 - - + -
135B ARG* 2.9 33.2 + - - +
167B ARG* 5.6 4.3 + - - +
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Residues in contact with ARG 75 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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39B PRO* 3.7 27.8 - - + +
69B ASP* 4.7 4.9 + - - -
71B ALA* 3.2 25.8 + - - +
72B ALA* 3.6 42.8 + - - +
73B GLY 3.3 0.2 - - - -
74B GLU* 1.3 77.1 - - + +
76B VAL* 1.3 62.5 - - - +
78B GLU* 3.4 6.9 + - - +
79B ALA* 3.2 21.0 + - - +
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Residues in contact with VAL 76 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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9B PHE* 4.9 1.8 - - + -
11B THR* 3.9 17.5 - - + -
37B VAL* 3.9 26.7 - - + +
38B THR* 3.8 23.6 - - - -
39B PRO* 4.0 6.1 - - + -
42B VAL* 4.1 14.1 - - + -
65B VAL* 4.1 23.8 - - + -
72B ALA* 3.1 16.9 + - + +
73B GLY 3.7 3.6 - - - +
75B ARG* 1.3 76.2 - - - +
77B PHE* 1.3 58.0 + - - +
79B ALA* 3.0 9.6 + - - +
80B VAL* 2.9 25.9 + - + +
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Residues in contact with PHE 77 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
65B VAL* 4.0 16.6 - - + +
73B GLY 2.8 21.0 + - - +
74B GLU* 3.7 4.3 - - - +
76B VAL* 1.3 72.2 - - - +
78B GLU* 1.3 65.9 + - - +
80B VAL* 3.2 9.5 + - + +
81B LYS* 3.1 48.6 + - + +
92B CYS* 3.6 35.9 - - + -
93B MET* 3.5 23.1 - - - -
94B LEU* 3.7 41.5 - - + -
274B VAL* 4.0 15.5 - - + -
275B PHE 4.4 3.8 - - - -
276B ASP* 4.2 17.7 - - + -
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Residues in contact with GLU 78 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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74B GLU* 3.0 22.8 + - + +
75B ARG* 3.8 7.0 - - - +
76B VAL 3.2 0.2 - - - -
77B PHE* 1.3 79.8 - - - +
79B ALA* 1.3 58.5 + - - +
81B LYS* 2.6 38.8 + - - +
82B LYS* 2.9 29.7 + - - +
167B ARG* 5.8 1.7 + - - -
276B ASP* 5.5 1.0 - - - +
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Residues in contact with ALA 79 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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39B PRO* 3.7 22.7 - - + +
42B VAL* 3.6 21.6 - - + +
43B GLY* 5.6 0.9 - - - -
75B ARG 3.2 13.1 + - - +
76B VAL 3.0 10.6 + - - +
78B GLU* 1.3 77.5 - - - +
80B VAL* 1.3 62.9 + - - +
82B LYS* 3.4 10.3 + - - +
83B ARG* 3.2 21.8 + - - +
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Residues in contact with VAL 80 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
9B PHE* 4.5 4.0 - - + -
42B VAL* 3.8 25.6 - - + -
46B VAL* 4.0 20.9 - - + -
63B ILE* 4.1 14.4 - - + -
65B VAL* 4.3 16.2 - - + -
76B VAL 2.9 20.2 + - - +
77B PHE* 3.4 10.8 - - + +
78B GLU 3.2 0.4 - - - -
79B ALA* 1.3 76.7 - - - +
81B LYS* 1.3 63.8 + - - +
83B ARG* 3.0 18.2 + - - +
84B PHE* 3.6 29.5 + - + -
92B CYS* 4.6 9.6 - - + -
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Residues in contact with LYS 81 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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77B PHE* 3.1 36.8 + - + +
78B GLU* 2.6 42.4 + - - +
80B VAL* 1.3 79.4 - - - +
82B LYS* 1.3 61.9 + - - +
84B PHE* 3.3 31.6 + - + +
89B ARG* 5.5 0.3 + - - -
92B CYS* 4.3 18.4 - - - -
167B ARG* 5.9 2.4 - - - +
274B VAL* 4.2 19.2 - - + +
276B ASP* 5.1 4.2 + - - -
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Residues in contact with LYS 82 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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78B GLU 2.9 18.6 + - - +
79B ALA* 3.7 10.3 - - - +
80B VAL 3.2 0.2 - - - -
81B LYS* 1.3 76.7 - - - +
83B ARG* 1.3 61.6 + - - +
84B PHE 3.5 6.8 + - - +
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Residues in contact with ARG 83 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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43B GLY* 3.3 34.5 + - - +
44B ALA* 4.2 3.8 - - - +
46B VAL* 3.9 20.0 - - + -
47B ASP* 2.9 42.4 + - - +
50B ILE* 4.3 7.6 - - + +
51B TYR* 5.5 1.4 + - - -
79B ALA 3.2 11.2 + - - +
80B VAL 3.0 12.3 + - - +
82B LYS* 1.3 74.0 - - - +
84B PHE* 1.3 69.7 + - - +
85B PHE* 3.6 4.9 + - - +
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Residues in contact with PHE 84 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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46B VAL* 3.8 22.2 - - + -
50B ILE* 4.1 9.6 - - + -
63B ILE* 4.6 0.4 - - + -
80B VAL* 3.9 19.1 - - + -
81B LYS* 3.7 30.5 - - + +
82B LYS 3.3 9.1 - - - +
83B ARG* 1.3 82.6 - - - +
85B PHE* 1.3 62.1 + - - +
88B PHE 3.5 8.7 - - - +
89B ARG* 3.5 45.7 + - + +
90B VAL* 3.3 44.0 - - + -
92B CYS* 4.3 15.0 - - - -
274B VAL* 5.9 3.1 - - + -
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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