Contacts of the helix formed by residues 76 - 92 (chain B) in PDB entry 4LVB
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 THR 76 (chain B).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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8B GLU* 6.0 0.2 - - - +
73B LYS* 4.4 20.9 - - + +
75B VAL* 1.3 79.7 - - - +
77B LYS* 1.3 64.2 + - - +
78B GLU* 3.4 15.8 + - - +
79B LYS* 3.0 40.4 + - + +
80B ILE* 3.1 24.1 + - - +
105B LEU* 3.9 11.4 - - - -
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Residues in contact with LYS 77 (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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76B THR* 1.3 72.8 - - - +
78B GLU* 1.3 76.5 + - - +
80B ILE* 3.3 7.2 + - - +
81B GLN* 3.0 27.9 + - - +
102B ASN* 5.7 2.5 - - - +
105B LEU* 3.6 23.4 - - + +
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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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76B THR* 3.6 17.8 + - - +
77B LYS* 1.3 96.1 + - - +
79B LYS* 1.3 60.5 + - + +
81B GLN* 3.3 5.9 + - - +
82B GLU* 2.8 31.8 + - - +
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Residues in contact with LYS 79 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
8B GLU* 3.3 30.4 + - - +
9B PHE* 3.0 27.8 + - - +
10B ASN* 3.2 40.0 + - + +
11B ILE 5.3 0.6 - - - +
12B LEU* 3.9 8.3 - - + +
73B LYS 4.9 3.2 + - - -
74B VAL* 3.7 30.9 + - - +
76B THR* 3.0 35.9 + - + +
78B GLU* 1.3 75.7 - - + +
80B ILE* 1.3 62.7 + - - +
82B GLU* 4.2 5.4 - - - +
83B ALA* 3.1 22.0 + - - +
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Residues in contact with ILE 80 (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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12B LEU* 3.7 15.3 - - + -
75B VAL* 3.8 25.4 - - + -
76B THR 3.1 12.5 + - - +
77B LYS* 3.5 8.7 - - - +
79B LYS* 1.3 77.8 - - - +
81B GLN* 1.3 62.5 + - - +
83B ALA 3.3 0.2 + - - -
84B LYS* 3.1 21.7 + - - +
96B PHE* 3.7 12.4 - - + -
98B GLU* 3.9 33.9 - - + +
101B TRP* 3.8 13.5 - - + +
102B ASN* 3.5 32.1 - - - +
105B LEU* 4.0 8.5 - - + -
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Residues in contact with GLN 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 LYS 3.0 15.8 + - - +
78B GLU* 3.3 6.7 + - - +
80B ILE* 1.3 78.2 - - - +
82B GLU* 1.3 62.5 + - - +
84B LYS* 3.3 25.9 + - - +
85B ASP* 3.1 54.0 + - - +
98B GLU* 4.6 5.9 - - - +
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Residues in contact with GLU 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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8B GLU 5.2 5.4 - - - +
10B ASN* 3.1 25.6 + - - +
13B LEU* 3.7 17.2 - - + +
78B GLU 2.8 17.5 + - - +
79B LYS* 3.6 11.9 - - - +
81B GLN* 1.3 78.3 - - - +
83B ALA* 1.3 62.2 + - - +
85B ASP* 3.4 6.8 + - - +
86B VAL* 3.1 32.7 + - + +
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Residues in contact with ALA 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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10B ASN* 4.4 0.2 - - - +
12B LEU* 3.8 24.2 - - + -
13B LEU* 3.9 23.8 - - + -
79B LYS 3.1 16.5 + - - +
80B ILE 3.9 2.9 - - - +
82B GLU* 1.3 73.6 - - - +
84B LYS* 1.3 65.2 + - - +
87B TYR* 2.9 42.5 + - + -
96B PHE* 4.1 9.2 - - + -
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Residues in contact with LYS 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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80B ILE 3.1 12.6 + - - +
81B GLN* 3.4 29.4 + - - +
83B ALA* 1.3 77.1 - - - +
85B ASP* 1.3 65.5 + - - +
87B TYR* 4.0 0.9 - - - +
88B LYS* 3.0 28.6 + - + +
94B ASP* 4.2 24.9 - - - +
96B PHE* 3.9 23.6 - - + +
98B GLU* 2.9 39.5 + - - +
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Residues in contact with ASP 85 (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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81B GLN* 3.1 42.3 + - - +
82B GLU* 3.8 6.1 - - - +
84B LYS* 1.3 79.7 - - - +
86B VAL* 1.3 64.1 + - + +
88B LYS* 3.6 6.6 + - - +
89B GLU* 3.6 23.2 + - - +
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Residues in contact with VAL 86 (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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221A VAL* 4.0 17.7 - - + -
224A LEU* 4.2 16.2 - - + -
228A LYS* 6.2 1.6 - - - +
237A VAL* 4.7 6.8 - - + +
13B LEU* 3.9 30.1 - - + -
82B GLU* 3.1 23.7 + - + +
83B ALA 3.9 3.4 - - - +
84B LYS 3.3 0.2 - - - -
85B ASP* 1.3 77.8 - - + +
87B TYR* 1.3 60.8 + - + +
89B GLU* 3.3 7.2 + - - +
90B HIS* 3.0 23.8 + - + +
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Residues in contact with TYR 87 (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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221A VAL* 4.0 31.2 - - + +
12B LEU 2.7 28.2 + - - -
13B LEU* 3.5 15.5 - - + -
15B THR* 4.0 6.1 - - - +
17B SER* 5.0 1.8 - - - -
20B VAL* 3.4 28.1 - - + +
83B ALA* 2.9 34.1 + - + +
84B LYS 4.2 1.3 - - - +
86B VAL* 1.3 76.0 - - + +
88B LYS* 1.3 65.2 + - - +
90B HIS* 4.0 11.4 - + + -
91B PHE* 2.9 52.2 + + + -
93B ASP 3.6 4.4 - - - +
95B VAL* 5.4 0.4 - - + -
96B PHE* 3.7 34.8 - + + +
147B TRP* 4.6 0.4 - + - -
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Residues in contact with LYS 88 (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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84B LYS* 3.0 21.9 + - + +
85B ASP* 3.8 9.2 - - - +
86B VAL 3.2 0.2 - - - -
87B TYR* 1.3 76.8 - - - +
89B GLU* 1.3 69.5 + - - +
92B GLN* 3.1 8.4 + - - -
93B ASP* 3.0 39.3 + - - +
94B ASP* 3.4 39.6 + - - +
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Residues in contact with GLU 89 (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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236A PRO* 3.4 32.0 - - + +
237A VAL* 3.8 23.1 - - + -
240A TYR* 3.5 10.7 - - - -
85B ASP 3.6 12.5 + - - +
86B VAL 3.3 6.5 + - - +
88B LYS* 1.3 90.2 - - - +
90B HIS* 1.3 64.8 + - - +
92B GLN* 2.8 34.3 + - - +
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Residues in contact with HIS 90 (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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218A THR* 3.2 25.2 + - + -
221A VAL* 5.2 3.1 - - + +
224A LEU* 3.6 24.5 - - + +
237A VAL* 4.3 2.0 - - - +
239A GLY 2.9 25.7 + - - -
240A TYR* 3.4 29.1 - - - +
241A SER* 3.2 30.5 + - - +
17B SER* 2.7 37.3 + - - -
86B VAL 3.0 17.8 + - - +
87B TYR* 3.2 15.7 + + + +
89B GLU* 1.3 77.4 - - - +
91B PHE* 1.3 68.9 + + - +
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Residues in contact with PHE 91 (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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241A SER* 3.6 41.2 - - - +
242A VAL* 4.3 14.4 - - - -
243A PRO* 4.5 7.1 - - + +
272A VAL* 6.1 1.0 - - - +
17B SER* 3.1 35.9 - - - -
18B TYR* 4.8 0.9 - - - -
20B VAL* 4.0 14.6 - - + -
21B THR* 4.4 11.7 - - + -
87B TYR* 2.9 49.4 + + + +
90B HIS* 1.3 79.8 - + - +
92B GLN* 1.3 70.5 + - - +
93B ASP* 3.4 16.9 + - + +
95B VAL* 3.6 20.6 - - + -
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Residues in contact with GLN 92 (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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237A VAL* 5.3 0.2 - - - +
240A TYR* 4.1 21.4 + - + -
88B LYS* 3.1 13.3 + - - -
89B GLU* 2.8 43.9 + - - +
91B PHE* 1.3 80.8 - - - +
93B ASP* 1.3 59.3 + - - +
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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