Contacts of the helix formed by residues 44 - 49 (chain B) in PDB entry 1LVB
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 ASN 44 (chain B).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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32B LEU* 3.8 11.0 - - + +
43B THR* 1.3 84.9 + - - +
45B LYS* 1.3 65.0 + - - +
46B HIS* 3.4 29.3 - - + +
47B LEU* 3.1 21.0 + - - +
81B ASP* 2.9 26.0 + - - +
83B ILE* 3.5 7.7 - - - +
151B ALA* 3.5 3.6 - - - +
152B GLY* 3.0 29.0 + - - -
166B ILE* 3.9 4.8 - - - +
167B HIS 3.0 23.8 + - - -
168B SER* 3.2 5.3 + - - +
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Residues in contact with LYS 45 (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 THR 3.8 0.2 + - - -
44B ASN* 1.3 67.7 - - - +
46B HIS* 1.3 58.0 + - - +
47B LEU 2.8 11.5 + - - -
48B PHE* 3.0 14.2 + - - +
76B LEU* 4.3 18.8 - - + +
77B ILE 2.8 30.8 + - - +
78B ASP* 4.7 0.6 - - - +
79B GLY* 4.2 5.7 - - - +
80B ARG 3.0 20.3 + - - +
81B ASP* 2.9 16.8 + - - +
82B MSE 3.6 22.1 - - - +
83B ILE* 4.0 10.1 - - - -
202B TRP* 3.2 46.2 - - + -
211B TRP* 3.6 24.3 - - + -
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Residues in contact with HIS 46 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
30B THR* 4.0 6.4 - - + +
32B LEU* 3.5 6.9 - - + +
44B ASN* 3.4 21.2 - - + +
45B LYS* 1.3 72.2 - - - +
47B LEU* 1.3 61.2 + - - +
48B PHE 3.0 2.6 + - - +
49B ARG* 3.3 16.2 + - - +
81B ASP* 2.9 37.7 + - - +
151B ALA* 4.2 7.5 - - + +
168B SER 4.2 0.9 - - - -
204B LEU* 4.2 13.2 - - + -
211B TRP* 4.6 1.3 - - + -
218B MSE 4.3 11.8 - - - +
306D PHE* 3.3 53.7 - + + +
308D SER* 3.3 34.1 - - - -
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Residues in contact with LEU 47 (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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21B LEU* 4.2 12.1 - - + -
23B ASN* 2.9 37.1 + - + +
30B THR* 3.9 22.5 + - + +
32B LEU* 3.6 32.1 - - + -
43B THR* 4.3 2.0 - - + -
44B ASN 3.1 17.9 + - - +
45B LYS 2.8 1.4 + - - +
46B HIS* 1.3 80.3 - - - +
48B PHE* 1.3 86.8 + - + +
49B ARG 3.3 3.2 + - - -
50B ARG 4.6 0.3 + - - -
55B LEU* 4.1 18.8 - - + -
85B ILE* 4.1 12.6 - - + -
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Residues in contact with PHE 48 (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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23B ASN* 3.8 12.8 - - - -
45B LYS 3.0 9.4 + - - -
46B HIS 3.0 0.8 - - - -
47B LEU* 1.3 91.4 - - + +
49B ARG* 1.3 60.8 + - - +
50B ARG 2.8 20.7 + - - +
51B ASN* 3.9 22.4 - - - -
55B LEU* 5.1 2.0 - - + -
69B THR* 4.6 7.4 - - + -
72B LEU* 4.2 20.2 - - + -
74B GLN* 3.7 19.7 - - + -
83B ILE* 3.7 27.8 - - + -
85B ILE* 3.8 32.8 - - + -
202B TRP* 3.8 22.6 - - + +
203B ARG* 3.2 2.9 - - - -
204B LEU* 2.8 21.7 + - - -
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Residues in contact with ARG 49 (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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30B THR* 4.3 13.9 - - + +
46B HIS 3.3 14.1 + - - +
47B LEU 3.3 3.0 + - - -
48B PHE* 1.3 76.6 - - - +
50B ARG* 1.3 87.3 + - + +
203B ARG* 4.7 0.2 - - - +
204B LEU* 3.0 31.2 + - + +
205B ASN* 3.8 10.1 - - - +
206B ALA* 3.1 41.0 + - - +
207B ASP* 2.9 30.3 + - - +
218B MSE 3.5 36.0 - - + +
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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