Contacts of the helix formed by residues 80 - 90 (chain F) in PDB entry 1LNU
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 GLY 80 (chain F).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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63F TYR 3.4 15.7 - - - -
64F VAL* 3.5 13.0 - - - -
75F ALA* 3.7 7.6 - - - -
77F THR 2.6 21.1 + - - -
78F GLU 2.7 1.0 + - - -
79F LEU* 1.3 72.2 - - - +
81F ARG* 1.3 64.9 + - - -
82F PRO* 3.2 3.6 - - - -
83F ASP* 2.8 19.6 + - - +
84F ALA 3.0 9.3 + - - -
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Residues in contact with ARG 81 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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75F ALA* 3.3 26.7 + - + +
78F GLU* 3.0 47.2 + - - +
80F GLY* 1.3 72.6 - - - +
82F PRO* 1.4 74.0 - - + +
84F ALA* 4.4 2.5 - - - -
85F GLU* 3.1 40.6 + - + +
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Residues in contact with PRO 82 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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77E ARG* 3.6 15.9 - - + +
12F VAL* 3.4 23.0 - - + +
14F GLY* 6.2 0.9 - - - -
78F GLU 3.6 8.5 - - - +
79F LEU* 3.9 5.8 - - - -
80F GLY 3.2 5.4 - - - -
81F ARG* 1.4 97.0 - - + +
83F ASP* 1.3 69.5 + - - +
85F GLU* 3.5 3.0 + - + +
86F TYR* 3.3 21.5 + - - +
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Residues in contact with ASP 83 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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77E ARG* 2.5 38.7 + - - -
11F ALA* 3.7 9.8 - - - +
12F VAL* 3.9 8.5 - - - +
63F TYR* 3.1 32.9 + - - -
64F VAL* 4.0 3.8 - - + -
80F GLY 2.8 10.2 + - - +
82F PRO* 1.3 69.8 - - - +
84F ALA* 1.3 63.3 + - - +
87F TRP* 3.0 61.7 + - + -
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Residues in contact with ALA 84 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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64F VAL* 4.5 4.4 - - + +
73F HIS* 4.0 22.1 - - + +
74F ARG 4.2 1.3 - - - -
75F ALA* 3.7 32.5 - - + +
80F GLY 3.0 10.6 + - - +
81F ARG* 3.9 6.5 - - - +
83F ASP* 1.3 76.6 - - - +
85F GLU* 1.3 62.9 + - + +
88F ASN* 3.1 36.1 + - - +
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Residues in contact with GLU 85 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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81F ARG* 3.1 32.0 + - + +
82F PRO* 3.9 2.7 - - + +
84F ALA* 1.3 81.5 - - + +
86F TYR* 1.3 66.9 + - - +
88F ASN* 3.0 13.3 + - - +
89F SER* 3.0 23.8 + - - -
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Residues in contact with TYR 86 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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10F LYS 5.2 1.8 - - - -
12F VAL* 3.1 37.5 - - + -
82F PRO 3.3 7.1 + - - +
83F ASP 4.2 1.1 - - - +
85F GLU* 1.3 76.8 - - - +
87F TRP* 1.3 71.6 + + - +
89F SER* 2.5 35.0 + - - -
90F GLN* 3.3 23.5 + - + +
93F ILE* 4.2 16.6 - - + -
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Residues in contact with TRP 87 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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70E ASN* 4.5 0.7 - - - -
9F ASN* 3.2 44.8 - - + +
10F LYS 2.6 33.7 + - - +
11F ALA* 3.9 2.7 - - - -
12F VAL 5.0 0.4 - - - +
56F TYR* 4.1 25.8 - + - -
63F TYR* 4.4 5.6 - - - -
64F VAL* 3.5 29.4 - - + -
73F HIS* 3.6 25.4 - + + +
83F ASP* 3.0 46.2 + - + +
86F TYR* 1.3 84.9 - + - +
88F ASN* 1.3 57.1 + - - +
89F SER 3.5 0.3 + - - -
90F GLN 3.9 2.7 - - - +
93F ILE* 3.8 27.6 - - + +
94F LEU* 3.0 31.0 + - - +
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Residues in contact with ASN 88 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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72F GLU* 3.0 25.9 + - - +
73F HIS* 2.7 40.1 + - - -
84F ALA* 3.1 20.4 + - - +
85F GLU* 3.0 15.8 + - - +
87F TRP* 1.3 76.4 - - - +
89F SER* 1.3 59.0 + - - +
94F LEU* 2.5 47.7 - - - +
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Residues in contact with SER 89 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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85F GLU 3.0 9.0 + - - -
86F TYR* 2.5 29.7 + - - -
88F ASN* 1.3 81.0 - - - +
90F GLN* 1.3 70.9 + - - +
91F PRO* 3.2 14.0 - - - +
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Residues in contact with GLN 90 (chain F).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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86F TYR* 3.3 22.7 + - + +
87F TRP 4.0 0.4 + - - -
88F ASN 3.7 0.4 - - - -
89F SER* 1.3 90.3 + - - +
91F PRO* 1.3 72.9 - - - +
92F GLU* 3.4 23.6 - - - +
93F ILE* 2.7 35.6 + - + +
94F LEU* 2.7 26.7 + - - +
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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