Contacts of the helix formed by residues 90 - 98 (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 GLN 90 (chain F).
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Specific contacts
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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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Residues in contact with PRO 91 (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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89F SER 3.2 11.4 - - - +
90F GLN* 1.3 90.9 - - - +
92F GLU* 1.3 66.8 + - + +
94F LEU* 5.0 2.7 - - + -
95F GLU* 2.9 46.2 + - + +
96F ARG 4.0 0.2 + - - -
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Residues in contact with GLU 92 (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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90F GLN* 3.4 23.6 - - + +
91F PRO* 1.3 84.0 - - + +
93F ILE* 1.3 58.9 + - + +
96F ARG* 3.5 29.1 + - - +
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Residues in contact with ILE 93 (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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9F ASN* 3.3 38.7 - - + +
10F LYS 6.0 1.1 - - - +
73F HIS* 4.7 0.4 - - - +
86F TYR* 4.2 17.9 - - + -
87F TRP* 3.8 35.2 - - + +
90F GLN* 2.7 26.3 + - + +
92F GLU* 1.3 82.5 - - + +
94F LEU* 1.3 64.7 + - - +
95F GLU 3.3 1.6 - - - -
96F ARG* 3.4 14.3 + - - +
97F THR* 3.3 25.6 + - - -
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Residues in contact with LEU 94 (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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66F TYR* 5.3 1.2 - - + -
71F GLY 4.5 0.2 - - - +
72F GLU* 4.0 11.9 - - + -
73F HIS* 3.1 24.2 - - + +
87F TRP 3.0 11.0 + - - +
88F ASN* 2.5 50.0 - - - +
90F GLN 2.7 15.8 + - - +
91F PRO* 5.0 1.6 - - + -
93F ILE* 1.3 74.7 - - - +
95F GLU* 1.3 62.2 + - + +
97F THR* 4.0 1.9 - - - +
98F ARG* 2.9 57.2 + - - +
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Residues in contact with GLU 95 (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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91F PRO* 2.9 34.7 + - + +
94F LEU* 1.3 81.8 - - + +
96F ARG* 1.3 63.3 + - - +
98F ARG* 3.4 44.5 + - - +
99F ALA* 3.3 21.7 + - - +
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Residues in contact with ARG 96 (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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7F LYS* 4.0 48.2 - - + +
8F ALA 5.1 4.4 + - - -
9F ASN* 3.6 23.0 + - - +
91F PRO 4.0 1.4 + - - -
92F GLU 3.5 24.0 + - - +
93F ILE* 3.4 13.1 + - - +
94F LEU 3.3 0.2 - - - -
95F GLU* 1.3 78.4 - - - +
97F THR* 1.3 65.5 + - - +
99F ALA* 3.1 19.3 + - + +
100F GLU* 3.4 16.1 + - + +
103F THR* 5.0 0.5 + - - -
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Residues in contact with THR 97 (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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7F LYS 5.3 2.6 + - - -
9F ASN* 3.9 20.3 + - - -
52F TYR* 4.1 7.3 - - + -
54F THR* 4.6 4.9 - - + +
56F TYR* 5.3 1.4 + - - +
66F TYR* 3.8 27.9 - - + -
73F HIS* 3.7 23.0 - - + -
93F ILE 3.3 15.1 + - - -
94F LEU 4.0 4.0 - - - +
96F ARG* 1.3 76.6 + - - +
98F ARG* 1.3 58.3 + - - +
99F ALA 2.8 10.7 + - - -
100F GLU* 2.8 40.9 + - - +
101F LEU 4.4 0.2 + - - -
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Residues in contact with ARG 98 (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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66F TYR* 3.4 26.4 + - - -
71F GLY* 2.9 33.2 + - - -
94F LEU* 2.9 45.7 + - - +
95F GLU* 3.4 32.4 + - - +
97F THR* 1.3 79.4 - - - +
99F ALA* 1.3 58.1 + - - +
100F GLU 3.5 0.2 - - - -
101F LEU* 4.3 9.2 + - - +
102F ASP* 4.5 5.4 - - - +
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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