Contacts of the helix formed by residues 89 - 96 (chain F) in PDB entry 4LQL
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 TRP 89 (chain F).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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12F VAL* 3.6 31.9 - - + -
13F VAL 4.4 8.7 - - - -
14F GLY* 4.9 1.6 - - - -
54F ALA 5.4 2.0 + - - -
60F ILE* 3.4 43.9 - - + +
78F THR* 3.3 26.2 - - - -
80F MET* 4.2 18.4 - - + +
84F SER* 2.4 33.4 + - - -
85F PRO 3.8 3.4 - - - -
86F ALA* 2.8 26.7 + - + +
88F ASN* 1.3 76.3 - - - +
90F ILE* 1.3 58.4 + - - +
91F ARG 3.6 0.9 - - - -
92F GLY 3.7 3.1 - - - +
93F THR* 2.8 48.2 + - - +
100F LEU* 6.0 2.7 - - + -
133F TYR* 4.7 14.1 - + + -
136F ILE* 4.0 14.4 - - + -
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Residues in contact with ILE 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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196A VAL* 4.3 17.9 - - + -
199A GLN* 3.3 56.1 - - + +
200A ILE* 3.7 28.0 - - + -
86F ALA 3.1 16.0 + - - +
87F LYS* 3.6 15.9 - - + +
88F ASN 3.3 0.4 - - - -
89F TRP* 1.3 77.8 - - - +
91F ARG* 1.3 55.8 + - + +
93F THR* 3.8 1.8 - - - -
94F GLU* 2.7 42.8 + - + +
136F ILE* 3.6 17.2 - - + +
140F LEU* 4.9 2.4 - - + +
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Residues in contact with ARG 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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174A PHE* 4.5 29.2 - - + +
199A GLN* 4.4 18.6 - - + +
200A ILE 5.7 2.0 - - - +
203A GLY* 5.5 2.0 - - - +
61F THR* 4.2 18.4 - - + +
88F ASN 5.1 2.0 + - - -
90F ILE* 1.3 76.8 - - + +
92F GLY* 1.3 69.1 + - - +
94F GLU* 3.8 10.1 - - + -
95F LEU* 3.1 26.3 + - + +
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Residues in contact with GLY 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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60F ILE* 4.1 12.8 - - - -
61F THR* 4.3 9.0 + - - +
64F MET* 3.7 27.4 - - - +
88F ASN 4.9 1.6 + - - -
89F TRP* 3.2 8.8 + - - +
90F ILE 3.2 0.8 - - - -
91F ARG* 1.3 83.0 - - - +
93F THR* 1.3 52.5 + - - +
95F LEU* 2.7 3.5 + - - +
96F LEU* 2.6 31.5 + - - +
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Residues in contact with THR 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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64F MET* 4.3 2.4 - - - +
89F TRP* 2.8 31.1 + - - -
90F ILE* 3.9 1.6 - - - -
92F GLY* 1.3 68.8 - - - -
94F GLU* 1.3 61.7 + - - +
96F LEU* 3.2 27.0 + - - +
100F LEU* 3.9 19.9 - - - +
133F TYR* 6.1 0.9 - - - -
136F ILE* 4.6 21.7 - - - +
137F ASN* 5.3 2.3 - - - +
140F LEU* 5.3 5.8 - - - +
142F VAL* 4.7 18.8 - - - +
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Residues in contact with GLU 94 (chain F).
Click here for Legend to table.
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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200A ILE* 3.8 33.0 - - + +
90F ILE* 2.7 38.1 + - + +
91F ARG* 3.8 11.2 - - + -
93F THR* 1.3 72.3 - - - +
95F LEU* 1.3 60.4 + - + +
96F LEU 4.9 1.6 - - - +
140F LEU* 3.9 16.8 - - + +
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Residues in contact with LEU 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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97A GLN* 4.7 22.6 - - + +
61F THR* 5.2 8.3 - - + -
64F MET* 5.1 5.6 - - + -
65F LYS* 5.0 16.8 - - + +
68F ASN* 3.5 18.4 + - - +
91F ARG* 3.1 23.4 + - + +
92F GLY* 2.7 10.2 + - - +
94F GLU* 1.3 73.8 - - + +
96F LEU* 1.3 64.4 + - - +
97F GLN* 3.2 8.1 + - - +
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Residues in contact with LEU 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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64F MET* 4.0 24.7 - - + +
67F ALA* 5.5 2.2 - - + -
68F ASN* 4.5 3.6 - - - +
76F VAL* 4.3 15.3 - - + -
92F GLY 2.6 17.0 + - - +
93F THR* 3.2 23.8 + - - +
94F GLU 4.9 1.2 - - - +
95F LEU* 1.3 68.6 - - - +
97F GLN* 1.3 62.0 + - - +
98F LYS* 3.1 38.2 + - + +
100F LEU* 3.6 42.4 - - + -
142F VAL* 5.0 6.5 - - + +
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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