Contacts of the helix formed by residues 163 - 171 (chain E) in PDB entry 1LWU
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 ALA 163 (chain E).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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105D LEU* 4.1 19.3 - - - +
109D GLU* 4.9 0.3 - - - +
164E GLN* 1.3 68.5 + - - +
165E LYS* 3.7 3.1 - - + +
166E GLU* 2.8 47.4 + - + +
167E ILE* 3.6 13.0 + - - +
83I LYS* 4.4 14.8 - - + +
86I GLN* 5.5 8.3 - - + +
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Residues in contact with GLN 164 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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101D TYR* 4.8 9.3 + - - +
105D LEU* 4.4 9.4 - - + +
163E ALA* 1.3 75.3 - - - +
165E LYS* 1.3 57.3 + - - +
166E GLU 3.1 1.6 - - - -
167E ILE* 2.7 30.7 + - - +
168E GLU* 2.9 24.9 + - - +
84F THR* 4.3 11.1 - - - +
85F VAL* 3.2 31.2 - - + +
88F ILE* 4.2 15.7 - - + -
83I LYS* 3.4 43.0 - - + +
84I THR* 3.6 22.0 + - - -
85I VAL 4.2 2.6 + - - -
86I GLN* 6.0 0.2 - - - +
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Residues in contact with LYS 165 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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163E ALA* 4.7 1.8 - - + +
164E GLN* 1.3 75.9 - - - +
166E GLU* 1.3 53.4 + - - +
168E GLU* 3.4 26.4 - - - +
169E ASN* 2.5 58.0 + - - +
83I LYS* 3.8 29.9 - - + +
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Residues in contact with GLU 166 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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109D GLU* 3.3 25.8 - - - +
163E ALA* 2.8 38.1 + - - +
164E GLN 3.1 0.2 - - - -
165E LYS* 1.3 79.5 - - - +
167E ILE* 1.3 59.9 + - - +
169E ASN* 3.3 13.6 + - - +
170E ARG* 3.4 25.0 + - + +
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Residues in contact with ILE 167 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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105D LEU* 3.5 44.6 - - + +
108D LEU* 3.5 25.1 - - + -
109D GLU* 4.0 21.8 - - + +
112D ILE* 4.2 11.4 - - + -
163E ALA 3.8 8.5 - - - +
164E GLN* 2.7 10.3 + - + +
166E GLU* 1.3 74.6 - - - +
168E GLU* 1.3 54.3 + - - +
169E ASN 2.7 15.2 + - - -
170E ARG* 3.0 6.3 + - - -
171E TYR* 2.9 23.4 + - - +
88F ILE* 3.3 34.3 - - + -
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Residues in contact with GLU 168 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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164E GLN* 2.9 28.6 + - - +
165E LYS* 3.0 36.3 + - + +
167E ILE* 1.3 76.5 - - - +
169E ASN* 1.3 59.0 + - - +
171E TYR* 4.3 10.4 - - + -
172E LYS* 3.1 28.0 + - - +
84F THR* 3.1 22.3 - - - +
88F ILE* 3.4 23.3 - - + +
83I LYS* 4.2 4.2 + - - -
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Residues in contact with ASN 169 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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165E LYS* 2.5 46.1 + - - +
166E GLU* 3.3 12.7 - - - +
167E ILE 2.7 1.2 + - - -
168E GLU* 1.3 78.2 - - - +
170E ARG* 1.3 69.1 + - + +
172E LYS* 2.8 22.2 + - - +
173E GLU* 3.2 15.4 + - - +
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Residues in contact with ARG 170 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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109D GLU* 5.5 15.6 - - + +
112D ILE* 4.0 18.6 - - + -
113D ILE* 3.1 37.9 - - - +
116D GLN* 3.3 31.1 + - - +
190D GLU* 2.7 58.1 + - - +
166E GLU* 3.4 13.8 + - + +
167E ILE* 3.0 8.5 + - - +
169E ASN* 1.3 78.1 - - + +
171E TYR* 1.3 63.0 + - - +
173E GLU* 3.0 25.3 + - - +
174E VAL* 3.3 13.2 - - - +
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Residues in contact with TYR 171 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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112D ILE* 3.5 24.6 - - + +
167E ILE 2.9 17.9 + - - +
168E GLU* 4.3 10.1 - - + -
170E ARG* 1.3 74.7 - - - +
172E LYS* 1.3 82.1 + - + +
174E VAL* 3.2 10.4 + - - +
175E LYS* 3.2 31.3 + - + +
88F ILE* 4.5 17.5 - - + -
91F GLU* 2.7 53.0 + - + +
92F VAL* 4.2 13.2 - - + -
95F LEU* 3.9 25.1 - - + -
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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