Contacts of the helix formed by residues 171 - 180 (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 TYR 171 (chain E).
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Specific contacts
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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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Residues in contact with LYS 172 (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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168E GLU 3.1 15.5 + - - +
169E ASN* 2.8 13.8 + - - +
171E TYR* 1.3 95.2 - - + +
173E GLU* 1.3 58.0 + - - +
174E VAL 2.9 6.4 + - - -
175E LYS* 3.3 26.5 + - - +
176E ILE* 3.1 22.9 - - + +
179E GLU* 5.6 0.8 + - - -
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Residues in contact with GLU 173 (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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116D GLN* 4.6 6.3 + - - +
186D PHE* 5.1 1.7 - - - -
188D ARG* 2.5 45.5 + - - +
190D GLU* 3.4 16.5 - - - +
169E ASN* 3.4 15.9 - - - +
170E ARG* 3.0 26.8 - - - +
172E LYS* 1.3 75.2 - - - +
174E VAL* 1.3 59.4 + - - +
176E ILE* 3.3 22.6 - - + +
177E ARG* 3.7 19.6 - - - +
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Residues in contact with VAL 174 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
112D ILE* 4.4 9.2 - - + +
115D LEU* 4.1 15.0 - - + -
116D GLN* 2.9 41.7 - - + +
119D ILE* 4.5 4.5 - - + -
170E ARG 3.3 17.3 - - - +
171E TYR* 3.7 6.7 - - - +
172E LYS 2.9 1.4 + - - -
173E GLU* 1.3 77.0 - - - +
175E LYS* 1.3 66.2 + - - +
176E ILE 2.8 5.5 + - - -
177E ARG* 3.1 5.1 + - - +
178E ILE* 2.9 46.7 + - + +
95F LEU* 3.9 11.2 - - + -
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Residues in contact with LYS 175 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
171E TYR* 3.2 37.9 + - + +
172E LYS* 3.3 22.9 + - - +
174E VAL* 1.3 79.1 - - - +
176E ILE* 1.3 66.2 + - - +
178E ILE* 4.6 0.2 - - - -
179E GLU* 2.8 70.9 + - - +
91F GLU* 3.9 14.8 - - - +
94F ILE* 6.5 0.7 - - - -
95F LEU* 3.8 29.5 - - + +
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Residues in contact with ILE 176 (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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172E LYS* 3.1 28.0 - - + +
173E GLU* 3.3 30.5 - - + +
174E VAL 2.8 0.4 + - - -
175E LYS* 1.3 73.2 - - - +
177E ARG* 1.3 81.8 + - + +
179E GLU* 2.7 17.6 + - - +
180E SER* 2.8 22.0 + - - +
181E THR* 4.8 3.1 - - - +
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Residues in contact with ARG 177 (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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119D ILE* 4.2 15.9 - - + -
183D ASN* 4.8 7.1 - - - +
184D LEU 5.1 1.0 + - - -
186D PHE* 3.1 61.2 - - + +
188D ARG* 5.8 0.4 - - - +
173E GLU 3.7 13.9 - - - +
174E VAL* 3.1 7.7 + - - +
176E ILE* 1.3 85.9 - - + +
178E ILE* 1.3 60.3 + - - +
181E THR* 2.8 56.6 + - + +
182E VAL* 2.8 32.9 + - - +
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Residues in contact with ILE 178 (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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115D LEU* 3.5 27.6 - - + -
119D ILE* 3.1 33.4 - - + -
174E VAL* 2.9 27.3 + - + +
175E LYS 4.2 1.6 - - - +
177E ARG* 1.3 76.1 - - - +
179E GLU* 1.3 63.3 + - + +
182E VAL* 4.4 5.8 - - - -
183E ALA* 3.4 6.8 + - - +
95F LEU* 3.7 27.6 - - + +
98F ILE* 3.7 28.5 - - + -
99F GLY* 4.8 4.3 - - - +
102F HIS* 3.0 26.4 - - + +
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Residues in contact with GLU 179 (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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172E LYS* 5.6 0.7 + - - -
175E LYS* 2.8 64.0 + - + +
176E ILE* 2.7 9.2 + - - +
178E ILE* 1.3 79.4 - - + +
180E SER* 1.3 61.3 + - - +
183E ALA* 3.7 16.0 - - - +
184E GLY* 4.5 1.6 + - - -
95F LEU* 5.2 2.7 - - + -
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Residues in contact with SER 180 (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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183D ASN* 5.7 0.2 + - - -
176E ILE* 2.8 23.2 + - - +
179E GLU* 1.3 77.7 + - - +
181E THR* 1.3 58.2 + - - -
182E VAL 2.7 16.2 + - - -
184E GLY* 2.8 26.7 + - - +
185E SER 4.0 0.2 + - - -
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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