Contacts of the helix formed by residues 143 - 147 (chain N) in PDB entry 1L0V
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 HIS 143 (chain N).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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102M PRO* 5.8 3.8 - - + +
127M ALA 6.3 0.2 - - - -
128M ALA* 4.9 16.9 - - + +
130M LYS* 5.7 4.5 - - + -
134M HIS* 4.5 14.8 - + - -
139N MET* 2.9 50.3 + - + +
140N ALA* 3.6 10.3 + - - +
142N TYR* 1.3 79.6 - - - +
144N GLN* 1.3 56.9 + - - +
146N SER* 2.5 48.4 + - - -
147N GLY 3.8 1.0 + - - -
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Residues in contact with GLN 144 (chain N).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
140N ALA 4.8 0.8 + - - -
142N TYR 3.5 0.4 - - - -
143N HIS* 1.3 79.4 - - - +
145N PHE* 1.3 62.1 + - - +
146N SER 3.3 0.7 + - - -
147N GLY* 3.6 9.0 + - - -
217N HIS* 3.6 23.7 + - - +
218N VAL* 3.3 31.0 - - - +
219N ASP* 3.8 22.6 + - - +
222N ALA* 5.7 0.2 - - - +
102O LYS* 2.5 44.5 + - - +
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Residues in contact with PHE 145 (chain N).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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141N LYS 4.0 20.0 - - - -
142N TYR* 3.1 12.1 + - + +
143N HIS 2.8 3.2 + - - -
144N GLN* 1.3 73.8 - - - +
146N SER* 1.3 60.5 + - - +
147N GLY 3.3 0.8 + - - -
148N CYS* 4.3 5.9 + - - +
174N THR* 3.6 33.2 - - + +
175N LEU* 5.0 4.0 - - - +
177N HIS* 3.8 21.1 - + - -
178N ARG* 4.0 20.1 - - + +
181N GLU* 5.7 0.4 - - + -
218N VAL* 3.4 28.8 - - - +
219N ASP 3.7 5.2 - - - -
222N ALA* 4.3 6.1 - - + -
223N ALA* 3.7 21.5 - - + -
226N GLN* 3.5 26.2 - - - -
95O ASN* 5.1 2.7 - - - -
102O LYS* 3.7 24.2 - - + -
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Residues in contact with SER 146 (chain N).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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102M PRO* 5.2 2.6 - - - +
133M PHE* 3.3 19.4 - - - -
134M HIS* 3.6 21.6 + - - -
137M HIS* 5.6 0.9 - - - -
142N TYR* 3.3 17.4 + - - -
143N HIS* 2.5 36.7 + - - -
145N PHE* 1.3 71.4 - - - +
147N GLY* 1.3 55.1 + - - +
148N CYS* 3.2 8.1 + - - +
175N LEU* 5.9 3.7 - - - +
178N ARG* 4.1 23.8 - - - +
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Residues in contact with GLY 147 (chain N).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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130M LYS* 4.1 16.1 + - - -
133M PHE* 3.9 11.2 - - - -
134M HIS* 5.0 1.1 - - - -
143N HIS 3.8 0.6 + - - -
144N GLN 3.6 9.2 + - - -
145N PHE 3.3 1.8 - - - -
146N SER* 1.3 79.7 + - - +
148N CYS* 1.3 63.3 + - - +
149N ILE* 3.2 5.9 + - - +
216N LYS* 2.9 27.4 - - - +
218N VAL* 3.8 7.2 - - - -
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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