Contacts of the helix formed by residues 146 - 152 (chain B) in PDB entry 1S5E
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 ARG 146 (chain B).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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122B SER* 3.6 3.7 + - - -
143B ARG 3.2 19.2 + - - -
144B GLY* 3.3 13.7 + - - +
145B TYR* 1.3 94.6 + - - +
147B ASP* 1.3 60.7 + - - +
148B ARG 3.5 1.6 - - - -
149B TYR* 3.6 17.7 + - + +
150B TYR* 3.1 36.5 + - + +
221B GLN* 4.6 9.7 + - - +
222B ILE* 3.8 32.1 + - + +
225B GLY* 6.2 0.8 - - - -
226B TYR* 4.1 21.6 + - - -
77M LEU 4.5 4.8 + - - -
78M THR* 3.3 54.5 + - - +
79M GLU* 3.8 9.6 - - - +
77N LEU 4.9 6.7 + - - -
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Residues in contact with ASP 147 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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2B ASP* 5.2 0.7 - - - +
4B LYS* 4.9 4.0 + - - -
125B TYR* 5.1 2.8 - - - -
145B TYR* 2.6 41.4 + - + -
146B ARG* 1.3 71.1 - - - +
148B ARG* 1.3 65.8 + - + +
151B SER* 2.9 44.5 + - - -
23M LYS* 3.6 18.0 + - - +
79M GLU* 2.8 19.2 + - - +
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Residues in contact with ARG 148 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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147B ASP* 1.3 76.7 - - + +
149B TYR* 1.3 63.2 + - - +
151B SER* 4.3 2.2 - - - -
152B ASN* 3.5 19.6 + - - +
80L ALA* 6.3 0.8 - - - +
103L ASN* 3.3 42.5 + - - +
23M LYS* 4.9 9.3 - - - +
24M ILE 4.3 7.7 + - - -
25M PHE* 5.3 1.4 + - - +
76M TYR* 2.9 58.6 + - - -
77M LEU* 4.0 12.5 + - - +
79M GLU* 2.8 39.2 + - - +
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Residues in contact with TYR 149 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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146B ARG* 3.6 13.1 + - + +
147B ASP 3.2 0.2 - - - -
148B ARG* 1.3 83.4 - - - +
150B TYR* 1.3 97.5 + + - +
152B ASN* 3.4 11.2 + - - +
153B LEU* 3.5 38.4 - - + +
214B TYR* 5.3 5.4 + - - -
217B LYS* 3.9 29.2 + - - +
218B VAL* 4.7 5.3 + - + +
221B GLN* 3.5 53.4 - - + +
78L THR 5.3 0.4 - - - -
79L GLU* 4.0 18.1 + - + -
79M GLU* 4.5 0.4 + - - -
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Residues in contact with TYR 150 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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89B ALA* 3.5 23.3 - - + -
90B THR 3.6 1.9 - - - +
91B ALA* 3.9 25.4 - - + -
120B PRO* 4.2 7.6 - - - +
122B SER* 2.7 51.5 + - - -
123B GLN* 3.7 29.8 + - + +
145B TYR* 4.1 7.4 - + + +
146B ARG* 3.1 28.3 + - + +
149B TYR* 1.3 110.8 - + - +
151B SER* 1.3 55.7 + - - +
152B ASN 3.2 0.7 - - - -
153B LEU* 3.1 9.6 + - + +
214B TYR* 4.4 3.4 - - - -
218B VAL* 4.5 9.4 - - - +
222B ILE* 5.4 1.0 - - + +
241B NA 2.4 29.7 - - - -
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Residues in contact with SER 151 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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1B ASN* 3.2 31.4 + - - -
2B ASP* 3.3 25.0 - - - +
145B TYR* 3.9 3.5 + - - -
147B ASP* 2.9 40.8 + - - -
148B ARG* 4.5 2.2 - - - -
150B TYR* 1.3 76.9 - - - +
152B ASN* 1.3 55.7 + - - +
153B LEU 3.3 1.6 - - - -
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Residues in contact with ASN 152 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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1B ASN 4.5 3.1 - - - +
148B ARG 3.5 16.4 + - - +
149B TYR* 3.4 6.2 + - - +
150B TYR 3.2 1.0 - - - -
151B SER* 1.3 77.3 - - - +
153B LEU* 1.3 67.8 + - + +
154B ASP* 5.0 1.8 - - - +
81L LYS* 5.7 4.0 + - - -
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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