Contacts of the helix formed by residues 146 - 152 (chain A) 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 A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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122A SER 3.5 3.6 + - - -
143A ARG 3.0 26.5 + - - -
144A GLY* 3.4 14.6 + - - +
145A TYR* 1.3 88.4 + - - +
147A ASP* 1.3 64.1 + - - +
148A ARG 3.5 1.3 - - - -
149A TYR* 4.0 17.5 - - + +
150A TYR* 3.1 31.2 + - + +
221A GLN* 4.1 8.8 + - - +
222A ILE* 3.8 33.8 + - + +
225A GLY* 6.1 1.6 - - - -
226A TYR* 4.1 21.8 + - - -
77G LEU 4.3 7.0 + - - -
78G THR* 3.2 53.6 + - - +
79G GLU* 3.7 8.5 - - - +
77H LEU 5.0 6.5 + - - -
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Residues in contact with ASP 147 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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2A ASP* 5.2 1.0 - - - +
4A LYS* 4.8 4.7 + - - -
125A TYR* 4.9 4.4 - - - -
145A TYR* 2.7 40.1 + - + -
146A ARG* 1.3 71.7 - - - +
148A ARG* 1.3 67.8 + - + +
151A SER* 2.9 45.8 + - - -
23G LYS* 4.6 16.5 + - - +
79G GLU* 2.8 20.1 + - - +
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Residues in contact with ARG 148 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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147A ASP* 1.3 81.0 - - + +
149A TYR* 1.3 65.3 + - - +
151A SER* 4.2 3.5 - - - -
152A ASN* 3.5 19.4 + - - +
80F ALA* 6.2 3.0 - - - +
81F LYS 6.1 0.4 - - - +
103F ASN* 3.3 42.2 + - - +
23G LYS* 4.7 10.9 - - - +
24G ILE 4.1 8.1 + - - -
25G PHE* 5.2 1.2 + - - +
76G TYR* 2.9 62.8 + - - -
77G LEU* 4.0 11.5 + - - +
79G GLU* 2.9 33.4 + - - +
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Residues in contact with TYR 149 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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146A ARG* 3.5 13.6 + - + +
147A ASP 3.2 0.4 - - - -
148A ARG* 1.3 82.3 - - - +
150A TYR* 1.3 96.9 + + - +
152A ASN* 3.3 13.3 + - - +
153A LEU* 3.6 35.6 - - + +
214A TYR* 5.4 4.5 + - - -
217A LYS* 3.8 30.2 + - - +
218A VAL* 5.0 4.1 - - + +
221A GLN* 3.5 49.1 - - + +
78F THR 5.1 1.1 - - - -
79F GLU* 3.6 26.7 + - + -
79G GLU* 4.5 0.6 + - - -
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Residues in contact with TYR 150 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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89A ALA* 3.6 22.7 - - + -
90A THR 3.5 2.0 - - - +
91A ALA* 4.0 25.4 - - + -
120A PRO* 4.6 1.4 - - - +
122A SER* 2.8 49.7 + - - -
123A GLN* 3.7 32.7 + - + +
145A TYR* 4.2 6.7 - + + +
146A ARG* 3.1 28.5 + - + +
149A TYR* 1.3 106.4 - + - +
151A SER* 1.3 53.1 + - - +
152A ASN 3.1 5.6 - - - -
153A LEU* 3.2 12.6 + - + +
214A TYR* 4.1 7.4 + - - -
218A VAL* 4.5 11.6 - - - +
221A GLN* 6.1 0.2 - - - +
222A ILE* 5.4 1.5 - - + +
241A NA 2.3 30.8 - - - -
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Residues in contact with SER 151 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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1A ASN* 3.1 32.3 - - - -
2A ASP* 3.4 24.1 - - - +
145A TYR* 4.0 2.6 + - - -
147A ASP* 2.9 40.6 + - - -
148A ARG* 4.2 3.1 - - - -
150A TYR* 1.3 75.9 - - - +
152A ASN* 1.3 56.3 + - - +
153A LEU 3.3 1.6 - - - -
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Residues in contact with ASN 152 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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1A ASN 4.5 3.4 - - - -
148A ARG 3.5 16.0 + - - +
149A TYR* 3.3 7.1 + - - +
150A TYR 3.1 0.8 - - - -
151A SER* 1.3 78.5 - - - +
153A LEU* 1.3 67.7 + - + +
154A ASP* 5.0 2.3 - - - +
23F LYS* 5.8 1.9 + - - -
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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