Contacts of the helix formed by residues 146 - 150 (chain I) in PDB entry 3STJ
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 ASN 146 (chain I).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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27I VAL 5.3 0.3 - - - -
28I SER* 2.4 30.5 + - - -
64I LEU* 3.5 18.3 - - + +
65I GLY 3.9 2.9 - - - +
66I SER* 2.9 16.3 + - - +
145I GLY* 1.3 70.4 - - - +
147I PRO* 1.4 68.2 - - - +
149I GLY* 3.2 31.4 + - - -
151I GLY* 3.1 41.4 - - - +
152I GLN* 3.7 3.1 + - - -
185I GLY* 3.3 18.8 + - - +
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Residues in contact with PRO 147 (chain I).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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215G ILE* 3.7 28.3 - - + -
145I GLY 3.6 5.6 - - - -
146I ASN* 1.4 86.5 - - - +
148I PHE* 1.4 61.4 + - + +
150I LEU* 3.0 33.1 + - + +
153I THR* 3.7 25.8 - - + +
155I THR* 6.1 0.4 - - + -
183I ASN* 3.9 17.0 - - + -
184I ARG 3.3 7.6 - - - +
185I GLY* 4.2 0.7 - - - -
186I ASN* 3.5 28.7 - - - +
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Residues in contact with PHE 148 (chain I).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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206G LEU* 3.7 36.6 - - + -
208G PRO* 4.4 21.3 - - + -
213G VAL* 4.1 10.3 - - + -
215G ILE* 3.8 27.6 - - + -
146I ASN 3.4 0.2 + - - -
147I PRO* 1.4 71.0 - - - +
149I GLY* 1.3 63.3 + - - +
150I LEU* 3.2 6.7 + - + +
183I ASN* 3.6 30.7 - - + -
184I ARG* 2.8 40.6 + - + -
185I GLY* 4.5 0.2 - - - -
210I GLY 5.5 1.6 - - - -
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Residues in contact with GLY 149 (chain I).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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64I LEU* 3.8 27.3 - - - +
146I ASN* 3.2 21.7 + - - -
147I PRO 3.1 2.2 + - - -
148I PHE* 1.3 77.3 - - - +
150I LEU* 1.4 59.8 + - - +
151I GLY 3.4 2.7 - - - -
185I GLY* 5.2 1.0 - - - -
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Residues in contact with LEU 150 (chain I).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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164G ARG* 3.5 30.2 + - - +
167G LEU* 3.6 30.2 - - + +
177G GLN* 3.9 15.0 - - - +
206G LEU* 3.8 23.6 - - + -
215G ILE* 3.6 33.2 - - + -
217G PHE* 4.3 4.3 - - + -
146I ASN* 3.5 0.6 - - - +
147I PRO* 3.0 20.0 + - + +
148I PHE* 4.2 9.2 - - + +
149I GLY* 1.4 77.8 - - - +
151I GLY* 1.3 58.3 + - - +
153I THR* 4.7 1.1 - - - +
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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