Contacts of the strand formed by residues 155 - 159 (chain J) in PDB entry 1I43
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 155 (chain J).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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150J VAL* 4.7 2.0 - - - +
153J GLY 5.5 0.2 - - - +
154J GLY* 1.3 74.0 - - - -
156J ILE* 1.3 70.1 + - - +
157J VAL* 4.2 12.6 - - + -
180J THR* 2.9 43.5 + - + +
181J ALA 3.4 14.8 - - - -
182J THR* 2.5 33.4 + - - -
195J ALA* 5.5 0.4 - - - +
199J LYS* 3.8 36.4 - - + +
200J LYS 3.6 17.8 + - - +
201J VAL* 4.3 7.9 - - + -
202J ASN* 2.9 39.3 + - - +
203J LEU 3.8 0.2 + - - -
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Residues in contact with ILE 156 (chain J).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
146J LEU* 3.3 35.0 - - + -
150J VAL* 4.3 9.2 - - + -
155J HIS* 1.3 76.9 + - - +
157J VAL* 1.3 61.7 + - - +
158J THR* 4.5 17.7 - - + -
170J ILE* 4.0 13.7 - - + -
174J LEU* 4.8 7.2 - - + -
179J ILE* 4.7 7.9 - - + -
180J THR 2.8 8.1 + - - +
181J ALA* 3.0 25.1 - - + -
182J THR 2.6 32.1 + - - -
203J LEU* 3.2 34.1 - - + +
205J PHE* 4.6 1.1 - - + -
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Residues in contact with VAL 157 (chain J).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
155J HIS* 4.2 2.7 - - + -
156J ILE* 1.3 79.4 - - - +
158J THR* 1.3 66.4 + - - +
182J THR* 3.3 23.8 - - + +
184J ILE* 4.4 13.7 - - + -
192J LEU* 3.9 16.4 - - + -
195J ALA* 4.5 6.7 - - + -
201J VAL* 3.5 39.5 - - + -
203J LEU 3.1 7.2 + - - +
204J PHE* 3.0 23.5 - - + -
205J PHE 2.8 32.1 + - - -
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Residues in contact with THR 158 (chain J).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
156J ILE* 4.4 12.6 + - + +
157J VAL* 1.3 82.1 - - - +
159J THR* 1.3 71.9 + - - +
162J CYS* 5.0 8.5 - - - +
167J ARG* 6.0 0.9 - - - -
170J ILE* 4.4 18.9 - - + +
181J ALA* 5.4 1.7 - - - +
182J THR 3.0 7.5 + - - +
183J VAL* 3.4 14.4 - - - +
184J ILE* 2.8 28.6 + - - +
204J PHE* 4.0 5.4 - - - -
205J PHE* 3.0 39.9 - - + +
206J THR* 5.5 0.2 - - - -
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Residues in contact with THR 159 (chain J).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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158J THR* 1.3 84.1 + - - +
160J THR* 1.3 62.8 + - - +
161J ASP* 3.2 13.9 + - - +
162J CYS* 3.6 21.4 + - - +
167J ARG* 5.1 2.4 + - - -
183J VAL* 3.4 11.8 - - - +
184J ILE* 2.8 13.7 - - + +
185J ASP 4.8 0.2 - - - -
186J PRO* 3.7 33.4 - - + +
204J PHE* 4.3 10.3 - - + -
205J PHE 4.1 0.8 + - - -
206J THR* 3.1 33.7 + - + +
207J GLU* 5.8 0.2 - - - +
210J THR* 4.5 2.6 + - - -
217J VAL* 4.8 2.0 - - + -
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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