Contacts of the strand formed by residues 180 - 184 (chain D) 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 THR 180 (chain D).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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153D GLY 4.4 4.9 - - - +
154D GLY 2.9 10.6 + - - +
155D HIS* 3.0 36.0 + - + +
156D ILE 2.8 23.0 + - - -
178D GLY 4.2 7.9 - - - +
179D ILE* 1.3 76.8 - - - +
181D ALA* 1.3 66.8 + - - +
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Residues in contact with ALA 181 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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155D HIS* 3.4 9.7 - - - -
156D ILE* 3.1 31.0 - - + -
158D THR* 5.3 3.4 - - - +
170D ILE* 4.0 18.2 - - + +
171D GLU* 6.4 1.6 - - + -
179D ILE* 5.6 0.7 - - + +
180D THR* 1.3 78.1 + - - +
182D THR* 1.3 61.9 + - - +
183D VAL* 4.1 7.3 + - + +
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Residues in contact with THR 182 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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155D HIS* 2.7 26.4 + - - -
156D ILE 2.7 9.9 + - - -
157D VAL* 3.4 9.3 - - + +
158D THR 3.1 24.7 + - - +
181D ALA* 1.3 72.3 + - - +
183D VAL* 1.3 63.5 + - - +
184D ILE* 3.7 22.0 - - + -
195D ALA* 3.9 18.3 - - + +
199D LYS* 3.2 21.4 + - - +
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Residues in contact with VAL 183 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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158D THR* 3.4 13.7 - - - +
159D THR 3.6 17.9 - - - +
160D THR* 3.3 32.0 - - + +
167D ARG* 4.4 29.8 - - - +
171D GLU* 4.9 5.8 - - + +
181D ALA* 4.2 6.9 + - + +
182D THR* 1.3 77.4 - - - +
184D ILE* 1.3 63.1 + - - +
415D TYR* 4.7 0.9 - - - +
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Residues in contact with ILE 184 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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157D VAL* 4.5 5.6 - - + -
158D THR 2.9 19.3 + - - +
159D THR* 3.0 10.6 - - + -
160D THR* 2.9 27.3 + - - -
182D THR* 3.7 22.2 - - + +
183D VAL* 1.3 78.6 - - - +
185D ASP* 1.3 65.7 + - - +
186D PRO 5.5 1.8 - - - +
188D ASP 3.5 20.4 - - - +
191D ALA* 3.6 30.3 - - + +
192D LEU* 3.7 31.0 - - + +
204D PHE* 4.4 10.1 - - + -
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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