Contacts of the strand formed by residues 141 - 145 (chain D) in PDB entry 1USK
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 ILE 141 (chain D).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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132D ILE* 4.6 4.5 - - + -
138D PRO* 3.6 36.8 - - + +
139D GLN 5.0 0.4 - - - +
140D ARG* 1.3 79.3 - - - +
142D ALA* 1.3 76.4 + - - +
143D ILE* 4.2 12.3 - - + -
162D LEU* 4.2 21.1 - - + -
167D ALA* 4.1 25.6 - - + -
168D ASN 3.1 19.6 + - - +
169D VAL* 3.7 7.2 - - + -
170D VAL* 2.8 33.0 + - - +
194D ILE* 4.0 2.2 - - - -
196D PHE* 3.4 19.5 - - + +
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Residues in contact with ALA 142 (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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141D ILE* 1.3 75.8 - - - +
143D ILE* 1.3 66.4 + - - +
144D ILE* 4.9 2.9 - - + -
169D VAL* 5.1 0.2 - - - -
171D PHE* 3.5 44.4 - - + -
189D LEU* 4.0 6.5 - - + -
194D ILE* 3.8 13.2 - - + -
196D PHE 2.9 7.1 + - - +
197D VAL* 3.3 9.3 - - + -
198D TYR 3.2 22.3 + - - -
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Residues in contact with ILE 143 (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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141D ILE* 4.2 9.2 - - + -
142D ALA* 1.3 81.1 - - - +
144D ILE* 1.3 64.2 + - - +
155D ALA* 3.7 36.1 - - + +
158D VAL* 4.4 2.5 - - + -
159D GLN* 3.5 41.7 - - + +
162D LEU* 4.1 15.9 - - + -
169D VAL* 4.1 13.2 - - + -
171D PHE 3.1 7.2 + - - +
172D PHE* 3.4 17.0 - - + -
173D ASP 3.1 24.1 + - - +
198D TYR* 3.4 19.1 - - + +
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Residues in contact with ILE 144 (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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142D ALA* 5.0 2.0 - - + -
143D ILE* 1.3 83.0 - - - +
145D HIS* 1.3 72.0 + - - +
155D ALA* 4.0 5.3 - - - +
171D PHE* 3.9 20.2 - - + -
173D ASP* 3.2 20.0 - - + +
175D ILE* 3.9 29.4 - - + -
185D LEU* 3.7 38.6 - - + -
189D LEU* 5.9 1.1 - - + -
197D VAL* 4.3 16.8 - - + -
198D TYR 3.0 10.1 + - - +
199D TYR* 3.4 21.2 - - + -
200D GLY 3.0 22.2 + - - -
209D MET* 4.6 1.6 - - + -
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Residues in contact with HIS 145 (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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144D ILE* 1.3 79.3 - - - +
146D ASP* 1.3 58.8 + - - +
147D LYS* 3.2 26.6 + - + -
152D GLU* 3.4 38.2 - - + +
155D ALA* 3.8 12.3 - - + -
156D ARG* 5.5 0.7 - - - -
172D PHE* 3.3 38.0 - + - -
173D ASP 3.2 24.6 + - - -
174D GLY* 3.5 19.4 + - - -
175D ILE* 2.9 28.6 + - - +
199D TYR* 3.9 7.4 - - - -
200D GLY 3.3 15.3 - - - +
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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