Contacts of the strand formed by residues 169 - 174 (chain B) 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 VAL 169 (chain B).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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141B ILE* 3.6 12.8 - - + +
143B ILE* 3.9 32.5 - - + -
159B GLN* 4.3 22.7 - - + +
162B LEU* 4.1 26.2 - - + -
163B LYS* 4.9 15.1 - - + -
167B ALA 3.0 11.2 + - - +
168B ASN* 1.3 72.9 + - - +
170B VAL* 1.3 61.5 - - - +
171B PHE* 4.0 19.0 - - - +
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Residues in contact with VAL 170 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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140B ARG* 3.7 30.5 - - + +
141B ILE 2.8 18.6 + - - +
168B ASN* 3.8 22.0 - - - +
169B VAL* 1.3 73.8 - - - +
171B PHE* 1.3 64.4 + - + +
192B GLU* 3.4 32.3 - - - +
194B ILE* 3.8 22.4 - - + -
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Residues in contact with PHE 171 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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141B ILE 3.8 1.6 + - - -
142B ALA* 3.4 24.9 - - + -
143B ILE 3.0 23.7 + - - -
144B ILE* 3.8 23.8 - - + -
169B VAL* 3.4 8.9 - - - +
170B VAL* 1.3 92.9 - - + +
172B PHE* 1.3 62.9 + - - +
173B ASP* 4.3 8.5 - - + -
185B LEU* 4.5 5.6 - - + -
188B ARG* 3.5 70.4 - - + +
189B LEU* 4.0 13.5 - - + -
192B GLU* 4.6 4.0 - - + -
194B ILE* 4.1 15.5 - - + -
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Residues in contact with PHE 172 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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143B ILE* 3.3 36.6 - - + -
145B HIS* 3.6 32.5 - + - -
152B GLU* 5.0 0.7 - - + -
155B ALA* 3.9 18.6 - - + -
156B ARG* 3.9 43.3 - - + -
159B GLN* 3.3 37.7 - - - +
169B VAL* 5.1 0.2 - - + -
171B PHE* 1.3 75.9 - - - +
173B ASP* 1.3 68.4 + - - +
188B ARG* 5.4 0.5 + - - -
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Residues in contact with ASP 173 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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143B ILE 3.1 6.9 + - - -
144B ILE* 3.2 42.4 - - + +
145B HIS* 3.3 7.4 + - - -
171B PHE* 4.3 9.4 - - + -
172B PHE* 1.3 82.0 - - - +
174B GLY* 1.3 76.3 + - - +
175B ILE* 6.5 0.2 - - + -
185B LEU* 6.2 0.2 - - + -
188B ARG* 3.6 17.2 + - - +
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Residues in contact with GLY 174 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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145B HIS* 3.2 31.1 + - - -
147B LYS* 3.7 19.7 + - - -
173B ASP* 1.3 89.7 + - - +
175B ILE* 1.3 64.9 + - - +
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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