Contacts of the strand formed by residues 141 - 147 (chain X) in PDB entry 1SHU
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 SER 141 (chain X).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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40X ARG* 5.6 0.4 - - - +
44X ASP* 3.4 11.0 + - - +
46X TYR* 4.1 6.4 + - - -
131X ILE* 3.8 34.1 - - - +
139X THR* 2.9 31.3 + - - +
140X SER* 1.3 70.3 - - - +
142X ILE* 1.3 66.4 + - - +
170X GLY 4.3 5.4 + - - +
171X ALA* 3.3 12.2 - - - -
172X SER* 3.1 23.1 + - - -
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Residues in contact with ILE 142 (chain X).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
43X PHE* 4.0 23.8 - - + -
44X ASP 2.9 6.4 + - - +
45X LEU* 3.5 21.3 - - + -
46X TYR* 2.8 34.0 + - - -
140X SER 5.3 0.2 - - - -
141X SER* 1.3 78.4 - - - +
143X ILE* 1.3 59.7 + - - +
144X ILE* 3.9 17.4 - - + +
172X SER* 3.4 9.4 - - - +
174X TYR* 3.6 34.8 - - + -
209X ILE* 5.9 0.2 - - + -
213X ILE* 3.7 30.1 - - + -
216X GLN* 4.5 13.0 - - - +
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Residues in contact with ILE 143 (chain X).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
46X TYR* 3.3 7.6 - - + -
48X VAL* 3.9 24.7 - - + -
124X LEU* 4.0 17.3 - - + -
127X ALA* 3.9 20.9 - - + -
128X ASN* 3.8 9.9 - - - +
131X ILE* 3.9 13.9 - - + -
142X ILE* 1.3 76.9 - - - +
144X ILE* 1.3 69.2 + - - +
145X ALA 4.4 1.3 - - - +
166X SER* 3.4 34.5 - - - +
171X ALA* 4.4 4.3 - - + -
172X SER 2.8 11.9 + - - +
173X VAL* 3.5 13.6 - - + -
174X TYR* 2.8 28.4 + - - -
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Residues in contact with ILE 144 (chain X).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
45X LEU* 5.0 8.1 - - + -
46X TYR 2.9 11.7 + - - +
47X PHE* 3.5 17.6 - - + -
48X VAL 2.9 24.9 + - - +
65X PHE* 4.0 6.1 - - + -
69X LEU* 3.4 33.0 - - + -
142X ILE* 3.9 18.4 - - + -
143X ILE* 1.3 77.9 - - - +
145X ALA* 1.3 61.4 + - - +
146X LEU* 3.8 22.5 + - + +
174X TYR* 3.5 11.9 - - + +
176X VAL* 3.8 20.9 - - + -
209X ILE* 4.1 17.3 - - + -
213X ILE* 5.4 0.4 - - + -
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Residues in contact with ALA 145 (chain X).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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48X VAL* 3.3 17.9 - - + +
120X ILE* 4.5 20.4 - - + -
124X LEU* 5.0 10.3 - - + -
143X ILE* 4.0 2.4 - - + -
144X ILE* 1.3 71.8 - - - +
146X LEU* 1.3 61.2 + - - +
147X THR* 3.9 3.7 + - + +
173X VAL* 5.4 0.9 - - + -
174X TYR 2.9 14.2 + - - +
175X CYS* 3.4 15.3 - - - +
176X VAL* 2.8 27.7 + - - +
189X ILE* 5.3 2.2 - - + -
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Residues in contact with LEU 146 (chain X).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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47X PHE* 4.8 2.0 - - + -
48X VAL 3.0 8.2 + - - +
49X LEU* 3.9 28.0 - - + -
50X ASP* 3.0 26.9 + - - +
62X ILE* 4.0 26.3 - - + +
65X PHE* 3.9 25.6 - - + -
85X PHE* 4.7 0.2 - - - -
144X ILE* 3.8 25.1 - - + +
145X ALA* 1.3 75.8 - - - +
147X THR* 1.3 60.7 + - - +
176X VAL* 3.4 31.2 - - + +
178X VAL* 4.4 3.6 - - + -
199X VAL* 4.1 13.9 - - + -
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Residues in contact with THR 147 (chain X).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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50X ASP* 2.7 28.5 + - - -
55X VAL* 5.0 0.2 - - - -
85X PHE* 4.4 1.1 - - - -
118X THR* 4.8 3.3 - - - +
120X ILE* 3.9 28.3 - - + +
145X ALA* 4.4 11.7 - - + +
146X LEU* 1.3 77.5 - - - +
148X ASP* 1.3 62.3 + - - +
149X GLY* 3.0 10.7 + - - +
151X LEU* 5.2 0.3 - - - +
175X CYS* 5.4 0.2 - - + -
176X VAL 3.2 5.3 + - - +
177X GLY* 3.3 9.2 - - - -
178X VAL* 3.0 27.5 + - - +
186X LEU* 3.6 29.2 - - + +
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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
------------------------------------------------------------
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