Contacts of the strand formed by residues 172 - 177 (chain X) in PDB entry 1SHT
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 172 (chain X).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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141X SER 3.0 6.0 + - - -
142X ILE* 3.4 15.2 - - - +
143X ILE 2.9 25.7 + - - +
170X GLY 4.7 1.7 + - - -
171X ALA* 1.3 73.3 - - - +
173X VAL* 1.3 60.4 + - - +
174X TYR* 3.9 8.8 - - - -
191X ASP* 3.2 12.1 - - - -
195X GLN* 4.0 2.2 - - - -
216X GLN 4.0 1.2 + - - -
217X SER* 2.6 51.1 + - - -
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Residues in contact with VAL 173 (chain X).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
124X LEU* 5.0 4.3 - - + -
143X ILE* 3.5 21.3 - - + +
145X ALA* 5.7 0.4 - - + -
163X ALA* 4.1 6.1 - - + +
166X SER* 3.8 29.2 - - - +
167X ARG* 3.5 24.5 - - + +
171X ALA 4.7 0.9 - - - +
172X SER* 1.3 74.3 - - - +
174X TYR* 1.3 69.1 + - - +
175X CYS* 4.9 0.2 - - - -
189X ILE* 3.5 28.5 - - + +
190X ALA* 3.3 6.7 - - - +
191X ASP* 2.8 30.5 + - - +
195X GLN* 3.0 14.4 - - - +
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Residues in contact with TYR 174 (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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142X ILE* 3.8 23.6 - - + -
143X ILE 2.8 10.4 + - - +
144X ILE* 4.3 6.7 - - + -
145X ALA* 2.9 24.2 + - - +
172X SER* 3.9 8.3 - - - -
173X VAL* 1.3 79.2 - - - +
175X CYS* 1.3 67.9 + - - +
195X GLN* 3.3 41.3 - - + +
197X PHE* 4.2 2.7 - + - -
209X ILE* 3.8 34.3 - - + -
212X SER* 2.7 47.5 + - - -
213X ILE* 3.4 18.7 + - + -
217X SER* 2.7 24.1 + - - -
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Residues in contact with CYS 175 (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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145X ALA* 3.3 14.4 - - - +
147X THR* 5.4 0.4 - - - -
174X TYR* 1.3 77.8 - - - +
176X VAL* 1.3 64.7 + - - +
177X GLY 4.0 0.2 - - - -
186X LEU* 3.7 50.3 - - + +
189X ILE* 3.6 32.3 - - - -
190X ALA* 3.9 4.7 - - - +
195X GLN 3.0 7.8 + - - +
196X VAL* 3.2 8.4 - - + +
197X PHE* 3.0 23.7 + - - +
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Residues in contact with VAL 176 (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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65X PHE* 4.0 24.2 - - + -
144X ILE* 3.8 24.5 - - + -
145X ALA 2.7 9.1 + - - +
146X LEU* 3.4 21.4 - - + -
147X THR 3.2 23.1 + - - +
175X CYS* 1.3 76.6 - - - +
177X GLY* 1.3 61.4 + - - +
178X VAL* 4.1 1.9 - - - +
186X LEU* 4.6 0.9 - - - -
197X PHE* 3.1 16.8 - - + +
198X PRO 4.1 1.8 - - - +
199X VAL* 3.7 31.4 - - + +
209X ILE* 4.1 11.7 - - + -
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Residues in contact with GLY 177 (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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147X THR 3.3 6.5 - - - -
175X CYS 4.0 1.4 - - - -
176X VAL* 1.3 71.9 - - - +
178X VAL* 1.3 59.9 + - - -
179X LEU 4.3 0.7 + - - -
181X PHE* 3.4 35.1 - - - -
186X LEU* 3.8 8.6 - - - +
197X PHE 2.8 13.9 + - - -
199X VAL* 2.9 28.6 + - - +
200X LYS 4.6 0.3 + - - -
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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