Contacts of the strand formed by residues 157 - 163 (chain B) in PDB entry 5E0T
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 ALA 157 (chain B).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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155B GLY 3.5 0.6 - - - -
156B ASP* 1.3 88.4 + - - +
158B VAL* 1.3 59.9 + - - +
159B VAL* 5.6 1.2 - - - +
170B SER 3.7 1.6 - - - +
171B ALA* 3.4 23.6 - - - +
172B SER 4.7 1.4 + - - +
206B THR* 4.0 18.4 - - + -
207B PHE 3.2 11.9 - - - +
209B LEU* 3.8 4.0 - - - +
254B LYS* 4.0 19.5 - - + +
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Residues in contact with VAL 158 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
147B ILE* 5.9 0.2 - - + -
148B CYS* 6.0 0.2 - - - -
151B LEU* 3.8 21.3 - - + -
157B ALA* 1.3 75.3 - - - +
159B VAL* 1.3 69.8 + - - +
160B ILE* 3.7 6.6 + - + -
169B PHE* 3.9 15.9 - - + -
170B SER 3.1 17.5 - - - +
205B LEU 3.8 0.2 - - - +
206B THR* 3.4 1.5 - - - -
207B PHE* 2.8 43.1 + - + +
209B LEU* 3.6 21.0 - - + +
212B LEU* 3.5 31.6 - - + -
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Residues in contact with VAL 159 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
157B ALA 5.6 1.1 - - - +
158B VAL* 1.3 73.8 - - - +
160B ILE* 1.3 59.9 + - - +
161B SER* 3.9 7.2 + - - +
168B LYS 3.4 6.1 - - - +
169B PHE* 3.4 0.9 - - - -
170B SER* 2.7 51.7 + - - +
204B GLN* 3.9 29.2 - - + +
205B LEU 3.4 9.9 - - - +
206B THR* 3.3 23.6 - - + +
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Residues in contact with ILE 160 (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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144B PHE* 5.7 1.8 - - + -
158B VAL* 4.3 7.2 - - + +
159B VAL* 1.3 75.5 - - - +
161B SER* 1.3 60.9 + - - +
162B CYS 4.2 0.2 - - - -
167B VAL* 4.0 13.7 - - + -
168B LYS 3.5 3.4 - - - +
169B PHE* 4.0 36.1 - - + -
203B VAL 3.8 0.9 - - - +
204B GLN* 3.3 3.8 - - - +
205B LEU 2.8 36.2 + - - +
207B PHE* 3.7 28.9 - - + -
212B LEU* 4.8 11.4 - - + -
227B LEU* 5.2 5.6 - - + -
229B MET* 3.4 33.8 - - + +
235B LEU* 4.4 13.7 - - + -
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Residues in contact with SER 161 (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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159B VAL* 3.9 6.5 + - - +
160B ILE* 1.3 71.8 - - - +
162B CYS* 1.3 62.0 + - - +
163B ALA* 4.1 2.9 + - - +
166B GLY 4.0 0.7 - - - +
167B VAL* 3.4 6.6 - - - +
168B LYS* 2.9 52.5 + - - +
203B VAL 3.5 4.3 - - - -
204B GLN* 3.2 31.3 + - - +
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Residues in contact with CYS 162 (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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135B CYS* 3.3 42.8 - - + -
137B VAL* 4.5 7.0 - - - -
160B ILE 4.2 0.6 - - - -
161B SER* 1.3 73.7 - - - +
163B ALA* 1.3 63.9 + - - +
166B GLY 4.0 4.5 - - - -
167B VAL* 4.4 10.8 - - + -
197B ILE* 3.9 26.7 - - - -
199B MET* 4.0 7.0 - - - -
202B PRO* 3.4 7.4 - - - +
203B VAL* 2.8 36.3 + - + +
229B MET* 5.0 7.2 - - + -
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Residues in contact with ALA 163 (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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161B SER* 5.4 3.4 - - - +
162B CYS* 1.3 74.5 - - - +
164B LYS* 1.3 66.4 + - + +
165B ASP* 2.7 12.3 + - - -
166B GLY 3.3 17.4 + - - +
199B MET* 3.4 23.3 - - - +
202B PRO* 4.7 3.6 - - + -
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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