Contacts of the strand formed by residues 174 - 180 (chain B) in PDB entry 5F0L
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 LEU 174 (chain B).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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169B GLY* 3.1 4.3 - - - -
170B ILE* 2.8 38.0 + - + +
173B CYS* 1.3 82.4 - - + +
175B HIS* 1.3 64.1 + - - +
176B ILE* 4.3 17.7 - - + -
197B PHE* 4.6 0.4 - - + -
199B LEU* 3.3 13.7 - - - +
200B VAL* 4.2 9.4 - - + -
202B ILE* 4.2 23.6 - - + -
204B ILE* 3.7 25.6 - - + -
278B LEU* 4.0 23.6 - - + -
286B TYR* 4.7 7.4 - - + -
557D LEU* 4.1 23.3 - - + -
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Residues in contact with HIS 175 (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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167B GLU* 5.7 3.8 - - + +
168B VAL 3.6 4.7 - - - +
170B ILE 3.9 2.0 - - - -
171B GLU* 3.9 12.4 + - - -
172B ASP* 3.8 20.4 + - - -
174B LEU* 1.3 83.6 - - - +
176B ILE* 1.3 67.3 + - - +
197B PHE* 4.1 0.2 - - - -
198B LEU* 3.0 42.5 + - + +
199B LEU* 3.0 43.2 + - + +
560D MET* 3.5 32.2 - - + +
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Residues in contact with ILE 176 (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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166B MET 3.8 0.2 - - - +
167B GLU* 3.4 6.4 - - - +
168B VAL* 2.9 57.5 + - + +
169B GLY* 5.4 0.2 - - - -
174B LEU* 4.3 14.1 - - + -
175B HIS* 1.3 79.5 - - - +
177B GLU* 1.3 61.1 + - - +
178B PHE* 4.8 4.0 - - + -
195B ILE* 4.4 10.8 - - + -
196B TYR 3.4 8.3 - - - +
197B PHE* 3.5 35.9 - - + -
198B LEU* 4.1 5.4 - - - +
276B LEU* 3.9 28.0 - - + -
278B LEU* 4.2 15.7 - - + -
557D LEU* 4.4 7.0 - - + -
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Residues in contact with GLU 177 (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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165B LYS* 3.8 31.2 + - + +
166B MET 3.4 11.2 - - - +
167B GLU* 4.3 17.1 + - + +
176B ILE* 1.3 74.1 - - - +
178B PHE* 1.3 66.9 + - - +
179B GLU* 5.7 0.9 - - + -
194B LYS* 3.8 2.6 + - - +
195B ILE* 3.7 1.1 - - - -
196B TYR* 2.8 47.1 + - + +
198B LEU* 4.2 13.9 - - + +
416B EDO 2.9 34.7 + - - -
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Residues in contact with PHE 178 (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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164B ILE* 4.0 12.3 - - + -
165B LYS* 3.4 3.1 - - - +
166B MET* 3.0 64.7 + - + -
168B VAL* 4.0 17.7 - - + -
176B ILE* 4.1 2.6 - - + +
177B GLU* 1.3 76.1 - - - +
179B GLU* 1.3 64.9 + - - +
180B TYR* 3.6 38.8 - + + +
194B LYS 3.3 4.5 - - - -
195B ILE* 3.4 26.2 - - + -
276B LEU* 4.1 13.9 - - + -
288B LYS* 3.8 24.9 - - + -
290B GLN* 3.7 23.1 - - + -
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Residues in contact with GLU 179 (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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163B SER* 3.7 16.5 + - - +
164B ILE 3.2 16.6 - - - +
165B LYS* 3.6 30.6 + - + +
177B GLU* 5.6 1.3 - - + +
178B PHE* 1.3 76.2 - - - +
180B TYR* 1.3 69.3 + - - +
181B ASN* 5.6 0.3 - - - -
193B GLY* 3.0 5.4 - - - -
194B LYS* 2.8 66.4 + - + +
11C LEU* 3.7 23.8 - - + +
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Residues in contact with TYR 180 (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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163B SER* 3.4 3.2 - - - -
164B ILE* 2.9 53.6 + - + +
178B PHE* 3.6 35.5 - + + -
179B GLU* 1.3 80.4 - - - +
181B ASN* 1.3 62.6 + - - +
182B LYS 3.2 6.5 + - - +
185B TYR* 3.6 13.2 - - + +
191B ILE* 4.3 15.5 - - + -
192B VAL 3.8 4.0 - - - -
193B GLY* 4.8 0.7 - - - -
195B ILE* 4.9 0.7 - - + -
209B LEU* 3.4 33.0 - - + +
248B ILE* 4.1 17.7 - - + -
274B LEU* 3.8 32.3 + - + -
276B LEU* 3.6 16.3 - - - +
288B LYS 4.8 1.2 + - - -
290B GLN* 4.1 9.4 - - + +
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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