Contacts of the strand formed by residues 203 - 208 (chain B) in PDB entry 1JLH
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 203 (chain B).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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148B ILE* 4.2 1.1 - - - -
150B ASP* 3.3 8.1 + - - +
152B ILE* 3.7 16.8 - - - -
198B LEU* 3.4 26.9 - - - +
199B ASN 2.9 21.5 + - - -
200B PRO 3.9 3.4 + - - +
201B GLU 3.8 1.2 - - - -
202B SER* 1.3 78.4 + - - +
204B LEU* 1.3 60.7 + - - +
205B PHE* 4.2 16.6 + - - -
227B TRP* 4.7 2.2 - - - -
241B HIS* 2.9 28.4 + - - +
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Residues in contact with LEU 204 (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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131B PHE* 3.7 30.1 - - + -
135B VAL* 4.2 21.1 - - + -
140B TRP* 4.5 5.4 - - + +
148B ILE* 3.7 20.2 - - + -
150B ASP 2.8 9.2 + - - +
151B VAL* 3.2 9.0 - - + +
152B ILE* 2.7 30.7 + - - -
203B SER* 1.3 74.6 - - - +
205B PHE* 1.3 61.0 + - - +
206B ILE* 5.0 2.0 - - + -
240B LYS 4.1 8.1 - - - +
241B HIS* 3.6 27.8 - - - +
242B PHE 4.1 1.8 - - - +
243B VAL* 4.2 20.0 - - + -
285B LEU* 4.5 11.4 - - + -
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Residues in contact with PHE 205 (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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152B ILE* 3.4 43.7 - - + +
154B ILE* 3.9 13.5 - - + -
195B LEU* 3.9 17.9 - - + -
198B LEU* 4.4 0.9 - - + -
203B SER* 4.2 15.0 - - - -
204B LEU* 1.3 75.9 - - - +
206B ILE* 1.3 63.0 + - - +
207B ILE* 4.0 6.7 - - + -
224B ALA* 3.8 14.8 - - + -
227B TRP* 3.6 34.5 - + - -
228B PHE* 5.1 3.8 - + + -
241B HIS 2.7 18.7 + - - -
242B PHE* 3.4 41.2 - + + -
243B VAL* 2.9 30.0 + - - +
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Residues in contact with ILE 206 (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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151B VAL* 3.5 31.0 - - + -
152B ILE 2.8 10.4 + - - +
153B ASN* 3.6 12.9 + - - +
154B ILE* 2.8 29.8 + - - +
204B LEU* 4.8 2.9 - - + +
205B PHE* 1.3 76.2 - - - +
207B ILE* 1.3 62.6 + - - +
208B ALA 3.5 0.7 + - - -
243B VAL* 3.6 17.0 - - + -
245B LEU* 3.5 42.8 - - + -
281B LEU* 4.2 5.2 - - + -
282B SER* 4.0 21.1 - - - +
285B LEU* 3.6 21.3 - - + -
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Residues in contact with ILE 207 (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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154B ILE* 3.8 20.9 - - + -
205B PHE* 4.3 2.9 - - + +
206B ILE* 1.3 78.1 - - - +
208B ALA* 1.3 60.6 + - - +
209B SER* 3.5 2.1 + - - -
212B PHE* 3.4 38.2 - - + -
217B THR* 4.0 17.3 - - + -
218B ILE* 4.5 3.4 - - + -
221B ALA* 3.7 33.9 - - + -
242B PHE* 4.2 21.3 - - + -
243B VAL 2.9 16.7 + - - +
244B ALA* 3.4 1.2 - - - -
245B LEU* 2.8 25.0 + - - -
255B PHE* 4.7 1.8 - - + -
257B ILE* 4.4 7.2 - - + -
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Residues in contact with ALA 208 (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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153B ASN* 4.5 6.5 - - - +
154B ILE 3.0 16.0 + - - +
155B GLY* 3.8 2.1 - - - -
156B ILE 4.9 0.2 + - - -
159B SER* 3.6 40.7 + - - +
206B ILE 3.5 1.2 + - - -
207B ILE* 1.3 69.3 - - - +
209B SER* 1.3 64.4 + - - +
217B THR* 3.6 12.5 + - - +
245B LEU* 3.8 27.4 - - + -
279B ILE* 4.0 6.3 - - + -
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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