Contacts of the strand formed by residues 203 - 208 (chain D) 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 D).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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148D ILE* 4.0 1.7 - - - +
150D ASP* 3.5 9.8 + - - +
152D ILE* 3.8 16.2 - - - +
198D LEU* 3.4 22.3 - - - +
199D ASN 2.9 21.5 + - - -
200D PRO 3.7 4.2 + - - +
201D GLU 3.7 0.4 - - - -
202D SER* 1.3 79.8 + - - +
204D LEU* 1.3 60.3 + - - +
205D PHE* 4.0 17.0 - - - -
227D TRP* 4.5 2.2 - - - -
241D HIS* 2.7 33.1 + - - +
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Residues in contact with LEU 204 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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131D PHE* 3.7 29.6 - - + -
135D VAL* 4.3 18.4 - - + -
140D TRP* 4.1 10.1 - - + +
148D ILE* 3.7 19.7 - - + +
150D ASP 2.9 7.4 + - - +
151D VAL* 3.4 14.0 - - + +
152D ILE* 2.8 25.9 + - - +
203D SER* 1.3 74.7 - - - +
205D PHE* 1.3 65.6 - - - +
206D ILE* 4.1 2.2 + - + -
240D LYS 4.0 8.5 - - - +
241D HIS* 3.5 27.1 - - - -
242D PHE 4.1 2.0 - - - +
243D VAL* 4.3 18.8 - - + -
285D LEU* 4.7 4.7 - - + -
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Residues in contact with PHE 205 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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152D ILE* 3.4 39.3 - - + +
154D ILE* 4.1 7.2 - - + -
191D ILE* 5.1 0.2 - - + -
195D LEU* 3.9 15.7 - - + -
203D SER* 4.0 15.9 - - - -
204D LEU* 1.3 74.5 - - - +
206D ILE* 1.3 62.7 + - - +
207D ILE* 3.9 6.7 + - + -
224D ALA* 3.8 22.7 - - + -
227D TRP* 3.3 39.5 - + - -
228D PHE* 5.1 4.0 - + + -
241D HIS 2.7 21.6 + - - +
242D PHE* 3.5 36.1 - + + +
243D VAL* 2.9 30.7 + - - +
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Residues in contact with ILE 206 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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151D VAL* 3.4 32.3 - - + -
152D ILE 2.8 11.0 + - - +
153D ASN* 3.6 12.8 + - + +
154D ILE 2.8 30.7 + - - +
204D LEU* 4.8 3.1 - - + +
205D PHE* 1.3 73.9 - - - +
207D ILE* 1.3 61.1 + - - +
208D ALA 3.4 0.9 + - - -
243D VAL* 3.7 16.2 - - + -
245D LEU* 3.5 43.3 - - + -
281D LEU* 4.4 3.4 - - + -
282D SER* 4.0 20.4 - - - +
285D LEU* 3.4 22.4 - - + -
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Residues in contact with ILE 207 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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154D ILE* 3.8 22.7 - - + -
205D PHE* 4.3 4.3 - - + +
206D ILE* 1.3 75.7 - - - +
208D ALA* 1.3 59.4 + - - +
209D SER 3.6 1.9 + - - -
212D PHE* 3.4 31.8 - - + -
217D THR* 4.1 16.4 - - + -
218D ILE* 4.3 3.6 - - + -
221D ALA* 3.7 34.3 - - + -
242D PHE* 4.2 25.6 - - + -
243D VAL 2.9 17.6 + - - +
244D ALA* 3.4 1.9 - - - -
245D LEU* 2.8 26.0 + - - +
255D PHE* 4.9 1.6 - - + -
257D ILE* 4.4 8.1 - - + -
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Residues in contact with ALA 208 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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153D ASN* 4.6 6.5 - - - +
154D ILE 2.9 17.2 + - - +
155D GLY* 3.9 2.1 - - - -
156D ILE 4.8 0.2 + - - -
159D SER* 3.6 42.2 + - - +
206D ILE 3.4 0.6 + - - -
207D ILE* 1.3 70.4 - - - +
209D SER* 1.3 62.3 - - - +
217D THR* 3.7 11.7 + - - +
245D LEU* 3.8 26.9 - - + -
279D ILE* 5.2 4.5 - - + -
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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