Contacts of the strand formed by residues 203 - 208 (chain C) 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 C).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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148C ILE* 4.3 1.3 - - - -
150C ASP* 3.5 8.3 + - - +
152C ILE* 4.1 10.6 - - - +
198C LEU* 3.6 19.6 - - - +
199C ASN 2.9 21.7 + - - -
200C PRO* 3.8 6.0 + - - +
201C GLU 3.8 1.2 - - - -
202C SER* 1.3 80.1 + - - +
204C LEU* 1.3 60.8 + - - +
205C PHE* 3.7 24.9 - - - -
227C TRP* 4.7 1.1 - - - -
228C PHE* 5.4 0.2 - - - -
241C HIS* 2.7 34.3 + - - +
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Residues in contact with LEU 204 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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131C PHE* 3.7 31.4 - - + -
135C VAL* 4.3 19.5 - - + -
140C TRP* 4.6 5.6 - - - +
148C ILE* 3.7 21.5 - - + +
150C ASP 2.9 9.6 + - - +
151C VAL* 3.2 9.4 - - + +
152C ILE 2.8 24.9 + - - +
203C SER* 1.3 72.5 - - - +
205C PHE* 1.3 66.9 + - - +
206C ILE* 4.9 4.3 - - + -
240C LYS 4.2 7.0 - - - +
241C HIS* 3.6 27.1 - - - +
242C PHE 4.1 0.2 - - - +
243C VAL* 4.1 19.7 - - + -
285C LEU* 4.4 12.8 - - + -
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Residues in contact with PHE 205 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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152C ILE* 3.4 30.7 - - + +
154C ILE* 3.9 10.3 - - + -
191C ILE* 5.0 0.4 - - + -
195C LEU* 3.9 16.2 - - + -
198C LEU* 4.5 0.4 - - + -
203C SER* 3.7 23.1 - - - -
204C LEU* 1.3 77.0 - - - +
206C ILE* 1.3 59.9 + - - +
207C ILE* 4.0 6.0 - - + +
224C ALA* 3.7 25.8 - - + -
227C TRP* 3.4 38.6 - + - -
228C PHE* 5.4 2.5 - + - -
241C HIS 2.7 20.1 + - - +
242C PHE* 3.4 32.5 - + + -
243C VAL* 2.9 29.9 + - - +
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Residues in contact with ILE 206 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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151C VAL* 3.5 30.3 - - + -
152C ILE 2.8 11.0 + - - +
153C ASN* 3.6 12.0 + - - +
154C ILE* 2.8 28.9 + - - +
204C LEU* 4.8 3.1 - - + +
205C PHE* 1.3 72.7 - - - +
207C ILE* 1.3 61.9 + - - +
208C ALA 3.4 2.1 + - - -
243C VAL* 3.6 18.4 - - + -
245C LEU* 3.5 42.2 - - + -
281C LEU* 4.0 9.9 - - + -
282C SER* 4.0 17.5 - - - +
285C LEU* 3.6 21.8 - - + -
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Residues in contact with ILE 207 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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154C ILE* 3.7 13.5 - - + -
205C PHE* 4.0 15.0 - - + +
206C ILE* 1.3 76.5 - - - +
208C ALA* 1.3 60.2 + - - +
209C SER* 3.5 2.7 + - - -
212C PHE* 3.2 34.9 - - + -
217C THR* 4.0 19.5 - - + -
218C ILE* 4.4 4.5 - - + -
221C ALA* 3.6 27.4 - - + -
242C PHE* 3.8 28.9 - - + -
243C VAL 3.0 13.8 + - - +
244C ALA* 3.5 2.9 - - - +
245C LEU 3.0 23.6 + - - -
255C PHE* 4.7 5.6 - - + -
257C ILE* 5.1 0.7 - - + -
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Residues in contact with ALA 208 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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153C ASN* 4.4 7.6 - - - +
154C ILE 2.9 16.5 + - - +
155C GLY* 3.8 1.6 - - - -
156C ILE 4.8 0.2 + - - -
159C SER* 3.6 42.4 + - - +
206C ILE 3.4 0.8 + - - -
207C ILE* 1.3 68.9 - - - +
209C SER* 1.3 63.6 + - - +
217C THR* 3.6 11.8 + - - +
245C LEU* 3.8 28.3 - - + -
279C ILE* 4.0 5.8 - - + -
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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