Contacts of the strand formed by residues 229 - 236 (chain D) in PDB entry 1JXQ
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 CYS 229 (chain D).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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155D LEU* 5.0 4.3 - - + -
162D CYS* 3.1 10.8 + - - +
163D GLY* 3.1 26.5 - - - -
164D HIS 3.6 1.2 + - - -
198D PHE* 3.6 27.7 - - + -
224D HIS* 5.3 0.9 + - - -
227D LEU* 3.8 2.9 - - - +
228D ASP* 1.3 81.1 - - + +
230D CYS* 1.3 78.9 + - - +
231D VAL* 4.4 1.1 - - - -
273D LEU* 4.5 5.2 - - - +
276D LYS* 4.9 2.7 - - - -
277D PRO* 3.2 30.1 - - + +
279D LEU* 4.1 17.7 - - - -
398D LEU* 4.4 4.5 - - - -
400D PHE* 5.3 0.9 - - - -
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Residues in contact with CYS 230 (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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164D HIS 3.5 8.3 - - - +
218D LEU* 3.6 33.9 - - - -
224D HIS* 4.2 7.9 - - + -
229D CYS* 1.3 77.0 - - - +
231D VAL* 1.3 73.1 + - - +
232D VAL* 4.7 2.2 - - - -
265D PHE* 3.9 15.3 - - - -
273D LEU* 3.6 28.4 - - + +
277D PRO 3.3 8.0 + - - +
278D LYS* 4.7 5.6 - - + -
279D LEU 3.0 25.6 + - - -
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Residues in contact with VAL 231 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
164D HIS 2.9 7.1 + - - +
165D CYS* 3.0 32.4 - - + -
166D LEU 2.8 29.3 + - - -
193D PHE* 4.0 27.8 - - + -
198D PHE* 4.0 23.1 - - + -
218D LEU* 4.5 0.2 - - - +
229D CYS* 4.4 2.7 - - - -
230D CYS* 1.3 83.2 - - - +
232D VAL* 1.3 67.0 + - - +
233D VAL* 4.0 13.0 - - + -
279D LEU* 3.4 19.5 - - + -
281D PHE* 4.3 5.2 - - + -
400D PHE* 5.2 0.2 - - + -
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Residues in contact with VAL 232 (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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166D LEU* 3.3 10.8 - - + +
168D ILE* 5.5 0.4 - - + -
215D LEU* 3.9 22.0 - - + -
218D LEU* 4.1 9.0 - - + -
230D CYS* 4.7 2.5 - - - -
231D VAL* 1.3 79.8 - - - +
233D VAL* 1.3 66.9 + - - +
234D ILE* 4.2 18.6 - - + -
261D ILE* 4.9 1.1 - - + -
265D PHE* 3.9 32.8 - - + -
279D LEU 2.9 8.2 + - - +
280D PHE* 3.4 25.8 - - + -
281D PHE* 2.8 26.7 + - - +
282D ILE* 5.2 1.3 - - + +
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Residues in contact with VAL 233 (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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166D LEU 2.7 12.7 + - - +
167D ILE* 3.3 18.5 - - + -
168D ILE* 2.6 33.1 + - - +
189D LEU* 3.9 26.7 - - + -
193D PHE* 3.8 31.6 - - + -
231D VAL* 4.0 8.5 - - + -
232D VAL* 1.3 80.4 - - - +
234D ILE* 1.3 63.0 + - - +
235D LEU* 3.9 12.6 - - + -
281D PHE* 3.2 22.0 - - + +
283D GLN 6.1 0.2 - - - +
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Residues in contact with ILE 234 (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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168D ILE* 3.4 22.7 - - + +
211D MET* 3.8 29.2 - - + -
215D LEU* 5.1 4.9 - - + -
232D VAL* 4.2 15.9 - - + -
233D VAL* 1.3 82.0 - - - +
235D LEU* 1.3 72.5 + - - +
236D SER* 4.1 2.8 + - - -
243D VAL* 4.0 19.2 - - + +
261D ILE* 3.8 30.7 - - + -
281D PHE 3.0 6.7 + - - +
282D ILE* 3.8 17.1 - - + +
283D GLN 3.2 26.5 + - - +
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Residues in contact with LEU 235 (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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167D ILE* 4.6 5.4 - - + -
168D ILE 2.8 14.8 + - - +
169D ASN* 3.9 10.5 - - + +
170D ASN* 2.9 29.3 + - - +
179D ARG* 3.3 17.7 - - - +
182D SER* 3.7 16.8 - - - +
185D ASP* 4.1 9.9 - - + +
186D CYS* 3.8 34.1 - - + +
189D LEU* 4.1 11.7 - - + -
233D VAL* 3.9 18.8 - - + -
234D ILE* 1.3 79.8 - - - +
236D SER* 1.3 63.1 + - - +
283D GLN* 3.7 23.3 - - + +
350D VAL* 5.3 0.9 - - + -
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Residues in contact with SER 236 (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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170D ASN* 3.3 17.0 - - - +
173D PHE* 3.3 5.2 - - - -
179D ARG* 3.3 20.4 + - - +
234D ILE* 4.0 12.2 - - - +
235D LEU* 1.3 77.9 - - - +
237D HIS* 1.3 71.4 + - - +
243D VAL* 4.5 6.1 - - - +
244D TYR 2.5 29.5 + - - -
283D GLN 3.4 5.1 + - - -
284D ALA* 3.2 5.4 - - - -
285D CYS 3.0 23.4 + - - -
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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
------------------------------------------------------------
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