Contacts of the strand formed by residues 235 - 244 (chain C) in PDB entry 5PAO
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 ALA 235 (chain C).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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231C LEU* 3.2 5.5 - - - -
232C VAL* 2.9 39.2 + - + +
233C ASN* 3.3 4.4 + - + +
234C GLY* 1.3 76.6 - - - +
236C GLN* 1.3 67.4 + - - +
237C LEU 3.2 0.2 + - - -
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Residues in contact with GLN 236 (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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229C LEU* 4.1 17.9 - - + +
230C LEU 3.9 4.5 - - - -
231C LEU* 3.9 8.2 - - + +
232C VAL* 5.5 0.9 - - - +
234C GLY 4.0 0.8 + - - -
235C ALA* 1.3 75.2 - - - +
237C LEU* 1.3 62.1 + - - +
238C CYS 4.5 5.4 - - - +
273C LEU* 4.1 17.0 - - + +
344C TRP* 3.0 42.4 + - - +
345C GLY* 4.1 0.2 - - - -
353C THR* 4.1 16.9 + - - +
402C GLY* 3.5 23.5 + - - +
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Residues in contact with LEU 237 (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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230C LEU* 2.8 24.7 + - + +
232C VAL* 4.1 24.0 - - + +
235C ALA 3.2 1.0 + - - +
236C GLN* 1.3 78.0 - - - +
238C CYS* 1.3 73.2 + - + +
254C CYS* 3.5 30.3 - - + +
255C PHE* 4.1 11.7 - - + -
258C ILE* 4.2 11.7 - - + -
264C LEU* 3.8 27.8 - - + -
402C GLY* 5.0 6.3 - - - -
506C 7Z7 3.6 25.3 - - + -
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Residues in contact with CYS 238 (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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229C LEU* 3.9 7.8 - - - +
230C LEU* 2.9 32.5 + - + +
236C GLN* 4.5 2.0 - - - +
237C LEU* 1.3 90.0 - - + +
239C GLY* 1.3 66.3 + - - +
254C CYS* 2.0 56.3 - - + -
402C GLY 4.2 13.0 - - - -
404C SER* 3.2 13.5 - - - +
506C 7Z7 3.8 12.8 - - - -
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Residues in contact with GLY 239 (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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227C GLN* 3.9 9.9 - - - -
228C VAL 3.3 11.2 - - - -
229C LEU* 4.8 0.9 - - - -
230C LEU* 3.6 7.2 - - - +
238C CYS* 1.3 75.2 - - - +
240C GLY* 1.3 52.8 + - - -
250C SER* 2.8 27.2 + - - -
344C TRP* 5.8 1.8 - - - -
402C GLY 4.1 5.9 + - - -
403C ASP* 4.3 2.9 + - - -
404C SER 2.8 11.9 + - - +
405C GLY* 3.3 10.5 - - - -
406C GLY* 4.0 4.9 - - - -
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Residues in contact with GLY 240 (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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227C GLN* 3.8 0.9 + - - -
228C VAL* 2.9 38.9 + - - -
230C LEU* 5.1 0.4 - - - -
239C GLY* 1.3 73.5 - - - -
241C THR* 1.3 65.6 + - - -
248C VAL* 4.1 6.3 - - - -
249C VAL 3.3 7.0 - - - -
250C SER* 4.3 1.8 - - - -
405C GLY 3.1 13.2 + - - -
406C GLY* 3.9 1.8 - - - -
407C PRO* 3.7 10.4 - - - +
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Residues in contact with THR 241 (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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226C TRP* 3.5 8.1 - - + +
228C VAL* 3.9 3.4 - - - -
240C GLY* 1.3 71.7 - - - -
242C LEU* 1.3 73.4 + - - +
243C ILE* 3.5 7.9 + - + +
248C VAL* 3.2 3.7 - - - +
249C VAL* 2.8 40.7 + - - +
321C LEU* 3.7 32.8 - - + -
405C GLY 4.2 0.5 + - - -
406C GLY 3.9 1.4 - - - -
407C PRO* 3.1 34.8 - - + +
418C LEU* 4.0 15.9 - - + +
421C ILE* 6.0 0.9 - - - +
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Residues in contact with LEU 242 (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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226C TRP* 2.9 18.8 + - - +
228C VAL* 3.6 3.3 - - + +
241C THR* 1.3 74.3 - - - +
243C ILE* 1.3 60.2 + - - +
244C ASN 3.1 24.9 - - - +
245C THR 4.6 2.9 - - - +
247C TRP 3.7 8.1 - - - +
248C VAL* 4.0 13.7 - - + -
268C LEU* 3.9 26.9 - - + -
308C LEU* 4.6 2.9 - - + -
312C VAL* 3.9 28.7 - - + -
314C LEU* 4.3 5.2 - - + -
318C VAL* 4.1 6.7 - - + -
319C VAL 3.9 5.8 - - - -
320C PRO* 3.8 25.6 - - + -
321C LEU* 2.8 25.4 + - - +
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Residues in contact with ILE 243 (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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175A HIS* 5.5 4.5 + - - -
195A CYS* 5.4 1.9 - - - +
241C THR* 3.5 6.7 + - + +
242C LEU* 1.3 77.5 - - - +
244C ASN* 1.3 61.7 + - - +
247C TRP* 3.0 26.1 + - + +
249C VAL* 3.7 34.1 - - + -
305C LEU* 4.5 3.8 - - + -
320C PRO* 3.5 12.8 - - - +
321C LEU 3.6 19.6 - - - +
323C LEU* 4.2 26.4 + - + +
418C LEU* 4.1 17.0 - - + -
447C LEU* 5.2 1.3 - - + -
451C MET* 3.7 33.2 - - + -
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Residues in contact with ASN 244 (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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176A GLU* 5.3 10.7 + - - +
242C LEU* 3.1 22.6 - - - +
243C ILE* 1.3 78.1 - - + +
245C THR* 1.3 83.3 + - - +
246C ILE* 3.1 3.7 + - - +
247C TRP* 3.4 32.2 + - + -
320C PRO* 3.7 11.6 - - - +
451C MET* 5.2 5.2 - - - -
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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