Contacts of the strand formed by residues 236 - 241 (chain g) in PDB entry 5OA3
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 ILE 236 (chain g).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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196g ASN* 3.1 26.9 + - + +
197g THR* 6.0 0.4 - - - -
210g GLY* 3.9 11.2 - - - -
211g GLY 3.3 18.4 + - - +
214g GLY 4.2 13.0 - - - +
215g GLN 4.0 4.0 - - - -
216g ALA* 3.6 42.6 - - + +
233g GLY 5.5 0.7 - - - +
235g ILE* 1.3 78.2 - - - +
237g ASN* 1.3 59.1 + - - +
238g ALA 4.1 4.7 - - - +
239g LEU* 3.7 34.8 - - + -
250g ALA* 4.9 5.4 - - + -
251g ALA 3.4 11.0 - - - +
252g THR* 4.5 8.5 - - - +
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Residues in contact with ASN 237 (chain g).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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196g ASN* 3.4 19.2 - - - +
197g THR* 2.3 29.0 + - - -
235g ILE* 3.4 31.7 - - - +
236g ILE* 1.3 72.8 - - - +
238g ALA* 1.3 53.9 + - - +
251g ALA 2.7 11.6 + - - +
253g GLY* 3.8 21.3 + - - -
285g GLN* 4.2 5.1 + - - +
286g CYS 3.1 29.2 + - - +
287g THR* 3.7 13.4 - - - +
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Residues in contact with ALA 238 (chain g).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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20g GLN* 5.1 7.2 - - - +
155g ARG* 5.9 0.4 - - - +
197g THR* 3.6 8.7 - - + +
236g ILE* 4.1 0.9 - - - +
237g ASN* 1.3 78.9 - - - +
239g LEU* 1.3 65.8 + - - +
249g CYS 4.0 0.4 - - - +
251g ALA* 2.9 32.8 + - + +
287g THR 4.0 1.3 - - - +
288g SER* 3.5 17.0 - - - +
289g LEU* 3.4 33.9 - - + +
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Residues in contact with LEU 239 (chain g).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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155g ARG* 4.5 7.1 + - - -
197g THR* 3.7 21.4 - - - +
199g THR* 2.4 35.9 + - - +
208g ALA* 4.0 7.4 - - + +
209g SER* 3.6 11.7 - - - +
210g GLY* 3.5 28.3 - - - +
216g ALA* 4.8 10.1 - - + -
236g ILE* 3.7 16.8 - - + -
238g ALA* 1.3 79.0 - - - +
240g CYS* 1.3 60.2 + - - +
248g LEU* 4.0 20.0 - - + -
249g CYS 3.2 7.2 - - - +
250g ALA* 3.6 32.1 - - + -
289g LEU* 5.2 1.3 - - - -
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Residues in contact with CYS 240 (chain g).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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155g ARG* 6.2 0.4 - - - +
199g THR* 3.9 5.4 - - + -
239g LEU* 1.3 77.6 - - - +
241g PHE* 1.3 64.2 + - - +
242g SER 3.9 0.9 + - - -
247g TRP 3.9 0.2 - - - +
248g LEU* 4.7 0.9 - - - +
249g CYS* 2.9 52.3 + - - +
289g LEU* 3.9 30.3 - - - +
290g ALA* 4.2 0.9 - - - -
291g TRP* 3.9 35.2 - - + +
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Residues in contact with PHE 241 (chain g).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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199g THR* 3.8 18.0 - - + +
200g VAL 5.2 0.2 - - - +
201g SER* 3.9 39.7 - - - +
202g PRO* 4.6 5.1 - - + +
206g LEU* 3.9 17.7 - - + -
208g ALA* 3.5 29.8 - - + -
218g LEU* 3.4 25.6 - - + -
240g CYS* 1.3 74.9 - - - +
242g SER* 1.3 65.4 + - - +
243g PRO* 3.7 5.7 - - - +
246g TYR* 5.7 3.1 - + - -
247g TRP 3.9 7.2 - - - -
248g LEU* 3.5 25.6 - - + -
261g LEU* 3.4 24.5 - - + -
291g TRP* 4.3 8.1 - - - +
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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