Contacts of the strand formed by residues 226 - 234 (chain I) in PDB entry 1M8V
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 GLU 226 (chain I).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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218I LEU* 4.0 28.0 - - + +
219I VAL 3.2 14.6 - - - +
220I ILE* 3.9 23.9 - - - +
221I LEU* 4.3 1.3 - - - +
224I GLY 3.7 14.9 - - - +
225I PHE* 1.3 79.8 - - - +
227I PHE* 1.3 66.3 + - - +
228I ARG* 5.6 1.1 + - - +
247I MET* 3.8 2.3 - - - -
248I ILE* 2.8 48.3 + - + +
250I ASP 6.0 0.3 + - - -
347J MET* 6.1 0.2 - - - +
355J LYS* 4.8 13.3 + - - +
357J TYR* 5.0 1.9 + - - -
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Residues in contact with PHE 227 (chain I).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
120H ILE* 5.2 1.3 - - + -
168H LEU* 4.6 10.3 - - + -
169H ALA* 5.3 0.4 - - + -
217I VAL 4.0 0.2 - - - +
218I LEU* 3.5 6.5 - - - +
219I VAL* 2.7 36.3 + - + +
221I LEU* 3.3 36.1 - - + -
225I PHE* 3.9 4.7 - + - -
226I GLU* 1.3 75.6 - - - +
228I ARG* 1.3 59.7 + - - +
242I LEU* 3.8 18.8 - - + -
245I ALA* 4.7 9.9 - - + -
246I GLU 3.4 14.8 - - - -
247I MET* 3.6 42.2 - - + -
248I ILE* 4.9 0.7 - - - -
257I TYR* 3.6 17.5 - + - -
260I ILE* 4.1 16.6 - - + -
262I ILE* 3.9 22.2 - - + -
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Residues in contact with ARG 228 (chain I).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
216I ASP* 5.9 4.3 - - + -
217I VAL 3.4 11.7 - - - +
218I LEU* 3.7 27.4 - - + +
226I GLU* 5.6 1.0 + - - +
227I PHE* 1.3 75.1 - - - +
229I GLY* 1.3 59.7 + - - +
242I LEU* 4.9 2.7 - - - -
244I ASP 3.9 1.4 - - - +
245I ALA* 3.4 2.3 - - - -
246I GLU* 2.9 47.7 + - - +
248I ILE* 3.1 35.7 - - + +
273I THR* 4.2 21.6 + - + +
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Residues in contact with GLY 229 (chain I).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
216I ASP* 3.4 8.4 - - - -
217I VAL* 2.9 33.8 + - - +
227I PHE 4.3 0.2 - - - -
228I ARG* 1.3 76.7 - - - +
230I ARG* 1.3 63.1 + - - -
231I LEU 3.7 0.5 + - - -
242I LEU* 4.4 12.2 - - - +
243I ALA 3.8 1.8 - - - -
244I ASP 3.8 14.1 - - - -
245I ALA* 4.4 2.9 - - - -
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Residues in contact with ARG 230 (chain I).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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214I ASP* 3.0 54.5 + - - -
215I LYS* 3.4 5.8 - - - +
216I ASP* 4.0 12.0 + - - +
229I GLY* 1.3 71.7 - - - -
231I LEU* 1.3 61.4 + - - +
232I ILE* 3.2 26.6 + - - +
242I LEU* 3.2 5.1 - - - -
243I ALA* 2.8 51.8 + - + +
244I ASP* 3.6 22.3 + - + +
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Residues in contact with LEU 231 (chain I).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
209I ILE* 3.5 42.2 - - + +
212I SER* 3.6 22.9 - - - +
213I LEU* 3.4 9.3 - - + +
214I ASP* 2.4 36.0 + - - -
215I LYS 2.9 11.0 + - - +
217I VAL* 4.1 15.0 - - + -
229I GLY 3.7 2.8 + - - -
230I ARG* 1.3 68.5 - - - +
232I ILE* 1.3 57.2 + - - +
233I GLY 3.0 31.6 - - - +
234I TYR* 4.6 0.2 - - + -
240I VAL* 3.9 17.9 - - + -
241I VAL 3.4 10.5 - - - +
242I LEU* 4.2 7.6 - - + +
270I ILE* 5.7 4.9 - - + -
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Residues in contact with ILE 232 (chain I).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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103H GLU* 2.8 37.6 - - + +
213I LEU* 3.8 7.5 - - - +
214I ASP* 4.6 2.2 - - + +
230I ARG* 3.2 38.1 - - - +
231I LEU* 1.3 77.9 - - - +
233I GLY* 1.3 55.6 - - - +
241I VAL* 2.8 43.9 + - + +
243I ALA* 3.8 22.4 - - + +
259I LYS* 3.8 24.0 - - + +
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Residues in contact with GLY 233 (chain I).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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103H GLU* 3.4 16.6 - - - -
105H PRO* 4.4 0.2 - - - -
213I LEU* 3.8 4.0 - - - +
231I LEU* 3.0 15.0 - - - +
232I ILE* 1.3 81.5 - - - +
234I TYR* 1.3 65.5 + - - +
241I VAL* 2.9 26.5 + - - -
1R U 3.6 11.7 - - - -
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Residues in contact with TYR 234 (chain I).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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104H ARG* 4.2 3.6 - - - +
105H PRO* 3.7 15.2 - - - +
206I LEU* 4.7 19.5 - - + -
209I ILE* 3.8 23.3 - - + -
210I HIS* 2.5 54.1 + - + +
213I LEU* 4.0 13.7 - - + -
231I LEU* 4.6 1.3 - - + -
233I GLY* 1.3 79.1 - - - +
235I ASP* 1.3 74.7 + - - +
238I LEU* 5.5 1.8 - - + -
239I ASN 3.1 15.9 - - - +
240I VAL* 4.0 11.0 - - + -
1R U 2.7 71.8 + + + +
2R U 4.2 1.9 + - - -
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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