Contacts of the strand formed by residues 233 - 242 (chain E) in PDB entry 5AJI
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 233 (chain E).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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190E ILE 3.6 1.0 - - - +
191E GLY* 3.2 2.4 - - - -
192E VAL* 2.8 42.7 + - + +
193E ALA 4.6 1.6 - - - +
194E TYR* 3.2 58.3 - - + +
196E SER* 6.2 0.2 - - - -
198E ILE* 5.8 5.4 - - + -
225E LEU* 3.4 17.0 - - + -
227E GLU 3.7 3.8 - - - -
228E LEU* 4.1 18.2 - - + -
232E SER* 1.3 71.3 - - - +
234E ASN* 1.3 60.2 + - - +
235E PHE* 3.1 35.9 - - + -
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Residues in contact with ASN 234 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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189E ILE* 4.2 20.3 - - + +
190E ILE 3.3 4.3 - - - +
191E GLY* 3.4 8.3 - - - -
225E LEU* 3.8 1.6 - - - +
226E ASN* 2.8 35.7 + - + +
227E GLU* 2.9 54.1 + - + +
229E GLY* 4.5 4.2 - - - -
232E SER* 2.8 31.7 + - - -
233E ILE* 1.3 75.2 - - - +
235E PHE* 1.3 55.4 + - - +
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Residues in contact with PHE 235 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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188E PHE 3.6 0.7 - - - +
189E ILE* 3.3 6.3 - - - -
190E ILE* 2.7 42.7 + - + +
192E VAL* 3.7 15.7 - - + -
196E SER* 5.7 0.4 - - - -
198E ILE* 4.2 22.0 - - + -
201E VAL* 3.3 39.0 - - + -
202E LYS* 4.1 20.0 - - + -
205E LEU* 4.2 19.5 - - + -
223E VAL* 5.3 0.2 - - + -
224E ARG* 3.2 20.0 - - - +
225E LEU* 3.5 22.0 - - + -
226E ASN* 4.5 0.9 - - - -
233E ILE* 3.1 30.3 - - + -
234E ASN* 1.3 72.5 - - - +
236E VAL* 1.3 61.4 + - - +
237E VAL* 4.1 0.4 + - - -
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Residues in contact with VAL 236 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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187E GLU* 3.8 14.1 - - + -
188E PHE 3.4 9.4 - - - +
189E ILE* 4.3 7.0 - - + -
222E THR* 3.9 11.6 - - + +
223E VAL* 3.4 1.6 - - - +
224E ARG* 2.9 49.6 + - + +
226E ASN* 3.9 32.0 - - + +
235E PHE* 1.3 74.7 - - - +
237E VAL* 1.3 67.3 + - - +
238E ARG* 3.6 38.1 - - + +
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Residues in contact with VAL 237 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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187E GLU* 3.3 4.2 - - - -
188E PHE* 2.8 60.1 + - + +
190E ILE* 4.7 8.3 - - + -
205E LEU* 3.8 37.5 - - + -
209E ILE* 4.1 26.5 - - + -
222E THR 3.2 10.5 - - - +
223E VAL* 4.1 11.4 - - + -
235E PHE 4.9 0.7 - - - +
236E VAL* 1.3 80.4 - - - +
238E ARG* 1.3 64.2 + - - +
239E VAL* 4.3 6.5 - - + -
253E VAL* 5.9 0.7 - - + -
257E ILE* 5.6 1.3 - - + -
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Residues in contact with ARG 238 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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185E ARG* 3.8 30.4 - - - +
186E ASN 3.3 2.7 - - - -
187E GLU* 2.7 41.0 + - + +
220E GLU* 3.4 29.5 + - - +
221E MET* 3.4 3.6 + - - -
222E THR* 2.9 40.5 + - - +
226E ASN* 5.2 6.7 + - - +
236E VAL* 3.6 21.9 - - + +
237E VAL* 1.3 78.6 - - - +
239E VAL* 1.3 64.7 + - - +
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Residues in contact with VAL 239 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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185E ARG* 4.1 3.1 - - - +
186E ASN* 3.1 31.1 + - + +
188E PHE* 3.8 28.7 - - + -
209E ILE* 3.7 34.8 - - + -
215E ILE* 3.8 35.4 - - + -
220E GLU 4.0 4.9 - - - -
221E MET* 4.2 7.4 - - + -
237E VAL* 4.3 4.3 - - + -
238E ARG* 1.3 81.4 - - - +
240E TRP* 1.3 64.6 + - - +
241E SER* 4.0 2.8 + - - -
249E VAL* 5.4 1.3 - - + -
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Residues in contact with TRP 240 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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183E VAL* 3.7 28.9 - - + -
184E ARG* 3.3 28.3 - - - -
185E ARG* 3.5 33.3 - - + +
215E ILE* 3.5 5.7 - - - +
216E LEU* 2.9 28.9 + - + -
219E ARG* 3.8 42.8 - - + +
220E GLU* 3.2 48.1 + - + +
239E VAL* 1.3 70.6 - - - +
241E SER* 1.3 66.0 + - - +
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Residues in contact with SER 241 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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183E VAL* 3.4 3.2 - - - +
184E ARG 2.9 30.2 + - - +
186E ASN* 4.0 9.5 + - - -
214E ARG 3.3 16.2 + - - -
215E ILE* 4.4 2.1 - - - +
216E LEU* 3.5 13.9 - - - -
239E VAL 4.0 1.9 + - - -
240E TRP* 1.3 76.5 + - - +
242E ASN* 1.3 68.3 + - - +
245E ASP* 4.1 2.0 - - - -
246E LEU* 4.5 8.9 - - - +
249E VAL* 3.8 31.9 - - - +
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Residues in contact with ASN 242 (chain E).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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182E PRO* 3.4 9.5 - - - +
183E VAL* 4.0 13.9 - - - +
214E ARG 4.4 0.4 + - - -
216E LEU* 3.9 16.8 - - - +
241E SER* 1.3 76.2 - - - +
243E SER* 1.3 66.8 + - - +
244E GLY* 3.2 4.9 - - - +
245E ASP* 2.8 34.5 + - - +
246E LEU* 3.1 10.8 + - - -
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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