Contacts of the strand formed by residues 233 - 242 (chain D) 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 D).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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190D ILE 3.6 1.0 - - - +
191D GLY* 3.2 2.3 - - - -
192D VAL* 2.8 42.0 + - + +
193D ALA 4.6 1.3 - - - +
194D TYR* 3.2 57.0 - - + -
198D ILE* 5.8 3.1 - - + -
225D LEU* 3.4 15.0 - - + -
227D GLU 3.7 3.4 - - - -
228D LEU* 4.1 12.8 - - + -
232D SER* 1.3 71.2 - - - +
234D ASN* 1.3 62.5 + - - +
235D PHE* 3.1 36.6 - - + -
258E LYS* 3.9 18.2 - - + +
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Residues in contact with ASN 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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189D ILE* 4.2 20.3 - - + +
190D ILE 3.3 3.8 - - - +
191D GLY* 3.4 8.5 - - - -
225D LEU* 3.8 1.4 - - - +
226D ASN* 2.8 34.9 + - + +
227D GLU* 2.9 57.1 + - + +
229D GLY* 4.5 4.0 - - - -
232D SER* 2.8 29.8 + - - -
233D ILE* 1.3 74.2 - - - +
235D PHE* 1.3 56.7 - - - +
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Residues in contact with PHE 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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188D PHE 3.6 0.5 - - - +
189D ILE* 3.4 5.6 - - - -
190D ILE* 2.7 43.8 + - + +
192D VAL* 3.7 16.4 - - + -
196D SER* 5.7 0.2 - - - -
198D ILE* 4.2 22.7 - - + -
201D VAL* 3.4 36.8 - - + -
202D LYS* 4.1 20.2 - - + -
205D LEU* 4.2 19.3 - - + -
224D ARG* 3.2 19.7 - - - +
225D LEU* 3.5 22.0 - - + -
226D ASN* 4.5 0.7 - - - -
233D ILE* 3.1 30.3 - - + -
234D ASN* 1.3 73.0 - - - +
236D VAL* 1.3 61.6 + - - +
237D VAL* 5.0 0.2 - - - -
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Residues in contact with VAL 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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187D GLU* 3.8 20.2 - - + -
188D PHE 3.4 4.0 - - - +
189D ILE* 4.3 6.5 - - + -
222D THR* 3.9 6.9 - - + +
223D VAL* 3.4 1.6 - - - +
224D ARG* 2.9 42.1 + - + +
226D ASN* 3.9 31.6 - - + +
235D PHE* 1.3 74.6 - - - +
237D VAL* 1.3 66.7 + - - +
238D ARG* 3.5 32.8 - - + +
251E TRP* 4.1 20.6 - - + +
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Residues in contact with VAL 237 (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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187D GLU* 3.3 3.6 - - - -
188D PHE* 2.8 59.4 + - + +
190D ILE* 4.7 8.7 - - + -
205D LEU* 3.8 37.9 - - + -
209D ILE* 4.1 25.6 - - + -
222D THR 3.2 10.1 - - - +
223D VAL* 4.1 11.7 - - + -
235D PHE 4.9 0.9 - - - +
236D VAL* 1.3 79.6 - - - +
238D ARG* 1.3 64.2 + - - +
239D VAL* 4.3 6.7 - - + -
253D VAL* 5.9 0.9 - - + -
257D ILE* 5.6 1.1 - - + -
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Residues in contact with ARG 238 (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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185D ARG* 3.8 30.0 - - - +
186D ASN 3.3 3.1 - - - -
187D GLU* 2.7 40.9 + - + +
220D GLU* 3.4 27.0 + - - +
221D MET* 3.5 3.8 + - - -
222D THR* 2.9 36.3 + - - -
226D ASN* 5.2 6.5 + - - +
236D VAL* 3.5 20.0 - - + +
237D VAL* 1.3 78.8 - - - +
239D VAL* 1.3 65.5 + - - +
247E GLN* 4.4 8.3 + - - +
251E TRP* 3.7 30.5 - - - -
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Residues in contact with VAL 239 (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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185D ARG* 4.1 3.2 - - - +
186D ASN* 3.1 31.4 + - + +
188D PHE* 3.8 29.4 - - + -
209D ILE* 3.7 34.5 - - + -
215D ILE* 3.8 36.3 - - + -
220D GLU 4.0 4.5 - - - -
221D MET* 4.2 7.0 - - + -
237D VAL* 4.3 5.2 - - + -
238D ARG* 1.3 81.2 - - - +
240D TRP* 1.3 64.4 + - - +
241D SER* 4.0 3.1 + - - -
249D VAL* 5.4 0.9 - - + -
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Residues in contact with TRP 240 (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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183D VAL* 3.7 28.3 - - + -
184D ARG* 3.3 27.6 - - - -
185D ARG* 3.4 18.0 - - + +
215D ILE* 3.4 6.0 - - - +
216D LEU* 2.9 28.7 + - + -
219D ARG* 3.8 42.6 - - + -
220D GLU* 3.2 47.6 + - + +
239D VAL* 1.3 71.3 - - - +
241D SER* 1.3 65.8 + - - +
156E ARG* 5.5 6.5 - - - -
157E THR 5.2 0.7 - - - -
158E ALA 3.4 26.9 - - - -
159E ASP 4.0 1.1 - - - -
160E GLY* 3.9 17.7 - - - -
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Residues in contact with SER 241 (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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183D VAL* 3.4 2.3 - - - +
184D ARG 2.9 29.8 + - - +
186D ASN* 4.0 9.4 + - - -
214D ARG 3.3 16.2 + - - -
215D ILE* 4.4 2.1 - - - +
216D LEU* 3.5 13.7 - - - -
239D VAL 4.0 2.6 + - - -
240D TRP* 1.3 76.9 + - - +
242D ASN* 1.3 68.8 + - - +
245D ASP* 4.1 0.9 - - - -
246D LEU* 4.5 9.3 - - - +
249D VAL* 3.8 31.8 - - - +
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Residues in contact with ASN 242 (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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182D PRO* 3.4 9.9 - - - +
183D VAL* 4.0 13.3 - - - +
214D ARG 4.4 0.8 + - - -
216D LEU* 3.9 17.1 - - - +
241D SER* 1.3 76.2 - - - +
243D SER* 1.3 67.2 + - - +
244D GLY 4.3 4.3 - - - +
245D ASP* 2.8 34.9 + - - +
246D LEU* 3.1 11.2 + - - -
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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