Contacts of the strand formed by residues 229 - 238 (chain D) in PDB entry 4BEI
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 THR 229 (chain D).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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189D ASP* 4.2 10.1 - - + +
190D LEU 3.5 17.0 - - - +
191D ASN* 4.2 11.3 - - + +
224D ILE* 4.9 2.2 - - - -
227D GLY 4.3 4.3 + - - -
228D ASP* 1.3 81.4 + - - +
230D TYR* 1.3 73.3 + - - +
231D SER* 3.6 16.7 + - - -
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Residues in contact with TYR 230 (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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96C VAL* 3.9 13.0 - - + +
188D VAL* 3.7 7.7 - - + +
189D ASP* 3.5 1.7 - - - -
190D LEU* 2.9 60.9 + - + +
202D PHE* 4.2 17.3 - + - -
220D GLU* 2.5 27.0 + - - -
222D TRP* 3.6 39.9 - + - -
224D ILE* 4.1 19.3 - - + +
229D THR* 1.3 70.3 - - - +
231D SER* 1.3 63.4 + - - +
232D LYS* 3.1 41.8 + - + +
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Residues in contact with SER 231 (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 VAL 3.3 3.6 - - - -
189D ASP* 2.6 25.4 + - - -
229D THR* 3.6 15.4 + - - -
230D TYR* 1.3 80.4 - - - +
232D LYS* 1.3 66.9 + - - +
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Residues in contact with LYS 232 (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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96C VAL* 3.5 15.1 - - + +
97C ASP 3.2 17.4 + - - -
187D THR* 3.7 3.1 - - - -
188D VAL* 2.8 47.5 + - + +
189D ASP* 5.3 0.2 - - - +
202D PHE* 4.6 3.8 - - - -
217D ASN* 3.0 31.0 - - - +
220D GLU* 3.2 16.8 + - - -
230D TYR* 3.1 31.1 + - + +
231D SER* 1.3 79.8 + - - +
233D VAL* 1.3 69.1 + - - +
234D ARG* 4.0 14.3 - - - +
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Residues in contact with VAL 233 (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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171D GLN* 3.9 16.8 - - - +
185D PRO* 4.0 15.0 - - + -
186D PHE 3.4 9.9 - - - +
187D THR* 4.4 13.0 - - + -
232D LYS* 1.3 86.4 - - - +
234D ARG* 1.3 69.3 + - - +
235D GLY 4.9 0.2 - - - +
1273D PEG 3.8 40.2 - - - +
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Residues in contact with ARG 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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97C ASP* 2.8 44.6 + - - -
98C THR* 3.5 15.2 + - - +
99C ALA* 2.7 30.5 + - - +
100C GLN* 3.2 16.9 + - - +
186D PHE* 2.8 43.5 + - - +
188D VAL* 4.4 10.3 - - + -
204D MET* 4.5 9.2 - - - +
216D VAL* 2.9 27.8 + - + +
217D ASN* 3.6 21.0 - - + +
232D LYS* 4.0 13.5 - - - +
233D VAL* 1.3 77.1 - - - +
235D GLY* 1.3 65.4 + - - +
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Residues in contact with GLY 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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100C GLN* 3.3 16.7 + - - +
183D PHE* 3.6 23.7 - - - -
184D VAL 3.4 12.1 - - - -
185D PRO* 3.7 4.5 - - - -
186D PHE* 4.8 0.2 - - - -
216D VAL* 4.5 5.7 - - - +
233D VAL* 4.3 1.6 - - - +
234D ARG* 1.3 90.4 + - - +
236D ILE* 1.3 61.3 + - - +
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Residues in contact with ILE 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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100C GLN* 4.7 1.8 - - - +
183D PHE* 3.5 5.3 - - - -
184D VAL 2.9 36.5 + - - +
186D PHE* 3.7 18.6 - - + -
206D ALA* 4.0 12.1 - - + -
214D ILE* 4.7 13.0 - - + -
215D PRO 5.6 0.2 - - - +
216D VAL* 4.0 32.1 - - + -
235D GLY* 1.3 74.1 - - - +
237D ASN* 1.3 70.9 + - - +
238D PHE* 3.6 43.9 + - + -
242D TYR* 4.9 4.7 - - + -
249D ILE* 4.4 5.4 - - + -
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Residues in contact with ASN 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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75C LYS* 5.5 4.0 - - - +
100C GLN* 3.6 26.0 + - + +
101C GLN* 5.9 2.0 + - - +
182D GLY* 3.5 17.1 + - - +
183D PHE* 3.9 15.9 - - + +
236D ILE* 1.3 75.0 - - - +
238D PHE* 1.3 62.2 + - - +
239D ASP* 3.0 25.8 + - - +
242D TYR* 3.4 16.1 + - - -
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Residues in contact with PHE 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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177D VAL* 3.8 24.7 - - + -
181D GLY* 3.1 4.2 - - - -
182D GLY 2.7 39.6 + - - +
184D VAL* 4.0 14.6 - - + -
236D ILE* 3.7 42.0 - - + -
237D ASN* 1.3 72.1 - - - +
239D ASP* 1.3 65.3 + - - +
242D TYR* 3.8 17.0 - + + -
247D TYR* 3.6 40.8 - + - -
249D ILE* 4.0 11.7 - - + -
268D VAL* 3.7 32.5 - - + -
270D LYS* 4.7 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