Contacts of the strand formed by residues 229 - 238 (chain G) 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 G).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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189G ASP* 4.2 10.3 - - + +
190G LEU 3.5 17.7 - - - +
191G ASN* 4.0 16.0 + - + -
224G ILE* 4.9 2.2 - - - -
227G GLY 4.3 3.1 + - - -
228G ASP* 1.3 81.1 + - - +
230G TYR* 1.3 73.6 + - - +
231G SER* 3.5 16.7 + - - -
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Residues in contact with TYR 230 (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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188G VAL* 3.7 8.4 - - + +
189G ASP* 3.5 2.4 - - - -
190G LEU* 2.9 56.7 + - + -
202G PHE* 4.3 17.0 - + - -
220G GLU* 2.5 27.8 + - - -
222G TRP* 3.6 39.7 - + - -
224G ILE* 4.1 26.6 - - + +
229G THR* 1.3 70.1 - - - +
231G SER* 1.3 64.3 + - - +
232G LYS* 3.1 43.1 + - + +
96H VAL* 4.1 10.1 - - + +
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Residues in contact with SER 231 (chain G).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
188G VAL 3.4 3.1 - - - -
189G ASP* 2.6 24.8 + - - -
229G THR* 3.5 14.7 + - - -
230G TYR* 1.3 81.3 - - - +
232G LYS* 1.3 66.6 + - - +
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Residues in contact with LYS 232 (chain G).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
187G THR* 3.7 3.3 - - - +
188G VAL* 2.8 47.8 + - + +
189G ASP* 5.3 0.3 - - - +
202G PHE* 4.6 4.3 - - - -
217G ASN* 3.0 31.4 - - - +
220G GLU* 3.2 17.0 + - - -
230G TYR* 3.1 31.3 + - + +
231G SER* 1.3 79.3 + - - +
233G VAL* 1.3 69.2 + - - +
234G ARG* 4.0 14.3 - - - +
96H VAL* 3.7 13.3 - - + +
97H ASP 3.2 16.4 + - - -
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Residues in contact with VAL 233 (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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171G GLN* 3.9 24.9 - - - +
183G PHE* 6.5 0.2 - - + -
185G PRO* 4.0 14.8 - - + -
186G PHE 3.4 9.4 - - - +
187G THR* 4.4 15.7 - - + -
232G LYS* 1.3 86.3 - - - +
234G ARG* 1.3 68.0 + - - +
235G GLY 4.3 0.7 - - - +
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Residues in contact with ARG 234 (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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186G PHE* 2.8 41.5 + - - +
188G VAL* 4.4 10.3 - - + -
204G MET* 4.5 9.4 - - - +
216G VAL* 2.9 27.0 + - + +
217G ASN* 3.6 25.0 - - + +
232G LYS* 4.0 13.9 - - - +
233G VAL* 1.3 79.1 - - - +
235G GLY* 1.3 73.3 + - - +
97H ASP* 2.8 41.7 + - - -
98H THR* 3.3 17.0 + - - +
99H ALA 2.6 31.3 + - - +
100H GLN* 4.3 8.2 + - - -
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Residues in contact with GLY 235 (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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183G PHE* 3.6 24.4 - - - -
184G VAL 3.4 11.0 - - - -
185G PRO* 3.7 4.5 - - - -
186G PHE* 4.8 0.2 - - - -
216G VAL* 4.6 6.1 - - - +
233G VAL* 4.9 1.6 - - - +
234G ARG* 1.3 92.3 + - - +
236G ILE* 1.3 62.2 + - - +
100H GLN* 3.8 13.6 + - - +
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Residues in contact with ILE 236 (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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183G PHE* 3.5 4.9 - - - -
184G VAL 2.9 34.7 + - - +
186G PHE* 3.7 20.9 - - + -
206G ALA* 4.0 11.4 - - + -
214G ILE* 4.7 12.8 - - + -
215G PRO 5.6 0.4 - - - +
216G VAL* 4.0 31.6 - - + -
235G GLY* 1.3 75.0 - - - +
237G ASN* 1.3 74.9 + - - +
238G PHE* 3.6 41.4 + - + -
242G TYR* 4.9 4.0 - - + -
249G ILE* 4.4 5.2 - - + -
100H GLN* 4.0 5.4 - - - +
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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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172B PHE* 3.0 64.4 - - + +
182G GLY 3.5 14.0 + - - +
183G PHE* 3.8 4.4 - - + -
236G ILE* 1.3 76.8 - - - +
238G PHE* 1.3 59.2 + - - +
239G ASP* 3.0 33.0 + - - +
242G TYR* 3.4 16.5 + - - -
75H LYS* 5.8 1.8 - - - +
100H GLN* 3.4 20.1 + - + +
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Residues in contact with PHE 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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177G VAL* 3.8 25.4 - - + -
181G GLY* 3.1 4.7 - - - -
182G GLY 2.7 38.3 + - - +
184G VAL* 3.8 16.2 - - + -
236G ILE* 3.7 43.3 - - + -
237G ASN* 1.3 70.9 - - - +
239G ASP* 1.3 67.7 + - - +
242G TYR* 3.8 13.7 - + + -
247G TYR* 3.7 38.4 - + + -
249G ILE* 4.0 11.2 - - + -
268G VAL* 3.7 32.3 - - + -
270G LYS* 4.7 7.6 - - + -
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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