Contacts of the strand formed by residues 222 - 229 (chain B) in PDB entry 2G5T
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 PHE 222 (chain B).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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215B TRP 4.0 0.2 - - - +
216B TRP* 3.5 8.0 - - - -
217B SER* 2.8 40.8 + - - +
221B THR* 1.3 87.4 - - + +
223B LEU* 1.3 60.2 + - - +
224B ALA 4.0 0.4 - - - -
270B VAL* 3.9 6.7 - - + -
271B VAL 3.4 12.6 - - - +
272B ASN* 3.7 29.6 - - + -
273B THR* 4.8 0.2 - - - -
305B TRP* 3.4 21.8 - + + -
308B GLN 3.4 27.4 - - - -
309B GLU* 4.4 9.4 - - + -
330B TYR* 3.9 31.6 - + - -
337B TRP* 3.8 32.3 - + - -
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Residues in contact with LEU 223 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
165B ALA* 3.9 21.8 - - + -
172B ILE* 4.2 17.5 - - + -
174B VAL* 4.1 18.6 - - + -
185B ILE* 5.9 0.2 - - + -
214B LEU* 4.2 13.7 - - + -
215B TRP 3.8 19.3 - - - +
216B TRP* 4.0 23.3 - - + +
221B THR 4.3 0.2 + - - -
222B PHE* 1.3 73.5 - - - +
224B ALA* 1.3 70.7 + - - +
225B TYR* 4.1 4.9 - - + -
270B VAL* 3.7 2.0 - - - -
271B VAL* 2.8 49.3 + - + +
273B THR* 3.9 12.3 - - + +
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Residues in contact with ALA 224 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
214B LEU* 3.1 5.2 - - - +
215B TRP* 2.6 50.7 + - + +
222B PHE 4.0 0.8 - - - -
223B LEU* 1.3 74.5 - - - +
225B TYR* 1.3 61.3 + - - +
268B PHE* 3.5 25.8 - - + -
269B PHE 3.2 7.9 - - - +
270B VAL* 4.2 3.8 - - + +
305B TRP* 3.9 8.0 - - + +
311B ILE* 3.8 17.7 - - + -
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Residues in contact with TYR 225 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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172B ILE* 3.3 35.0 - - + -
185B ILE* 4.3 16.0 + - + +
186B THR* 4.8 6.9 + - - -
196B ASN* 4.1 16.2 - - + -
197B GLY* 4.3 1.3 - - - -
213B ALA 3.4 14.6 - - - +
214B LEU* 4.0 5.2 - - + +
215B TRP* 4.0 5.8 - - - -
223B LEU* 4.1 10.5 - - + -
224B ALA* 1.3 77.6 - - - +
226B ALA* 1.3 71.8 + - - +
227B GLN* 4.9 0.2 - - + -
268B PHE* 3.6 5.4 - - - -
269B PHE* 2.8 73.1 + + + +
271B VAL* 4.5 7.2 - - + -
284B SER* 2.8 33.7 + - - -
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Residues in contact with ALA 226 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
195B TYR 3.7 1.2 - - - +
197B GLY* 3.2 24.1 + - - -
213B ALA* 3.1 8.1 + - + +
215B TRP* 3.9 11.8 - - + -
225B TYR* 1.3 78.2 - - - +
227B GLN* 1.3 61.8 + - - +
228B PHE* 3.8 27.9 - - + -
266B VAL* 4.3 1.3 - - + -
267B LYS 3.3 9.2 - - - +
268B PHE* 4.5 0.4 - - - -
300B LEU* 3.8 25.1 - - + -
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Residues in contact with GLN 227 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
186B THR* 4.8 0.8 + - - -
188B THR* 3.2 23.0 + - - +
194B ILE* 4.0 15.5 - - + +
195B TYR 3.2 6.7 - - - +
196B ASN* 3.0 27.7 + - - +
225B TYR* 4.9 0.6 - - + -
226B ALA* 1.3 74.7 - - - +
228B PHE* 1.3 66.1 + - - +
229B ASN* 4.2 4.1 + - - +
265B THR 3.8 0.3 - - - +
266B VAL* 3.3 5.5 - - - -
267B LYS* 2.8 56.9 + - + +
269B PHE* 3.9 25.2 - - + -
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Residues in contact with PHE 228 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
193B ILE 3.5 0.9 - - - +
194B ILE* 3.3 7.3 - - - +
195B TYR* 2.8 44.8 + - + -
198B ILE 3.3 25.8 - - - -
199B THR* 3.8 13.5 - - + -
200B ASP* 4.5 6.5 - - + -
203B TYR* 3.4 57.0 - + - -
208B PHE* 4.1 12.1 - + - -
213B ALA* 4.0 8.5 - - + -
226B ALA* 3.8 26.5 - - + -
227B GLN* 1.3 75.2 - - - +
229B ASN* 1.3 60.9 + - - +
230B ASP* 4.1 11.7 - - - +
264B PRO* 5.1 1.1 - - + -
265B THR 3.5 4.5 - - - +
266B VAL* 3.7 18.6 - - + -
300B LEU* 5.4 0.4 - - + -
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Residues in contact with ASN 229 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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193B ILE 3.4 4.3 - - - +
194B ILE* 4.2 17.5 - - + +
227B GLN* 4.2 4.7 + - - +
228B PHE* 1.3 73.8 - - - +
230B ASP* 1.3 61.2 + - - +
231B THR* 2.5 36.7 + - - -
233B VAL* 4.6 0.2 - - - +
264B PRO* 3.2 5.2 - - - +
265B THR* 3.1 45.4 + - - +
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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