Contacts of the strand formed by residues 266 - 273 (chain B) in PDB entry 3A4T
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 266 (chain B).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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71B SER* 3.6 26.0 - - - +
72B SER* 3.9 12.6 - - - -
75B PRO* 3.7 24.2 - - + -
97B LYS* 3.7 25.1 - - - -
163B ASP* 3.9 7.6 - - - -
210B SER* 3.9 11.4 - - - -
211B THR 3.4 13.0 - - - -
212B CYS* 3.8 14.4 - - + -
213B SER 3.8 6.7 + - - +
214B MET* 4.7 0.7 - - - +
258B ARG* 3.4 9.1 - - - +
259B VAL* 2.9 35.0 + - + -
264B GLU* 3.2 30.0 + - - +
265B PRO* 1.3 80.3 - - - +
267B PHE* 1.3 60.7 + - - +
268B ILE* 3.5 22.2 - - + -
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Residues in contact with PHE 267 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
209B TYR* 4.2 13.5 - + - -
210B SER* 3.2 8.5 - - - -
211B THR* 2.9 30.3 + - + +
213B SER 3.7 0.2 - - - +
219B ASN* 3.2 66.2 - - + +
220B GLU* 3.6 26.0 - - + -
223B ILE* 4.0 13.9 - - + -
256B THR* 3.5 39.9 - - + -
257B LEU 3.1 22.0 - - - -
258B ARG* 4.4 8.1 - - + -
266B PHE* 1.3 75.1 - - - +
268B ILE* 1.3 62.7 + - - +
269B ALA* 4.1 9.2 - - + -
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Residues in contact with ILE 268 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
74B ILE* 3.9 43.5 - - + -
75B PRO* 4.5 5.6 - - + -
78B VAL* 4.6 3.6 - - + -
208B VAL* 3.6 28.3 - - + -
209B TYR 3.4 3.4 - - - +
210B SER* 4.4 4.3 - - - -
238B ILE* 3.9 15.2 - - + +
248B ILE* 5.3 0.2 - - + -
256B THR* 3.3 5.5 - - - -
257B LEU* 2.8 54.8 + - + +
259B VAL* 5.0 3.8 - - + -
266B PHE* 3.5 28.5 - - + -
267B PHE* 1.3 83.5 - - - +
269B ALA* 1.3 63.8 + - - +
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Residues in contact with ALA 269 (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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208B VAL* 3.3 6.9 - - - +
209B TYR* 2.8 32.8 + - - +
223B ILE* 3.8 28.9 - - + -
235B LEU* 4.7 4.9 - - + -
238B ILE* 3.9 8.7 - - - -
255B GLY 5.1 0.2 - - - -
256B THR* 3.5 26.7 - - + +
267B PHE* 4.1 2.9 - - + -
268B ILE* 1.3 74.8 - - - +
270B LYS* 1.3 60.5 + - - +
271B LEU* 5.3 1.3 - - + -
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Residues in contact with LYS 270 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
78B VAL* 2.8 40.5 + - + +
79B LEU* 3.6 9.1 + - - +
80B ASN* 4.8 2.8 - - - +
206B GLU* 3.2 45.5 + - - -
207B LEU 3.3 9.0 - - - +
208B VAL* 3.9 5.2 - - + +
235B LEU* 3.7 7.0 - - - +
236B ILE* 2.9 60.2 + - + +
238B ILE* 4.1 14.6 - - + +
269B ALA* 1.3 76.3 - - - +
271B LEU* 1.3 67.2 + - - +
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Residues in contact with LEU 271 (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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194B ILE* 4.0 19.3 - - + -
198B ILE* 3.9 28.3 - - + -
201B LEU* 4.8 0.6 - - - +
206B GLU* 3.2 6.6 - - - +
207B LEU* 2.8 50.7 + - + +
209B TYR* 5.6 0.2 - - + -
223B ILE* 4.5 10.3 - - + -
226B ILE* 4.1 11.9 - - + -
227B LEU* 4.1 18.4 - - + -
233B VAL* 4.3 7.4 - - + -
234B GLU 3.3 14.4 - - - +
235B LEU* 3.9 27.6 - - + -
236B ILE* 4.0 5.4 - - - +
269B ALA 5.3 0.7 - - - -
270B LYS* 1.3 76.7 - - - +
272B ARG* 1.3 61.1 + - - +
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Residues in contact with ARG 272 (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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201B LEU* 4.9 0.9 - - - -
204B ASP* 4.1 18.5 + - - +
205B GLY 3.3 11.2 - - - +
206B GLU* 3.7 22.1 + - + +
233B VAL* 3.3 9.0 - - - +
234B GLU* 2.9 59.1 + - + +
236B ILE* 3.6 31.7 - - + +
271B LEU* 1.3 74.6 - - - +
273B LYS* 1.3 68.8 + - - +
274B ILE* 3.7 17.6 + - - -
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Residues in contact with LYS 273 (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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156B PHE* 6.0 0.2 - - - -
198B ILE* 2.5 38.9 + - + +
199B ASP* 4.1 8.7 + - - +
201B LEU* 3.1 37.2 + - + +
202B LYS 3.7 16.4 - - - +
203B LYS* 3.9 15.0 - - + +
204B ASP* 2.8 31.9 + - - +
205B GLY 3.0 11.3 + - - +
230B ARG* 4.5 4.3 - - - +
232B ASP* 3.3 28.7 - - - +
233B VAL* 4.6 2.7 - - - -
272B ARG* 1.3 73.7 - - - +
274B ILE* 1.3 64.6 + - - +
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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