Contacts of the strand formed by residues 245 - 254 (chain B) in PDB entry 3THT
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 245 (chain B).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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183B PHE* 4.7 18.6 - - + -
190B VAL 4.8 5.4 - - - -
191B ASP* 5.3 0.9 - - + -
223B GLN* 4.2 17.5 - - + -
240B ASP* 4.2 13.2 - - + -
241B THR* 3.5 17.9 + - - +
242B HIS 3.6 12.6 - - - +
244B ALA* 1.3 103.9 - - + +
246B GLU* 1.3 71.3 + - - +
249B ILE* 4.6 2.0 - - + -
287B ARG* 2.9 14.8 + - - +
288B TYR* 4.7 0.3 + - - -
334B ARG* 3.8 61.7 - - + -
335B LYS 3.4 7.2 - - - +
336B VAL* 4.3 12.6 - - + -
337B ARG* 3.7 6.9 + - - +
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Residues in contact with GLU 246 (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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219B HIS* 6.2 0.4 - - + -
245B PHE* 1.3 71.5 - - - +
247B ASP* 1.3 63.8 + - - +
248B GLU 4.7 4.5 - - - +
249B ILE* 4.0 5.9 - - - +
287B ARG* 2.4 27.6 + - - -
288B TYR* 3.9 2.9 - - - -
335B LYS* 2.8 42.9 + - + +
336B VAL 4.2 6.7 - - - +
337B ARG* 3.1 49.7 + - - +
338B GLN 4.6 1.4 + - - -
339B THR* 5.1 0.3 + - - -
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Residues in contact with ASP 247 (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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246B GLU* 1.3 75.3 - - - +
248B GLU* 1.3 67.5 + - - +
249B ILE* 3.0 7.8 + - - +
282B MET 3.4 1.4 - - - +
283B THR* 2.9 14.9 - - - -
284B GLY* 2.9 37.1 + - - -
287B ARG* 3.1 19.3 - - - +
288B TYR* 3.5 28.4 + - + +
337B ARG* 5.5 0.4 - - - +
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Residues in contact with GLU 248 (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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216B TYR 3.9 4.5 - - - +
217B ILE* 3.0 30.4 - - + +
218B LYS* 2.6 52.9 + - - +
219B HIS* 2.9 26.4 + - + +
246B GLU* 3.8 5.7 - - - +
247B ASP* 1.3 79.1 + - - +
249B ILE* 1.3 63.2 + - - +
250B VAL 4.3 0.2 - - - -
281B VAL* 4.9 3.6 - - + +
282B MET 3.7 3.6 - - - -
283B THR* 4.1 19.9 - - + +
333B PHE 4.5 0.2 - - - +
334B ARG* 4.2 14.4 - - - +
335B LYS* 4.5 4.0 + - - +
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Residues in contact with ILE 249 (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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240B ASP* 3.1 42.2 - - + +
245B PHE* 4.6 3.8 - - + -
246B GLU 4.0 3.6 - - - +
247B ASP 3.2 13.9 - - - +
248B GLU* 1.3 76.2 - - - +
250B VAL* 1.3 61.4 + - - +
280B LEU 3.6 0.9 - - - +
281B VAL 3.7 0.2 - - - -
282B MET* 2.7 64.4 + - + +
287B ARG* 3.7 26.0 - - + +
332B THR* 4.2 16.8 - - + -
333B PHE 3.9 9.6 - - - +
334B ARG* 4.3 13.5 - - + -
403B AKG 6.1 0.2 - - - +
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Residues in contact with VAL 250 (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 LEU* 6.1 0.2 - - + -
211B TRP* 5.2 6.7 - - + -
217B ILE* 3.2 35.2 - - + -
221B PRO* 5.5 2.0 - - + -
248B GLU 4.3 0.4 + - - -
249B ILE* 1.3 78.2 - - - +
251B SER* 1.3 61.2 + - - +
252B LEU 4.2 0.2 - - - -
279B LEU* 4.1 19.7 - - + -
280B LEU 3.0 4.7 - - - +
281B VAL* 3.8 26.9 - - + -
282B MET* 5.8 0.4 - - - -
331B PHE 4.5 0.2 - - - -
332B THR* 3.3 7.7 - - - +
333B PHE* 2.9 59.5 + - + +
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Residues in contact with SER 251 (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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250B VAL* 1.3 74.0 - - - +
252B LEU* 1.3 62.4 + - - +
253B SER* 3.5 8.2 + - - -
274B LEU* 6.1 0.7 - - - -
278B SER 3.6 0.5 - - - +
279B LEU* 3.6 2.5 - - - -
280B LEU* 2.8 54.1 + - - +
282B MET* 5.1 4.9 - - - -
328B ARG* 5.7 0.9 - - - -
330B SER* 4.6 1.3 - - - -
331B PHE 3.4 3.5 + - - -
332B THR* 2.7 28.8 + - - +
403B AKG 3.6 22.4 + - - +
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Residues in contact with LEU 252 (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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143B ILE* 3.8 28.7 - - + -
144B ILE* 4.1 21.1 - - + -
152B LEU* 3.9 25.6 - - + -
207B PHE* 6.4 1.1 - - + -
211B TRP* 4.8 7.0 - - + +
251B SER* 1.3 69.6 - - - +
253B SER* 1.3 60.9 + - - +
254B LEU* 3.8 13.8 + - + +
278B SER 3.5 7.4 - - - +
279B LEU* 3.9 15.2 - - + +
330B SER* 3.3 5.3 - - - -
331B PHE* 2.8 60.9 + - + +
333B PHE* 4.3 10.1 - - + -
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Residues in contact with SER 253 (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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251B SER* 3.8 7.3 + - - -
252B LEU* 1.3 72.5 - - - +
254B LEU* 1.3 67.3 + - - +
256B SER 5.5 1.1 - - - -
274B LEU* 4.0 19.0 - - - +
275B PRO 4.0 8.1 - - - -
276B ARG* 4.7 1.6 - - - -
277B ARG* 3.0 26.5 + - - -
278B SER* 2.8 29.1 + - - -
280B LEU 5.3 0.3 + - - -
328B ARG* 3.7 29.5 + - - +
329B THR 4.3 1.8 - - - -
330B SER* 4.5 0.2 - - - -
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Residues in contact with LEU 254 (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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144B ILE* 3.1 33.9 - - + -
149B GLU* 3.2 19.3 - - + +
152B LEU* 3.6 36.3 - - + -
153B LEU* 3.6 22.0 - - + -
252B LEU* 4.1 17.3 - - + +
253B SER* 1.3 84.0 - - - +
255B GLY* 1.3 61.7 + - - +
256B SER 3.1 7.7 + - - -
276B ARG* 4.8 1.8 - - - +
277B ARG 4.5 2.0 - - - +
328B ARG* 3.3 6.7 - - - +
329B THR 2.9 36.3 + - - +
331B PHE* 4.7 10.1 - - + -
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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