Contacts of the strand formed by residues 237 - 243 (chain B) in PDB entry 3THW
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 ALA 237 (chain B).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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231B LYS* 3.6 21.7 + - - -
234B HIS* 3.3 14.1 + - + +
236B ASP* 1.3 82.0 + - - +
238B VAL* 1.3 64.2 + - - +
239B LEU* 3.5 11.0 + - + +
253B ASP* 4.7 0.7 - - - -
294B LYS* 3.2 22.4 - - + +
296B GLY 4.2 4.7 - - - +
324B LEU* 4.0 27.4 - - + -
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Residues in contact with VAL 238 (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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236B ASP 4.0 2.3 + - - +
237B ALA* 1.3 70.5 - - - +
239B LEU* 1.3 58.2 + - - +
240B CYS* 5.0 1.6 - - - -
249B PHE* 4.1 21.3 - - + -
253B ASP* 3.8 22.2 - - + +
256B ILE* 4.4 20.0 - - + -
257B ALA* 6.0 0.2 - - + -
288B LEU* 4.0 22.9 - - + -
293B TYR* 4.1 28.5 - - + -
294B LYS 2.8 14.0 + - - +
295B VAL* 3.4 10.6 - - + +
296B GLY 2.7 32.7 + - - +
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Residues in contact with LEU 239 (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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227B TYR* 4.1 17.8 - - + -
230B MET* 4.6 8.3 - - + +
231B LYS* 3.9 38.4 - - + +
234B HIS* 5.1 9.9 - - + +
237B ALA* 3.8 18.8 - - + +
238B VAL* 1.3 81.5 - - - +
240B CYS* 1.3 63.2 + - - +
241B VAL* 3.9 8.8 - - + +
248B ARG 3.8 6.1 - - - +
249B PHE* 3.2 22.3 - - - -
250B PHE 5.2 0.5 + - - -
253B ASP* 3.6 14.6 + - - +
296B GLY* 3.5 19.5 - - - +
298B VAL* 4.6 17.3 - - + -
321B LEU* 4.6 6.1 - - + -
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Residues in contact with CYS 240 (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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238B VAL* 5.0 1.6 - - - -
239B LEU* 1.3 70.5 - - - +
241B VAL* 1.3 59.6 + - - +
247B TYR* 3.6 24.9 - - + -
248B ARG 4.1 3.4 - - - -
249B PHE* 3.2 31.2 - - + -
276B ILE* 5.3 0.9 - - - -
281B LEU* 4.5 16.2 - - + -
284B HIS 6.5 0.7 - - - -
285B VAL* 5.0 4.0 - - - -
288B LEU* 5.5 3.4 - - - -
295B VAL* 4.3 17.7 - - - -
296B GLY 2.9 15.5 + - - +
297B VAL* 4.5 4.3 - - + -
298B VAL* 2.7 34.1 + - - +
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Residues in contact with VAL 241 (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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223B LEU* 4.6 11.9 - - + -
227B TYR* 4.4 16.8 - - + -
230B MET* 5.2 5.8 - - + -
239B LEU* 4.7 6.3 - - + +
240B CYS* 1.3 74.6 - - - +
242B GLU* 1.3 60.6 + - - +
243B CYS* 3.1 7.4 + - + -
247B TYR* 3.3 2.8 - - - -
248B ARG* 2.8 45.9 + - + +
250B PHE* 4.1 23.1 - - + -
298B VAL* 3.7 20.9 - - + -
319B ARG* 3.7 32.5 - - - +
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Residues in contact with GLU 242 (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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241B VAL* 1.3 69.8 - - - +
243B CYS* 1.3 58.9 - - - +
244B GLY 4.3 13.9 - - - +
246B LYS 3.8 5.2 - - - +
247B TYR* 3.7 24.5 + - + -
278B THR* 4.8 8.0 - - + +
298B VAL 2.8 20.0 + - - +
299B LYS* 3.4 11.8 - - - +
300B GLN* 2.6 56.8 + - - +
319B ARG* 2.9 27.0 + - - +
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Residues in contact with CYS 243 (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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223B LEU* 4.1 24.2 - - + -
241B VAL* 3.1 5.7 + - + +
242B GLU* 1.3 72.1 - - - +
244B GLY* 1.3 65.0 + - - +
245B TYR 3.1 0.9 + - - -
246B LYS* 2.8 35.5 + - - +
248B ARG* 4.0 32.3 - - + +
319B ARG* 3.7 9.4 - - - +
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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