Contacts of the strand formed by residues 219 - 228 (chain B) in PDB entry 3V4K
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 TYR 219 (chain B).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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197B MET* 4.3 10.3 - - + -
201B THR* 3.5 23.9 - - + +
205B ASN* 3.5 34.3 - - + -
206B PHE* 3.8 24.6 - + + -
217B GLU* 3.2 37.1 + - + -
218B THR* 1.3 78.4 - - - +
220B LEU* 1.3 60.9 + - - +
221B CYS 4.3 0.2 - - - -
241B PHE* 4.1 27.1 - + - -
242B LEU 3.5 6.3 - - - -
243B ALA* 3.7 19.5 - - + +
282B PHE 3.8 0.7 - - - +
283B THR* 3.3 3.6 - - - -
284B SER* 2.9 33.4 + - - +
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Residues in contact with LEU 220 (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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218B THR* 5.1 0.9 - - + -
219B TYR* 1.3 75.3 - - - +
221B CYS* 1.3 69.5 + - - +
222B TYR* 4.0 13.7 - - + -
241B PHE* 3.1 2.6 - - - -
242B LEU* 2.9 45.5 + - + +
258B ALA* 4.3 13.7 - - + +
259B GLU* 4.3 16.2 - - + -
262B PHE* 3.9 46.2 - - + -
281B CYS* 4.0 12.8 - - + -
282B PHE 3.4 4.3 - - - -
283B THR* 3.8 24.5 - - + +
295B MET* 5.7 1.6 - - + -
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Residues in contact with CYS 221 (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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197B MET* 3.6 31.0 - - - -
202B PHE* 5.9 0.9 - - - -
206B PHE* 4.3 15.7 - - - -
220B LEU* 1.3 74.5 - - - +
222B TYR* 1.3 60.4 + - - +
240B GLY 3.4 5.4 - - - -
241B PHE* 3.8 5.4 - - - -
280B THR 3.8 0.5 - - - +
281B CYS* 3.2 4.0 - - - -
282B PHE* 2.8 41.1 + - + +
346B CYS* 4.9 5.2 - - - -
350B PHE* 3.6 40.8 - - + -
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Residues in contact with TYR 222 (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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220B LEU* 4.0 17.5 - - + -
221B CYS* 1.3 75.8 - - - +
223B GLU* 1.3 65.8 + - - +
238B ARG 4.1 3.4 - - - -
239B ARG* 3.2 18.8 + - - -
240B GLY* 2.8 66.5 + - - -
241B PHE* 3.9 4.4 + - - -
242B LEU* 4.3 17.7 - - + -
262B PHE* 3.8 25.6 - + + -
265B VAL* 4.8 10.0 - - + +
269B TRP* 3.5 37.6 + + + -
279B VAL* 5.1 0.9 - - + -
280B THR 3.2 9.4 - - - +
281B CYS* 4.5 0.4 - - - -
350B PHE* 3.4 7.4 - - - -
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Residues in contact with GLU 223 (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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222B TYR* 1.3 77.7 - - - +
224B VAL* 1.3 66.3 + - - +
225B GLU* 5.5 2.1 - - - +
234B LYS* 3.4 31.8 + - + +
238B ARG 3.6 9.0 - - - +
239B ARG* 4.6 6.5 - - + -
278B ARG 3.9 0.6 - - - +
279B VAL* 3.6 1.6 - - - +
280B THR* 3.0 46.3 + - - +
282B PHE* 3.8 17.7 - - + -
345B HIS* 3.0 33.0 + - - -
349B THR* 4.2 5.4 - - - +
350B PHE* 4.0 12.3 - - + -
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Residues in contact with VAL 224 (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 GLU* 1.3 83.4 - - - +
225B GLU* 1.3 72.3 + - - +
234B LYS* 3.8 3.8 - - - +
235B LEU* 2.9 45.4 + - + +
238B ARG* 3.5 29.6 + - + +
269B TRP* 3.4 35.7 - - + -
271B LEU* 4.7 8.3 - - + -
277B TYR* 4.0 12.3 - - + -
278B ARG 3.4 6.7 - - - +
279B VAL* 4.2 12.3 - - + -
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Residues in contact with GLU 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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223B GLU* 5.5 2.7 - - - +
224B VAL* 1.3 78.0 - - - +
226B ARG* 1.3 62.1 + - - +
232B TRP* 3.6 25.8 - - + +
233B VAL 3.2 8.3 - - - +
234B LYS* 3.7 42.4 - - + +
235B LEU* 3.9 3.8 - - - -
277B TYR* 3.2 9.5 - - - +
278B ARG* 2.7 78.3 + - - +
280B THR* 4.3 6.9 + - - -
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Residues in contact with ARG 226 (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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225B GLU* 1.3 75.3 - - - +
227B MET* 1.3 67.1 + - - +
228B HIS* 2.9 32.8 + - + +
232B TRP* 3.7 2.9 - - - -
233B VAL* 2.8 34.9 + - - +
235B LEU* 3.5 45.6 - - + +
275B GLN* 3.5 26.6 - - + +
276B ASP 3.4 8.5 - - - +
277B TYR* 3.7 29.4 + - + -
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Residues in contact with MET 227 (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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226B ARG* 1.3 73.3 - - - +
228B HIS* 1.3 72.3 + - - +
229B ASN 5.1 0.4 - - - +
230B ASP* 3.4 19.3 - - - +
231B THR 3.2 32.3 - - - +
232B TRP* 3.4 47.5 - - + +
275B GLN* 4.5 7.1 - - - +
276B ASP* 2.8 36.6 + - + +
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Residues in contact with HIS 228 (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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226B ARG* 2.9 54.5 + - - +
227B MET* 1.3 77.3 + - - +
229B ASN* 1.3 72.8 + - + +
230B ASP 3.3 1.6 - - - -
231B THR* 2.8 29.0 + - - +
233B VAL* 3.8 25.5 - - + +
275B GLN* 3.8 19.0 + - - -
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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