Contacts of the strand formed by residues 248 - 256 (chain B) in PDB entry 5DVX
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 248 (chain B).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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227B LEU* 6.1 0.2 - - + -
228B HIS 3.2 15.5 - - - +
229B TRP* 4.1 11.4 - - + -
237B SER* 3.7 12.5 - - - +
246B PHE* 3.3 0.7 + - - +
247B PRO* 1.3 82.1 - - - +
249B GLU* 1.3 64.7 + - - +
278B PHE* 3.6 4.3 - - - +
279B LEU* 2.9 46.1 + - + +
356B LEU* 4.5 7.2 - - + -
359B LEU* 4.2 8.5 - - + -
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Residues in contact with GLU 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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227B LEU* 3.4 6.8 - - - +
228B HIS* 2.9 37.6 + - + +
237B SER* 3.5 13.3 - - - -
238B GLU* 2.8 29.3 + - - +
239B HIS* 2.8 33.5 + - - -
248B ALA* 1.3 78.9 - - - +
250B ILE* 1.3 63.7 + - - +
251B HIS* 2.7 34.7 + - + +
276B ALA* 3.8 5.3 - - - +
277B ALA 3.3 18.6 - - - +
278B PHE* 3.5 10.2 - - + -
279B LEU* 3.9 4.6 - - - +
344B VAL* 6.2 0.4 - - - -
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Residues in contact with ILE 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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225B LEU* 4.4 21.1 - - + -
226B HIS 3.7 6.7 - - - +
227B LEU* 3.6 20.9 - - + -
249B GLU* 1.3 72.0 - - - +
251B HIS* 1.3 73.3 + - - +
252B VAL* 4.7 3.8 - - + -
275B LEU 3.6 0.3 - - - +
276B ALA* 3.2 6.9 - - - -
277B ALA* 2.9 54.5 + - + +
279B LEU* 3.8 6.2 - - + +
289B TYR* 3.3 28.7 - - + +
316B LEU* 4.0 22.0 - - + +
317B LEU* 4.1 15.9 - - + -
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Residues in contact with HIS 251 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
225B LEU* 3.1 6.5 - - - +
226B HIS* 2.9 48.6 + - + +
228B HIS* 3.1 10.0 + + - -
238B GLU* 3.1 23.6 - - + -
249B GLU* 2.7 31.7 + - + +
250B ILE* 1.3 86.6 - - - +
252B VAL* 1.3 63.3 + - - +
253B VAL* 4.1 0.6 + - + -
274B VAL* 3.8 12.6 - - + -
275B LEU 3.4 2.2 - - - -
276B ALA* 3.7 11.7 - - + -
332B THR* 4.7 0.2 - - + -
342B TRP* 3.6 22.4 - + - -
401B ZN 2.0 32.9 - - - -
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Residues in contact with VAL 252 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
185B PHE* 4.7 8.3 - - + -
206B LEU* 4.0 19.3 - - + -
222B ALA* 4.3 4.5 - - + -
224B GLN 3.6 9.6 - - - +
225B LEU* 4.1 16.8 - - + -
250B ILE* 4.7 3.4 - - + -
251B HIS* 1.3 74.2 - - - +
253B VAL* 1.3 61.4 + - - +
254B HIS* 3.0 36.9 + - + +
274B VAL* 3.4 1.1 - - - -
275B LEU* 2.9 33.2 + - + +
313B ILE* 5.4 2.7 - - + -
317B LEU* 4.1 33.4 - - + -
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Residues in contact with VAL 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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222B ALA* 3.7 2.4 - - - +
223B LEU* 2.8 36.6 + - + +
224B GLN* 2.9 36.4 + - + +
226B HIS* 3.8 21.5 - - + -
252B VAL* 1.3 76.6 - - - +
254B HIS* 1.3 61.4 + - - +
272B LEU* 5.4 4.3 - - + -
273B ALA 3.7 3.4 - - - +
274B VAL* 4.3 24.5 - - + -
331B LEU* 5.0 9.4 - - + -
402B GOL 3.6 26.7 - - - +
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Residues in contact with HIS 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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185B PHE* 4.0 6.6 - + - -
212B MET* 3.5 46.8 - - + +
220B TYR* 3.5 18.6 - - + -
221B ARG 3.2 7.6 - - - +
222B ALA* 3.5 31.8 - - + +
223B LEU* 4.2 5.8 - - - +
252B VAL* 3.0 47.7 + - + +
253B VAL* 1.3 73.5 - - - +
255B LEU* 1.3 59.9 + - - +
272B LEU* 3.3 13.0 - - - +
273B ALA 2.7 39.2 + - - +
275B LEU* 4.1 11.7 - - + -
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Residues in contact with LEU 255 (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 TYR* 3.3 2.6 - - - -
221B ARG* 2.9 58.8 + - - +
223B LEU* 4.1 24.3 - - + +
254B HIS* 1.3 73.2 - - - +
256B SER* 1.3 76.8 + - - +
257B THR 3.5 0.2 + - - -
259B TYR* 3.7 13.5 - - + +
260B ALA 3.8 15.7 - - - +
261B ARG* 3.9 18.8 - - - +
262B VAL* 4.1 7.9 - - + +
265B ALA* 3.5 31.6 - - + -
271B GLY 3.8 1.6 - - - +
272B LEU* 3.9 7.0 - - + -
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Residues in contact with SER 256 (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 GLU 3.6 4.0 + - - -
220B TYR* 3.4 17.4 - - - -
221B ARG* 3.4 2.1 + - - -
255B LEU* 1.3 75.7 - - - +
257B THR* 1.3 62.5 + - - +
258B LYS* 3.0 34.0 + - - +
259B TYR* 3.1 26.4 + - - +
270B GLY 3.5 17.8 + - - -
271B GLY* 2.9 25.4 + - - -
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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