Contacts of the strand formed by residues 251 - 258 (chain B) in PDB entry 3BEQ
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 SER 251 (chain B).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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218B TRP* 2.8 33.9 + - - -
219B ARG* 3.6 20.5 + - - +
242B THR* 3.3 4.5 - - - -
243B ASP 3.0 36.6 + - - -
250B ALA* 1.3 74.9 - - - +
252B TYR* 1.3 63.2 + - - +
267B GLU* 2.6 28.9 + - - -
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Residues in contact with TYR 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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240B ILE* 4.9 3.6 - - + -
241B MET 3.4 5.4 - - - +
242B THR* 3.7 5.8 - - + +
249B GLN* 3.4 12.1 + - - -
250B ALA* 3.1 50.9 + - + -
251B SER* 1.3 78.9 + - - +
253B LYS* 1.3 61.2 + - - +
267B GLU* 3.4 7.4 + - - +
268B LEU* 2.8 52.0 + - + -
270B ALA* 4.1 16.6 - - + -
273B TYR 2.7 23.8 + - - -
274B HIS* 3.3 10.5 - + - -
275B TYR* 3.4 58.8 - + + -
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Residues in contact with LYS 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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218B TRP* 3.6 62.9 - - + +
240B ILE* 3.3 7.9 - - - +
241B MET* 2.9 33.8 + - + +
252B TYR* 1.3 77.5 - - - +
254B ILE* 1.3 67.7 + - - +
255B LEU* 4.0 11.8 + - + +
265B SER* 4.8 15.2 + - - +
266B ILE 3.3 5.8 - - - +
267B GLU* 3.9 28.7 - - + +
268B LEU* 5.2 0.7 - - - -
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Residues in contact with ILE 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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239B THR 3.4 9.2 - - - +
240B ILE* 3.7 13.0 - - + -
253B LYS* 1.3 73.8 - - - +
255B LEU* 1.3 65.0 + - - +
265B SER* 3.1 9.0 - - - -
266B ILE* 2.9 48.7 + - + -
268B LEU* 3.7 29.4 - - + -
303B VAL* 4.5 0.9 - - + -
305B PHE* 3.5 54.7 - - + -
310B LEU* 3.7 16.9 - - + +
312B TYR* 3.8 15.9 - - + -
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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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215B ILE* 3.1 40.2 - - + -
218B TRP* 6.3 1.3 - - + -
237B CYS 3.8 0.2 - - - +
238B PHE* 3.2 10.9 - - - +
239B THR* 3.0 45.8 + - + +
241B MET* 3.7 30.5 - - + -
253B LYS* 4.5 15.5 - - + +
254B ILE* 1.3 77.7 - - - +
256B LYS* 1.3 59.5 + - - +
257B ILE* 4.1 12.1 - - + -
262B VAL* 4.7 7.6 - - + -
264B LYS 3.7 2.5 - - - +
265B SER* 3.6 23.3 - - - -
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Residues in contact with LYS 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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236B SER* 3.4 28.2 + - - -
237B CYS 3.6 3.6 - - - -
238B PHE* 3.6 20.6 - - + -
255B LEU* 1.3 73.2 - - - +
257B ILE* 1.3 57.8 + - - +
258B GLU* 3.5 14.5 + - - +
262B VAL* 3.4 4.5 - - - -
263B THR* 2.8 40.6 + - - +
264B LYS* 2.8 34.3 + - + +
308B GLN* 3.0 35.1 + - - +
309B ASN* 5.1 1.2 - - - +
310B LEU* 4.1 6.9 - - + +
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Residues in contact with ILE 257 (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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190B LEU* 3.8 29.2 - - + -
192B ILE* 3.9 20.0 - - + -
205B LEU* 4.0 17.9 - - + -
235B GLY 4.4 0.2 - - - +
236B SER* 3.4 2.6 - - - -
237B CYS* 2.8 48.9 + - - +
239B THR* 4.1 17.5 - - + -
255B LEU* 4.3 10.1 - - + -
256B LYS* 1.3 79.3 - - - +
258B GLU* 1.3 63.9 + - - +
259B LYS 4.3 0.7 + - - -
260B GLY* 3.5 35.2 - - - +
261B LYS 3.2 4.3 - - - +
262B VAL* 4.2 9.4 - - + -
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Residues in contact with GLU 258 (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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235B GLY 4.1 9.1 - - - +
236B SER* 3.4 26.5 + - - +
256B LYS* 3.5 13.4 + - - -
257B ILE* 1.3 75.2 - - - +
259B LYS* 1.3 74.6 + - + +
260B GLY 3.1 0.4 - - - -
261B LYS* 2.8 26.7 + - - +
263B THR* 2.7 38.3 + - + +
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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