Contacts of the strand formed by residues 276 - 283 (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 GLU 276 (chain B).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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224B ARG* 2.8 36.8 + - + +
242B THR* 4.3 6.1 - - + -
246B SER* 3.4 3.1 - - - -
274B HIS* 3.4 27.6 - - + +
275B TYR* 1.3 78.8 - - - +
277B GLU* 1.3 70.6 + - + +
278B CYS* 3.2 4.6 + - - -
291B CYS* 3.4 2.2 - - - +
292B ARG* 2.9 40.6 + - - +
294B ASN* 3.3 11.9 - - - +
1004B GOL 2.5 49.4 + - - +
3004B ACT 5.6 0.7 - - - +
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Residues in contact with GLU 277 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
224B ARG* 6.3 0.4 - - - +
225B THR 3.9 10.5 + - - -
226B GLN 3.4 13.2 - - - +
227B GLU* 4.0 7.6 - - + -
242B THR* 5.4 0.2 + - - -
276B GLU* 1.3 74.8 - - + +
278B CYS* 1.3 62.4 + - - +
279B SER* 3.5 1.6 + - - -
290B VAL 4.4 2.4 - - - +
291B CYS* 4.4 2.4 - - - -
292B ARG* 2.7 30.3 + - + -
350B LYS* 2.9 37.7 + - + +
351B GLY 4.5 1.2 - - - +
406B TYR* 2.6 30.9 + - - -
1004B GOL 3.4 10.3 + - - +
3004B ACT 2.4 43.0 + - - +
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Residues in contact with CYS 278 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
225B THR 5.1 0.2 - - - -
226B GLN* 3.0 35.7 + - + +
228B SER* 3.2 0.3 + - - -
240B ILE* 3.9 35.0 - - + -
275B TYR* 4.3 9.6 - - - -
276B GLU 3.2 4.1 + - - -
277B GLU* 1.3 76.5 - - - +
279B SER* 1.3 57.2 + - - +
280B CYS* 3.8 18.4 - - - -
289B CYS* 4.4 0.2 - - - -
290B VAL 3.8 0.9 - - - -
291B CYS* 2.2 48.0 - - - -
350B LYS* 3.1 6.3 + - - -
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Residues in contact with SER 279 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
228B SER* 3.8 6.4 + - - -
277B GLU 3.5 0.2 + - - -
278B CYS* 1.3 69.6 - - - +
280B CYS* 1.3 60.0 + - - +
281B TYR* 4.6 4.0 - - - -
288B MET 3.8 1.9 - - - +
289B CYS* 3.3 1.0 - - - -
290B VAL* 2.8 36.7 + - - +
350B LYS* 3.2 15.6 + - - -
351B GLY 2.9 25.7 + - - -
352B PHE* 3.6 18.2 - - - -
353B SER 5.5 0.5 - - - +
408B GLY* 3.5 14.0 - - - -
409B SER* 3.6 13.9 + - - -
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Residues in contact with CYS 280 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
226B GLN* 3.5 29.7 - - - +
228B SER* 4.7 0.4 + - - -
229B GLU* 3.6 19.6 + - - +
230B CYS 4.4 1.9 - - - +
231B ALA* 4.0 13.3 - - + +
238B PHE 5.1 1.6 - - - +
239B THR* 5.2 2.9 - - - -
240B ILE* 4.0 7.0 - - - -
278B CYS* 3.8 11.7 - - - -
279B SER* 1.3 73.6 - - - +
281B TYR* 1.3 61.2 + - - +
282B PRO* 4.6 0.2 - - - +
287B VAL* 4.0 8.7 - - + -
288B MET 3.2 4.5 - - - +
289B CYS* 2.1 45.5 - - - -
305B PHE* 5.5 0.2 - - - -
409B SER* 3.8 6.7 + - - -
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Residues in contact with TYR 281 (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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91B LEU* 4.0 22.0 - - + -
229B GLU* 5.5 1.3 - - - +
231B ALA* 4.0 5.2 - - - -
279B SER 4.6 4.7 - - - -
280B CYS* 1.3 77.8 - - - +
282B PRO* 1.3 81.6 - - + +
283B ASP* 3.8 20.0 - - + -
287B VAL* 3.4 0.9 - - - -
288B MET* 2.9 68.1 + - + +
290B VAL* 5.2 0.7 - - + -
353B SER 3.6 20.0 - - - -
354B PHE* 3.7 22.2 - + + -
355B ARG* 3.0 30.7 + - - +
409B SER* 4.4 11.0 - - - +
411B VAL* 3.8 16.4 - - + -
1006B GOL 4.3 1.6 + - - -
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Residues in contact with PRO 282 (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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87B GLY* 4.7 2.2 - - - +
91B LEU* 4.5 0.5 - - - +
229B GLU* 5.3 1.1 - - - +
231B ALA* 3.9 14.8 - - + -
232B CYS 3.8 7.2 - - - +
233B VAL* 3.7 24.5 - - + -
281B TYR* 1.3 93.4 - - + +
283B ASP* 1.3 64.0 + - - +
286B LYS 3.4 7.4 - - - +
287B VAL* 4.4 2.2 - - + -
411B VAL* 3.8 15.7 - - + -
412B HIS* 3.6 28.7 - - - +
418B MET* 3.6 28.2 - - + +
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Residues in contact with ASP 283 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
87B GLY 4.7 0.4 + - - -
89B SER 3.9 4.0 - - - -
90B SER* 3.4 4.2 - - - +
91B LEU* 3.6 15.1 - - + +
281B TYR* 3.8 12.4 + - + +
282B PRO* 1.3 76.1 - - - +
284B THR* 1.3 88.0 + - - +
285B GLY 3.3 1.3 - - - +
286B LYS 2.8 15.9 + - - +
355B ARG 4.3 0.5 - - - +
418B MET* 5.4 0.2 - - - -
1006B GOL 2.9 48.5 + - - -
1007B GOL 2.6 45.6 + - - -
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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