Contacts of the strand formed by residues 276 - 286 (chain A) in PDB entry 1B70
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 LYS 276 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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269A VAL 3.6 0.5 - - - +
270A TRP* 3.2 9.6 - - - -
271A TRP* 3.2 55.3 + - + +
274A GLY* 3.4 11.3 + - - -
275A GLY* 1.3 80.5 - - - +
277A TRP* 1.3 64.0 + - - +
278A LEU* 3.6 19.9 - - + +
325A LEU* 5.9 1.1 - - - -
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Residues in contact with TRP 277 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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250A LYS* 3.5 23.1 - - + -
251A VAL 3.8 7.9 - - - -
252A ARG* 3.0 58.9 + - + +
268A ALA* 3.4 20.4 - - + -
269A VAL 3.2 27.8 - - - -
270A TRP* 3.1 46.4 - + + -
276A LYS* 1.3 76.1 - - - +
278A LEU* 1.3 68.0 + - - +
279A GLU* 4.0 2.3 + - - +
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Residues in contact with LEU 278 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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245A PHE* 4.3 6.5 - - + -
268A ALA* 2.8 4.5 - - - -
269A VAL* 2.6 59.2 + - + +
271A TRP* 3.8 19.3 - - + -
276A LYS* 3.6 29.6 - - + +
277A TRP* 1.3 83.1 - - - +
279A GLU* 1.3 66.4 + - - +
280A LEU* 3.2 9.0 + - + -
322A LEU* 5.9 2.0 - - + -
325A LEU* 3.2 40.8 - - + -
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Residues in contact with GLU 279 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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252A ARG* 3.1 26.0 + - - +
254A GLN* 4.1 1.0 - - - +
266A GLN* 3.3 41.0 + - + +
267A PHE 3.5 9.4 - - - +
268A ALA* 3.6 10.7 - - + +
277A TRP 4.0 1.9 + - - +
278A LEU* 1.3 72.4 - - - +
280A LEU* 1.3 65.3 + - - +
281A GLY 3.9 0.7 - - - +
321A ARG* 5.5 7.1 - - - +
31B GLU* 4.1 10.5 - - - +
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Residues in contact with LEU 280 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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240A LEU* 5.5 9.6 - - + -
244A LEU* 5.6 3.8 - - + -
245A PHE* 5.4 1.1 - - + -
267A PHE* 2.9 33.3 + - + +
269A VAL* 3.2 42.0 - - + -
278A LEU* 3.2 9.1 + - + +
279A GLU* 1.3 78.9 - - - +
281A GLY* 1.3 57.6 + - - +
317A LEU* 3.2 26.3 - - + +
318A GLY* 3.5 15.7 + - - +
321A ARG* 5.8 3.6 - - + -
322A LEU* 4.4 35.0 - - + +
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Residues in contact with GLY 281 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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266A GLN* 3.6 4.5 - - - +
267A PHE* 3.0 39.3 + - - +
279A GLU 3.9 0.2 - - - -
280A LEU* 1.3 83.4 - - - +
282A GLY* 1.3 58.0 + - - -
316A GLY 3.2 13.0 - - - -
317A LEU* 4.1 1.1 - - - -
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Residues in contact with GLY 282 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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258A PHE* 4.1 9.8 - - - -
265A ALA 3.4 10.8 - - - -
266A GLN* 4.3 1.8 - - - -
267A PHE* 3.5 2.0 - - - -
281A GLY* 1.3 75.4 - - - -
283A ALA* 1.3 62.6 + - - +
315A PHE* 3.1 3.3 - - - +
316A GLY 2.8 31.4 + - - +
352A PHE* 3.4 21.6 - - - +
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Residues in contact with ALA 283 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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233A LEU* 3.6 23.1 - - + -
253A PHE* 5.1 1.8 - - + -
258A PHE* 4.5 0.3 - - - -
261A VAL* 3.8 4.7 - - - +
264A GLY* 3.8 2.9 - - - -
265A ALA* 3.0 30.4 + - + +
267A PHE* 3.9 11.6 - - + -
282A GLY* 1.3 74.1 - - - -
284A GLY* 1.3 60.2 + - - +
314A ALA 3.1 9.6 - - - +
315A PHE* 3.2 23.3 - - + -
352A PHE* 3.4 12.1 - - - -
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Residues in contact with GLY 284 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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230A MET* 4.0 5.4 - - - -
233A LEU* 3.6 10.4 - - - +
261A VAL* 3.7 8.0 - - - +
263A PRO 3.1 13.7 - - - -
283A ALA* 1.3 81.2 - - - +
285A MET* 1.3 67.6 + - - -
286A VAL 3.5 0.2 + - - -
313A PHE* 3.1 5.4 - - - +
314A ALA 3.0 27.6 + - - +
352A PHE* 4.4 0.2 - - - -
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Residues in contact with MET 285 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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228A ILE* 4.1 0.7 - - + -
229A ALA* 3.5 23.6 - - - +
230A MET* 3.4 35.9 - - + -
233A LEU* 5.1 0.2 - - - -
261A VAL* 3.1 2.7 - - - -
262A GLU 3.0 34.3 + - - +
263A PRO* 3.0 19.7 + - + -
284A GLY* 1.3 70.9 - - - -
286A VAL* 1.3 70.0 + - - +
311A THR* 3.3 33.4 - - + -
312A GLY 3.3 7.9 - - - +
313A PHE* 3.6 18.2 - - - -
414B LEU* 3.5 21.8 - - + -
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Residues in contact with VAL 286 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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183A GLN* 4.7 5.6 - - - +
187A MET* 5.3 2.7 - - + -
222A LEU* 3.7 30.5 - - + -
260A PHE 3.7 7.6 - - - +
261A VAL* 3.9 2.0 - - - -
262A GLU 4.8 1.2 - - - +
284A GLY 3.5 2.6 + - - -
285A MET* 1.3 73.7 - - - +
287A HIS* 1.3 76.9 + - - +
288A PRO* 3.6 4.3 - - - +
290A VAL* 4.0 18.6 - - + -
291A PHE* 3.7 36.6 - - + -
312A GLY* 2.8 27.0 + - - +
313A PHE 4.0 5.2 - - - +
314A ALA* 4.3 6.5 - - + -
457B GLU* 6.0 0.2 - - - +
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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