Contacts of the strand formed by residues 279 - 284 (chain D) in PDB entry 4BGG
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 LEU 279 (chain D).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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253C ASN* 6.3 2.0 - - + -
236D ILE* 3.5 3.7 - - - +
237D PHE* 3.0 41.4 + - + +
238D SER 4.1 14.6 - - - +
239D SER* 5.1 4.0 - - - -
242D GLU* 4.1 28.7 - - + -
245D TRP* 3.6 47.8 - - + -
246D PHE* 4.7 9.2 - - + -
269D ASP 3.7 3.6 - - - -
270D MET* 5.0 5.2 - - + -
278D GLN* 1.3 81.3 - - - +
280D TRP* 1.3 61.5 + - - +
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Residues in contact with TRP 280 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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205D ALA* 3.7 42.0 - - + -
208D ILE* 5.0 11.4 - - + -
234D VAL* 3.6 26.7 - - + -
235D LYS 3.3 2.7 - - - +
236D ILE* 3.6 25.3 - - + +
245D TRP* 3.1 11.8 + - - +
268D SER* 3.3 1.0 + - - -
269D ASP* 2.7 43.2 + - + +
271D THR* 4.3 16.1 - - + +
278D GLN* 2.9 32.7 + - + +
279D LEU* 1.3 87.8 - - - +
281D LEU* 1.3 59.8 + - - +
282D ILE* 3.9 17.5 - - + -
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Residues in contact with LEU 281 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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234D VAL* 3.5 2.1 - - - -
235D LYS* 2.7 38.6 + - + +
237D PHE* 3.8 19.9 - - + -
245D TRP* 4.7 2.7 - - + -
248D GLU* 3.7 35.7 - - + +
249D THR* 4.7 5.8 - - - +
252D TYR* 4.4 10.3 - - + -
263D LEU* 5.8 0.2 - - + -
265D PHE* 3.7 36.1 - - + -
267D ALA 3.9 1.8 - - - +
268D SER* 4.5 6.7 - - - +
280D TRP* 1.3 74.1 - - - +
282D ILE* 1.3 62.1 + - - +
283D THR* 4.1 12.6 - - + -
1000D 844 3.7 26.0 - - - +
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Residues in contact with ILE 282 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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204D VAL 5.8 6.3 - - - +
205D ALA* 5.7 2.9 - - - -
227D TRP* 6.3 1.1 - - + -
232D VAL* 4.0 26.7 - - + -
233D ALA 3.3 9.0 - - - +
234D VAL* 3.7 27.1 - - + -
265D PHE* 4.2 1.6 - - - -
266D ILE* 3.0 35.5 + - + -
267D ALA* 2.7 37.7 + - + +
268D SER* 4.7 1.8 - - - +
269D ASP* 5.5 4.7 - - + +
280D TRP* 3.9 22.4 - - + -
281D LEU* 1.3 77.9 - - - +
283D THR* 1.3 68.6 + - - +
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Residues in contact with THR 283 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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232D VAL* 3.6 8.8 - - - +
233D ALA* 2.9 34.3 + - - +
252D TYR* 5.3 3.1 - - + +
263D LEU* 3.7 24.3 - - + +
264D GLY 3.2 17.7 - - - +
265D PHE* 4.5 4.3 - - - -
266D ILE* 3.7 10.1 - - - +
281D LEU* 4.1 15.3 - - + -
282D ILE* 1.3 79.3 - - - +
284D HIS* 1.3 72.0 + - - +
1000D 844 3.2 28.6 - - - -
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Residues in contact with HIS 284 (chain D).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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231D ASN 5.3 3.4 - - - -
232D VAL* 5.1 0.9 - - - +
233D ALA* 3.6 4.0 - - - +
263D LEU* 3.7 11.2 - - + +
264D GLY* 3.1 33.1 + - - +
265D PHE 4.9 3.6 - - - -
266D ILE* 3.8 23.8 - - + +
283D THR* 1.3 90.5 + - - +
285D TYR* 1.3 60.5 + - - +
286D HIS* 4.3 18.8 - - + +
1000D 844 4.0 2.6 - - - -
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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