Contacts of the strand formed by residues 268 - 276 (chain D) in PDB entry 5BZZ
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 ASP 268 (chain D).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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206D PHE* 4.6 11.3 - - + +
258D PHE* 3.2 5.2 - - - +
259D HIS* 2.6 67.9 + - + +
261D GLN* 4.5 10.6 - - - +
266D LYS* 4.4 13.9 + - - +
267D LYS* 1.3 73.8 - - - +
269D LYS* 1.3 64.2 + - - +
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Residues in contact with LYS 269 (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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206D PHE* 3.8 11.5 - - - -
256D GLU* 2.5 36.6 - - + +
257D PHE 3.7 15.3 - - - +
258D PHE* 3.9 13.2 - - + -
266D LYS* 5.5 0.8 - - - +
267D LYS 3.7 2.2 + - - -
268D ASP* 1.3 74.4 - - - +
270D MET* 1.3 61.5 + - - +
271D PHE 4.0 4.0 - - - +
272D HIS* 2.8 37.5 + - - -
327D LYS* 3.5 49.9 + - + +
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Residues in contact with MET 270 (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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200D PHE* 4.5 4.0 - - + -
204D PRO* 3.3 41.1 - - + -
206D PHE* 3.6 27.8 - - + -
211D CYS* 3.9 11.4 - - - -
213D PRO* 4.4 12.1 - - - -
257D PHE* 2.9 15.4 + - - +
258D PHE 3.7 23.3 - - - +
259D HIS* 3.5 22.7 - - + +
269D LYS* 1.3 77.0 - - - +
271D PHE* 1.3 81.3 + - + +
327D LYS* 3.6 17.3 - - - +
337D PHE* 3.7 16.9 - - + -
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Residues in contact with PHE 271 (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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200D PHE* 3.7 17.3 - + - -
257D PHE* 2.8 62.6 + + + +
269D LYS* 4.0 5.4 - - - +
270D MET* 1.3 94.7 - - + +
272D HIS* 1.3 70.9 + - - +
273D PHE* 4.0 8.7 - + - -
325D LEU* 3.8 27.8 - - + -
327D LYS* 4.0 9.4 - - - -
328D ALA* 3.9 22.2 - - + +
337D PHE* 3.9 13.5 - + - -
341D PHE* 3.9 10.5 - + - -
343D VAL* 3.5 33.4 - - + -
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Residues in contact with HIS 272 (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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93D HIS 5.1 6.0 + - - -
94D ASN* 4.8 4.2 + - - -
168D ILE* 5.8 0.2 - - - +
254D LYS* 3.6 31.5 + - - -
255D VAL 3.2 15.7 - - - +
256D GLU* 3.7 15.3 - - + -
269D LYS* 2.8 30.1 + - - -
271D PHE* 1.3 79.9 - - - +
273D PHE* 1.3 69.7 + - - +
274D TRP* 4.4 5.6 - + - -
325D LEU* 3.8 2.4 - - - +
326D ASP* 2.9 64.9 + - + +
327D LYS* 4.4 4.0 + - + +
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Residues in contact with PHE 273 (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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170D SER* 3.8 7.9 - - - -
173D ARG* 4.2 9.4 - - - +
198D MET* 4.4 0.9 - - - -
253D ILE 5.3 0.7 - - - -
254D LYS* 3.4 5.1 - - - +
255D VAL* 2.9 71.7 + - + +
257D PHE* 4.9 1.1 - + - -
271D PHE* 4.0 17.7 - + - -
272D HIS* 1.3 79.2 - - - +
274D TRP* 1.3 65.5 + - - +
275D VAL* 4.0 14.1 - - + -
320D LEU* 3.5 21.5 - - + -
324D ASP 4.5 3.6 - - - +
325D LEU* 3.7 21.8 - - + -
326D ASP* 4.1 0.9 - - - -
343D VAL* 4.7 5.4 - - + -
345D LEU* 3.6 42.8 - - + -
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Residues in contact with TRP 274 (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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91D GLU* 6.5 1.1 - - - -
94D ASN* 2.8 30.3 + - + -
95D PRO* 3.5 37.5 - - + -
170D SER* 3.2 17.9 + - - +
173D ARG* 2.7 32.9 + - - -
174D TYR* 4.0 16.3 - + + -
218D CYS* 5.2 0.4 - - + -
220D LEU 3.9 19.5 - - - -
252D ASP* 4.0 22.4 - - + -
253D ILE 3.3 21.1 - - - -
254D LYS* 3.6 47.0 - - + +
272D HIS* 4.4 2.2 - + - -
273D PHE* 1.3 77.9 - - - +
275D VAL* 1.3 62.5 + - - +
326D ASP* 4.3 6.1 - - - -
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Residues in contact with VAL 275 (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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173D ARG* 4.3 9.2 - - - +
174D TYR* 3.8 5.0 + - - -
177D TYR* 3.6 11.7 - - - +
252D ASP* 3.7 1.6 - - - -
253D ILE* 2.8 41.8 + - + +
273D PHE* 4.0 23.7 - - + -
274D TRP* 1.3 79.8 - - - +
276D ASN* 1.3 64.5 + - - +
280D ILE* 3.7 30.5 - - + -
318D LEU* 3.6 26.9 - - + -
320D LEU* 4.5 4.7 - - + -
345D LEU* 4.6 4.9 - - + -
347D PHE* 5.2 1.1 - - + -
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Residues in contact with ASN 276 (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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98D LEU* 3.6 14.3 - - - +
174D TYR* 4.7 0.2 - - + -
177D TYR* 3.1 27.8 + - + -
188D TYR* 3.3 26.6 + - - -
251D GLY 3.3 7.8 - - - +
252D ASP* 2.5 32.1 + - - +
275D VAL* 1.3 79.9 - - - +
277D THR* 1.3 54.8 + - - +
278D PHE* 2.9 46.6 + - - +
279D PHE* 2.9 28.4 + - + +
280D ILE 3.9 2.4 + - - -
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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