Contacts of the strand formed by residues 272 - 277 (chain A) in PDB entry 2BQZ
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 MET 272 (chain A).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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245A TYR* 4.7 0.2 - - - -
250A ILE* 4.2 2.7 - - + -
255A ALA* 3.6 32.3 - - + +
258A ARG* 4.1 9.2 - - + -
259A GLU* 4.3 17.7 - - + +
262A TYR* 3.9 12.6 - - + -
270A CYS* 3.8 2.3 - - - -
271A TYR* 1.3 79.2 - - - +
273A TYR* 1.3 58.9 + - - +
274A TYR* 4.1 14.6 - - + +
283A CYS* 3.7 21.1 - - - -
284A VAL 3.6 2.2 - - - -
285A ASP* 3.3 40.6 - - - +
287A THR* 4.1 1.8 - - - +
18B HIS 5.9 1.1 - - - +
19B ARG* 3.8 8.4 - - + +
20B MLZ 3.0 28.6 + - - +
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Residues in contact with TYR 273 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
245A TYR* 3.7 38.1 - + + -
272A MET* 1.3 72.7 - - - +
274A TYR* 1.3 70.4 + - - +
275A PHE* 3.7 6.1 - - - -
283A CYS* 3.2 4.0 - - - -
284A VAL* 2.8 35.8 + - + +
307A THR* 2.7 39.8 + - + -
318A LEU* 3.6 16.4 - - + -
320A LEU* 5.9 0.4 - - + -
334A TYR* 3.5 31.5 - + - -
335A ASP 4.2 6.2 + - - -
336A TYR 4.8 0.7 - - - -
20B MLZ 3.5 27.1 - - + -
21B VAL 3.7 6.3 + - - -
22B LEU* 3.5 28.7 - - + +
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Residues in contact with TYR 274 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
252A ILE* 4.4 14.1 - - + -
255A ALA* 3.5 41.6 + - + +
256A LYS* 3.9 9.7 + - + +
259A GLU* 2.5 30.4 + - - +
272A MET* 4.1 11.8 - - + +
273A TYR* 1.3 77.3 - - - +
275A PHE* 1.3 61.9 + - - +
281A THR* 4.2 16.2 - - + -
282A TYR 3.3 10.1 - - - +
283A CYS* 3.9 9.9 - - + -
19B ARG* 3.7 27.4 - - + -
20B MLZ 2.9 18.8 + - - +
21B VAL* 3.5 12.8 - - + +
22B LEU 2.9 25.6 + - - -
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Residues in contact with PHE 275 (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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249A LEU* 3.7 14.6 - - + -
273A TYR 3.7 12.6 - - - -
274A TYR* 1.3 74.6 - - - +
276A GLN* 1.3 72.8 + - - +
277A TYR* 3.8 13.0 - - + -
281A THR* 3.4 5.9 - - - +
282A TYR* 2.8 62.3 + - + +
283A CYS 4.0 0.2 - - - -
284A VAL* 3.9 23.8 - - + -
309A LEU* 3.9 14.1 - - + -
316A PRO* 3.7 31.2 - - + -
318A LEU* 3.9 17.7 - - + -
21B VAL* 5.9 0.4 - - - -
22B LEU* 3.8 30.5 - - + -
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Residues in contact with GLN 276 (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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275A PHE* 1.3 82.3 - - - +
277A TYR* 1.3 63.5 + - - +
279A SER* 6.0 2.8 - - - +
280A LYS 3.3 8.7 - - - +
281A THR* 4.3 14.6 - - + +
309A LEU* 3.9 12.1 - - - +
22B LEU* 5.2 10.1 + - - +
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Residues in contact with TYR 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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275A PHE* 3.8 9.8 + - + -
276A GLN* 1.3 75.8 - - - +
278A LEU* 1.3 107.8 + - + +
279A SER 3.3 1.3 - - - -
280A LYS* 2.8 20.3 + - - +
282A TYR* 3.4 33.5 + + + -
309A LEU* 3.7 21.5 - - + -
311A ASP* 3.6 31.2 + - + +
314A GLY* 3.6 38.5 + - - -
316A PRO* 3.7 24.5 - - + -
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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