Contacts of the strand formed by residues 344 - 351 (chain A) in PDB entry 2AQ5
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 344 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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21A ALA* 5.0 8.5 - - - +
24A CYS* 4.1 16.0 - - + +
25A TYR 3.3 11.9 - - - +
26A GLU* 3.9 24.9 + - + +
28A VAL* 3.8 5.9 - - - +
30A VAL* 4.6 1.6 - - - +
339A LYS 3.6 0.4 - - - +
340A LEU* 3.4 5.4 - - - +
341A HIS* 2.9 66.9 + - + +
342A GLU 3.5 1.0 + - - -
343A ARG* 1.3 79.7 - - - +
345A CYS* 1.3 70.6 + - - +
346A GLU* 4.1 18.4 + - - -
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Residues in contact with CYS 345 (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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24A CYS* 3.3 5.9 - - - +
25A TYR* 2.9 53.0 + - + +
28A VAL* 4.2 0.6 - - + +
40A CYS* 4.3 1.1 - - - -
47A MET* 4.0 12.8 - - - -
49A LEU* 4.0 13.0 - - + -
338A TYR* 3.8 36.8 - - - -
339A LYS 3.4 3.8 - - - -
340A LEU* 3.7 22.4 - - + -
344A LYS* 1.3 73.3 - - - +
346A GLU* 1.3 61.1 + - - +
347A PRO* 3.7 0.4 - - - +
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Residues in contact with GLU 346 (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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18A PRO* 3.4 27.2 - - + +
19A ALA 4.5 3.0 - - - +
24A CYS* 3.9 13.9 - - - -
310A PHE* 6.0 0.2 - - - -
314A GLU* 4.6 6.3 - - - +
338A TYR* 4.3 1.1 - - - -
339A LYS* 2.8 53.5 + - - +
341A HIS* 2.9 36.9 + - - +
344A LYS* 4.1 14.1 + - - -
345A CYS* 1.3 74.6 - - - +
347A PRO* 1.3 73.4 - - - +
348A ILE* 3.6 7.3 + - + +
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Residues in contact with PRO 347 (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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18A PRO* 3.5 2.8 - - - +
19A ALA* 2.8 37.1 + - + -
23A GLN 3.5 25.4 - - - +
24A CYS* 3.8 9.0 - - - -
25A TYR* 4.3 5.4 - - + +
336A ARG* 4.2 11.2 - - - -
337A PHE 3.2 8.1 - - - +
338A TYR* 3.6 34.7 - - + +
345A CYS 3.7 8.3 - - - +
346A GLU* 1.3 85.2 - - - +
348A ILE* 1.3 59.2 + - - +
349A ALA 4.1 0.9 - - - -
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Residues in contact with ILE 348 (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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16A GLY* 4.0 8.7 - - - -
17A GLN 3.5 25.4 - - - +
18A PRO* 4.1 12.1 - - + -
292A ILE* 4.5 9.6 - - + -
310A PHE* 3.7 33.7 - - + -
336A ARG* 3.3 4.1 - - - +
337A PHE* 2.7 42.0 + - + +
339A LYS* 3.8 34.3 - - + -
346A GLU* 3.8 10.8 - - + +
347A PRO* 1.3 78.1 - - - +
349A ALA* 1.3 64.9 + - - +
350A MET* 3.7 10.2 + - - +
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Residues in contact with ALA 349 (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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15A PHE 3.4 1.2 - - - +
16A GLY* 3.2 5.2 - - - -
17A GLN* 2.8 45.0 + - + +
333A GLU* 3.2 28.7 - - + +
335A ALA 3.8 0.9 - - - -
336A ARG* 4.1 1.5 - - + +
347A PRO* 4.1 1.2 - - - +
348A ILE* 1.3 72.7 - - - +
350A MET* 1.3 61.1 + - - +
351A THR* 4.0 12.7 + - - +
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Residues in contact with MET 350 (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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14A VAL* 4.0 13.7 - - + -
15A PHE 3.4 2.2 - - - -
16A GLY* 3.7 22.2 - - - +
283A TYR* 4.1 15.7 - - + +
292A ILE* 5.3 3.6 - - + -
294A TYR* 3.7 30.7 - - + -
310A PHE* 4.9 7.0 - - + -
333A GLU* 3.4 4.0 - - - -
334A ILE* 2.9 30.7 + - + +
335A ALA* 2.8 30.4 + - + +
337A PHE* 3.8 30.5 - - + -
348A ILE* 4.2 11.9 - - - +
349A ALA* 1.3 81.0 - - - +
351A THR* 1.3 60.9 + - - +
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Residues in contact with THR 351 (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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14A VAL* 3.2 7.7 - - - +
15A PHE* 2.9 65.3 + - + +
17A GLN* 5.3 2.8 - - - +
331A LYS 3.7 20.2 + - - +
332A CSO 3.5 3.6 - - - +
333A GLU* 4.4 5.5 - - - +
349A ALA* 4.1 15.4 + - - +
350A MET* 1.3 75.2 + - - +
352A VAL* 1.3 77.5 + - - +
353A PRO* 4.8 0.9 - - + -
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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