Contacts of the strand formed by residues 333 - 341 (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 GLU 333 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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327A LEU* 3.5 19.8 - - + +
328A GLU* 2.8 49.2 + - + +
331A LYS* 3.1 5.4 - - + +
332A CSO 1.3 76.9 + - - -
334A ILE* 1.3 56.0 + - - +
335A ALA 3.4 19.1 - - - +
336A ARG* 2.7 41.4 + - - +
349A ALA* 3.2 26.0 - - + +
350A MET 3.4 7.9 - - - +
351A THR* 4.4 4.9 - - - +
364A TYR* 2.7 22.9 + - - -
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Residues in contact with ILE 334 (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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11A PHE* 4.0 4.9 - - + -
14A VAL* 3.8 22.4 - - + -
276A ASP* 4.1 4.2 - - - +
279A THR* 4.7 7.6 - - + -
281A ILE* 3.6 30.3 - - + -
283A TYR* 3.7 12.2 + - - +
321A TYR* 5.1 0.9 + - - -
324A LYS* 3.1 28.2 + - - +
327A LEU* 3.5 10.2 - - - +
332A CSO 3.5 3.6 + - - +
333A GLU* 1.3 75.8 - - - +
335A ALA* 1.3 62.4 + - - +
350A MET* 2.9 18.6 + - + +
352A VAL* 3.7 25.1 - - + -
363A LEU* 4.6 16.4 - - + +
364A TYR* 4.0 16.6 - - + +
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Residues in contact with ALA 335 (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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276A ASP* 5.9 0.2 - - - +
283A TYR* 3.6 29.8 - - + +
321A TYR* 4.2 17.5 - - + +
322A MET 5.3 1.3 - - - -
327A LEU* 3.8 10.5 - - - +
333A GLU* 3.4 7.5 - - - +
334A ILE* 1.3 80.1 - - - +
336A ARG* 1.3 63.4 + - - +
337A PHE* 4.4 2.5 - - + -
350A MET* 2.8 38.2 + - + -
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Residues in contact with ARG 336 (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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64A LEU* 4.6 6.1 - - - +
321A TYR* 3.6 3.3 - - - -
322A MET* 2.9 44.5 + - + +
326A GLY 3.1 27.0 + - - -
327A LEU* 3.7 13.4 - - + +
328A GLU* 3.7 18.5 + - - +
333A GLU* 2.7 39.3 + - - +
335A ALA* 1.3 77.8 - - - +
337A PHE* 1.3 65.9 + - - +
338A TYR* 3.0 37.5 + - + -
347A PRO* 4.2 9.9 - - - -
348A ILE 3.3 20.6 - - - +
349A ALA* 4.1 0.9 - - - +
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Residues in contact with PHE 337 (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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274A PHE* 4.0 12.3 - + - -
283A TYR* 3.5 49.1 - + + -
285A CYS* 3.8 18.8 - - - -
292A ILE* 4.1 21.3 - - + -
319A MET* 3.5 31.0 - - + -
320A GLY 3.4 7.0 - - - -
321A TYR* 3.6 26.5 - + - -
335A ALA* 4.4 2.9 - - + -
336A ARG* 1.3 74.7 - - - +
338A TYR* 1.3 62.6 + - - +
339A LYS 3.8 0.7 - - - -
346A GLU 3.6 0.2 - - - +
347A PRO* 3.2 3.8 - - - +
348A ILE* 2.7 45.6 + - + +
350A MET* 3.8 22.0 - - + -
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Residues in contact with TYR 338 (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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25A TYR* 4.0 16.4 + + - -
40A CYS* 3.7 22.6 - - - -
42A VAL* 3.7 25.4 - - + -
47A MET* 4.2 2.2 - - + -
64A LEU* 3.6 12.5 - - + +
319A MET* 3.2 6.4 - - - -
320A GLY 2.8 34.9 + - - +
322A MET* 3.5 25.7 - - + +
336A ARG* 3.0 51.7 + - + -
337A PHE* 1.3 76.2 - - - +
339A LYS* 1.3 62.6 + - - +
340A LEU 3.6 0.7 + - - -
345A CYS* 3.8 22.0 - - - -
346A GLU 3.7 2.7 - - - -
347A PRO* 3.6 23.6 - - + +
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Residues in contact with LYS 339 (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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289A ASP 5.1 0.4 - - - -
290A SER* 4.1 5.4 + - - +
292A ILE* 5.7 1.1 - - + -
310A PHE* 4.8 3.8 - - + -
312A SER* 2.8 24.4 + - - -
314A GLU* 2.8 36.9 + - - +
315A SER 4.2 0.2 - - - -
316A GLN* 4.0 23.3 - - + +
319A MET* 3.6 24.7 - - + -
337A PHE 3.8 0.2 - - - -
338A TYR* 1.3 73.5 - - - +
340A LEU* 1.3 63.4 + - - +
341A HIS* 3.7 19.7 - - + -
344A LYS 3.6 0.9 - - - +
345A CYS* 3.4 2.1 - - - -
346A GLU* 2.8 53.2 + - - +
348A ILE* 3.8 24.7 - - + -
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Residues in contact with LEU 340 (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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30A VAL* 3.8 30.7 - - + -
39A PHE* 3.7 38.6 - - + +
40A CYS* 3.9 15.5 - - + -
49A LEU* 3.8 19.3 - - + -
50A ILE 5.3 0.4 - - - +
316A GLN* 3.3 4.7 - - - -
317A ARG* 2.6 33.4 + - - -
318A GLY* 2.9 25.7 + - - +
338A TYR 3.6 0.2 + - - -
339A LYS* 1.3 70.7 - - - +
341A HIS* 1.3 60.3 + - - +
344A LYS 3.4 3.6 - - - +
345A CYS* 3.7 32.5 - - + -
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Residues in contact with HIS 341 (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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30A VAL* 5.4 0.2 - - - +
314A GLU* 3.7 35.4 - - + +
315A SER 3.2 23.1 - - - +
317A ARG* 4.1 3.4 - - - -
339A LYS* 3.7 24.2 - - + -
340A LEU* 1.3 76.1 - - - +
342A GLU* 1.3 74.4 + - + +
343A ARG 3.0 0.9 + - - -
344A LYS* 2.9 56.8 + - + +
346A GLU* 2.9 37.2 + - + +
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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